fix(codeql): fix high-severity CodeQL issues

- Replace MD5 with SHA-256 for finding ID generation (4 locations)
- Use crypto.randomBytes() instead of Math.random() for temp files (2 files)
- Fix TOCTOU race conditions by using try/catch instead of existsSync (5 files)
- Add __dir__() to lazy import module for static analysis

Fixes the following CodeQL alerts:
- Use of broken/weak cryptographic hashing algorithm
- Insecure temporary file creation
- Potential file system race conditions (TOCTOU)
- Explicit export not defined in __all__

All 3841 frontend tests pass.

.github/FUNDING.yml

@@ -0,0 +1,3 @@
+# These are supported funding model platforms
+
+github: AndyMik90

.github/ISSUE_TEMPLATE/config.yml

@@ -1,8 +1,8 @@
 blank_issues_enabled: false
 contact_links:
   - name: 💡 Feature Request
-    url: https://github.com/AndyMik90/Auto-Claude/discussions/new?category=ideas
+    url: https://github.com/AndyMik90/Auto-Claude/discussions
     about: Suggest new features in GitHub Discussions
   - name: 💬 Discord Community
-    url: https://discord.gg/KCXaPBr4Dj
+    url: https://discord.gg/QhRnz9m5HE
     about: Questions and discussions - join our Discord!

.github/ISSUE_TEMPLATE/question.yml

@@ -5,7 +5,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        **Before asking:** Check [Discord](https://discord.gg/KCXaPBr4Dj) - your question may already be answered there!
+        **Before asking:** Check [Discord](https://discord.gg/QhRnz9m5HE) - your question may already be answered there!
 
   - type: checkboxes
     id: checklist

.github/PULL_REQUEST_TEMPLATE.md

@@ -33,6 +33,21 @@ Follow conventional commits: `<type>: <subject>`
 
 **Example:** `feat: add user authentication system`
 
+## AI Disclosure
+
+<!-- Check the box below if any part of this PR was written with AI assistance. -->
+
+- [ ] This PR includes AI-generated code (Claude, Codex, Copilot, etc.)
+
+<!-- If checked, please also fill in: -->
+**Tool(s) used:** <!-- e.g., Claude Code, GitHub Copilot, ChatGPT -->
+**Testing level:**
+- [ ] Untested -- AI output not yet verified
+- [ ] Lightly tested -- ran the app / spot-checked key paths
+- [ ] Fully tested -- all tests pass, manually verified behavior
+
+- [ ] I understand what this PR does and how the underlying code works
+
 ## Checklist
 
 - [ ] I've synced with `develop` branch
@@ -40,9 +55,21 @@ Follow conventional commits: `<type>: <subject>`
 - [ ] I've followed the code principles (SOLID, DRY, KISS)
 - [ ] My PR is small and focused (< 400 lines ideally)
 
+## Platform Testing Checklist
+
+**CRITICAL:** This project supports Windows, macOS, and Linux. Platform-specific bugs are a common source of breakage.
+
+- [ ] **Windows tested** (either on Windows or via CI)
+- [ ] **macOS tested** (either on macOS or via CI)
+- [ ] **Linux tested** (CI covers this)
+- [ ] Used centralized `platform/` module instead of direct `process.platform` checks
+- [ ] No hardcoded paths (used `findExecutable()` or platform abstractions)
+
+**If you only have access to one OS:** CI now tests on all platforms. Ensure all checks pass before submitting.
+
 ## CI/Testing Requirements
 
-- [ ] All CI checks pass
+- [ ] All CI checks pass on **all platforms** (Windows, macOS, Linux)
 - [ ] All existing tests pass
 - [ ] New features include test coverage
 - [ ] Bug fixes include regression tests

.github/actions/finalize-macos-notarization/action.yml

@@ -0,0 +1,160 @@
+name: 'Finalize macOS Notarization'
+description: 'Wait for Apple notarization to complete and staple tickets to DMG files'
+
+inputs:
+  apple-id:
+    description: 'Apple ID for notarization'
+    required: true
+  apple-app-specific-password:
+    description: 'Apple app-specific password'
+    required: true
+  apple-team-id:
+    description: 'Apple Team ID'
+    required: true
+  intel-notarization-id:
+    description: 'Notarization request ID for Intel build'
+    required: false
+    default: ''
+  arm64-notarization-id:
+    description: 'Notarization request ID for ARM64 build'
+    required: false
+    default: ''
+  intel-dmg-file:
+    description: 'Filename of the Intel DMG'
+    required: false
+    default: ''
+  arm64-dmg-file:
+    description: 'Filename of the ARM64 DMG'
+    required: false
+    default: ''
+  intel-artifact-path:
+    description: 'Path to Intel build artifacts'
+    required: false
+    default: 'intel'
+  arm64-artifact-path:
+    description: 'Path to ARM64 build artifacts'
+    required: false
+    default: 'arm64'
+  timeout:
+    description: 'Timeout in seconds for notarization wait'
+    required: false
+    default: '3600'
+
+outputs:
+  intel-stapled:
+    description: 'Whether Intel DMG was successfully stapled'
+    value: ${{ steps.staple.outputs.intel_stapled }}
+  arm64-stapled:
+    description: 'Whether ARM64 DMG was successfully stapled'
+    value: ${{ steps.staple.outputs.arm64_stapled }}
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Wait for notarization and staple
+      id: staple
+      shell: bash
+      env:
+        APPLE_ID: ${{ inputs.apple-id }}
+        APPLE_APP_SPECIFIC_PASSWORD: ${{ inputs.apple-app-specific-password }}
+        APPLE_TEAM_ID: ${{ inputs.apple-team-id }}
+        INTEL_NOTARIZATION_ID: ${{ inputs.intel-notarization-id }}
+        ARM64_NOTARIZATION_ID: ${{ inputs.arm64-notarization-id }}
+        INTEL_DMG: ${{ inputs.intel-dmg-file }}
+        ARM64_DMG: ${{ inputs.arm64-dmg-file }}
+        INTEL_PATH: ${{ inputs.intel-artifact-path }}
+        ARM64_PATH: ${{ inputs.arm64-artifact-path }}
+        TIMEOUT: ${{ inputs.timeout }}
+      run: |
+        intel_stapled=false
+        arm64_stapled=false
+
+        if [ -z "$APPLE_ID" ]; then
+          echo "Skipping notarization wait: APPLE_ID not configured"
+          echo "intel_stapled=false" >> "$GITHUB_OUTPUT"
+          echo "arm64_stapled=false" >> "$GITHUB_OUTPUT"
+          exit 0
+        fi
+
+        # Warn if no notarization IDs provided (could indicate submission failure)
+        if [ -z "$INTEL_NOTARIZATION_ID" ] && [ -z "$ARM64_NOTARIZATION_ID" ]; then
+          echo "::warning::No notarization IDs provided - nothing to finalize. Check if notarization submission succeeded."
+          echo "intel_stapled=false" >> "$GITHUB_OUTPUT"
+          echo "arm64_stapled=false" >> "$GITHUB_OUTPUT"
+          exit 0
+        fi
+
+        # Wait for Intel notarization
+        if [ -n "$INTEL_NOTARIZATION_ID" ]; then
+          echo "Waiting for Intel notarization: $INTEL_NOTARIZATION_ID"
+          if ! xcrun notarytool wait "$INTEL_NOTARIZATION_ID" \
+            --apple-id "$APPLE_ID" \
+            --password "$APPLE_APP_SPECIFIC_PASSWORD" \
+            --team-id "$APPLE_TEAM_ID" \
+            --timeout "$TIMEOUT"; then
+            echo "::error::Intel notarization failed or timed out"
+            exit 1
+          fi
+          # Verify notarization was accepted (not just processed)
+          INTEL_STATUS=$(xcrun notarytool info "$INTEL_NOTARIZATION_ID" \
+            --apple-id "$APPLE_ID" \
+            --password "$APPLE_APP_SPECIFIC_PASSWORD" \
+            --team-id "$APPLE_TEAM_ID" \
+            --output-format json | jq -r '.status // "Unknown"')
+          if [ "$INTEL_STATUS" != "Accepted" ]; then
+            echo "::error::Intel notarization status is '$INTEL_STATUS', expected 'Accepted'"
+            exit 1
+          fi
+          echo "Intel notarization status: $INTEL_STATUS"
+          # Verify DMG file exists before stapling
+          if [ ! -f "$INTEL_PATH/$INTEL_DMG" ]; then
+            echo "::error::Intel DMG not found at $INTEL_PATH/$INTEL_DMG"
+            exit 1
+          fi
+          echo "Stapling Intel DMG: $INTEL_PATH/$INTEL_DMG"
+          if ! xcrun stapler staple "$INTEL_PATH/$INTEL_DMG"; then
+            echo "::error::Failed to staple Intel DMG"
+            exit 1
+          fi
+          echo "Successfully stapled Intel DMG"
+          intel_stapled=true
+        fi
+
+        # Wait for ARM64 notarization
+        if [ -n "$ARM64_NOTARIZATION_ID" ]; then
+          echo "Waiting for ARM64 notarization: $ARM64_NOTARIZATION_ID"
+          if ! xcrun notarytool wait "$ARM64_NOTARIZATION_ID" \
+            --apple-id "$APPLE_ID" \
+            --password "$APPLE_APP_SPECIFIC_PASSWORD" \
+            --team-id "$APPLE_TEAM_ID" \
+            --timeout "$TIMEOUT"; then
+            echo "::error::ARM64 notarization failed or timed out"
+            exit 1
+          fi
+          # Verify notarization was accepted (not just processed)
+          ARM64_STATUS=$(xcrun notarytool info "$ARM64_NOTARIZATION_ID" \
+            --apple-id "$APPLE_ID" \
+            --password "$APPLE_APP_SPECIFIC_PASSWORD" \
+            --team-id "$APPLE_TEAM_ID" \
+            --output-format json | jq -r '.status // "Unknown"')
+          if [ "$ARM64_STATUS" != "Accepted" ]; then
+            echo "::error::ARM64 notarization status is '$ARM64_STATUS', expected 'Accepted'"
+            exit 1
+          fi
+          echo "ARM64 notarization status: $ARM64_STATUS"
+          # Verify DMG file exists before stapling
+          if [ ! -f "$ARM64_PATH/$ARM64_DMG" ]; then
+            echo "::error::ARM64 DMG not found at $ARM64_PATH/$ARM64_DMG"
+            exit 1
+          fi
+          echo "Stapling ARM64 DMG: $ARM64_PATH/$ARM64_DMG"
+          if ! xcrun stapler staple "$ARM64_PATH/$ARM64_DMG"; then
+            echo "::error::Failed to staple ARM64 DMG"
+            exit 1
+          fi
+          echo "Successfully stapled ARM64 DMG"
+          arm64_stapled=true
+        fi
+
+        echo "intel_stapled=$intel_stapled" >> "$GITHUB_OUTPUT"
+        echo "arm64_stapled=$arm64_stapled" >> "$GITHUB_OUTPUT"

.github/actions/merge-macos-manifests/action.yml

@@ -0,0 +1,194 @@
+name: 'Merge macOS Manifests'
+description: 'Merge Intel and ARM64 macOS manifests for electron-updater'
+
+inputs:
+  dist-path:
+    description: 'Path to the dist directory containing build artifacts'
+    required: false
+    default: 'dist'
+  output-path:
+    description: 'Path to output the merged manifest'
+    required: false
+    default: 'release-assets'
+  copy-other-manifests:
+    description: 'Whether to copy Windows/Linux manifests as well'
+    required: false
+    default: 'true'
+  yq-version:
+    description: 'Version of yq to use for YAML merging'
+    required: false
+    default: 'v4.44.3'
+
+outputs:
+  merged:
+    description: 'Whether manifests were merged (true) or single architecture used (false)'
+    value: ${{ steps.merge.outputs.merged }}
+  file-count:
+    description: 'Number of files in the merged manifest'
+    value: ${{ steps.validate.outputs.file_count }}
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Merge macOS manifests
+      id: merge
+      shell: bash
+      env:
+        # yq SHA256 checksum for v4.44.3 linux_amd64
+        # When updating yq-version, update this checksum and the one in validate step
+        YQ_SHA256: "a2c097180dd884a8d50c956ee16a9cec070f30a7947cf4ebf87d5f36213e9ed7"
+      run: |
+        echo "=== Merging macOS update manifests ==="
+
+        # Find all latest-mac.yml files from different build artifacts
+        intel_manifest=$(find "${{ inputs.dist-path }}" -path "*/macos-intel-builds/latest-mac.yml" -type f 2>/dev/null | head -1)
+        arm64_manifest=$(find "${{ inputs.dist-path }}" -path "*/macos-arm64-builds/latest-mac.yml" -type f 2>/dev/null | head -1)
+
+        echo "Intel manifest: ${intel_manifest:-not found}"
+        echo "ARM64 manifest: ${arm64_manifest:-not found}"
+
+        mkdir -p "${{ inputs.output-path }}"
+
+        if [ -n "$intel_manifest" ] && [ -n "$arm64_manifest" ]; then
+          echo "Both architectures found - merging manifests..."
+          echo "merged=true" >> "$GITHUB_OUTPUT"
+
+          # Install yq for YAML merging (pinned version with checksum verification)
+          YQ_VERSION="${{ inputs.yq-version }}"
+          YQ_URL="https://github.com/mikefarah/yq/releases/download/${YQ_VERSION}/yq_linux_amd64"
+
+          echo "Downloading yq ${YQ_VERSION}..."
+          if ! wget -qO /tmp/yq "$YQ_URL"; then
+            echo "::error::Failed to download yq ${YQ_VERSION}"
+            exit 1
+          fi
+
+          # Verify checksum
+          echo "Verifying yq checksum..."
+          ACTUAL_SHA256=$(sha256sum /tmp/yq | cut -d' ' -f1)
+          if [ "$ACTUAL_SHA256" != "$YQ_SHA256" ]; then
+            echo "::error::yq checksum verification failed!"
+            echo "Expected: $YQ_SHA256"
+            echo "Actual:   $ACTUAL_SHA256"
+            rm -f /tmp/yq
+            exit 1
+          fi
+          echo "Checksum verified successfully"
+
+          sudo mv /tmp/yq /usr/local/bin/yq
+          sudo chmod +x /usr/local/bin/yq
+          echo "Installed yq version:"
+          yq --version
+
+          # Merge the files arrays from both manifests using two-step approach
+          # Step 1: Collect all files from both manifests into a temp file
+          yq eval-all '[.files] | flatten' "$intel_manifest" "$arm64_manifest" > /tmp/merged-files.yml
+
+          # Step 2: Replace files array in first manifest with merged files
+          yq eval '.files = load("/tmp/merged-files.yml")' "$intel_manifest" > "${{ inputs.output-path }}/latest-mac.yml"
+
+          echo "Merged manifest contents:"
+          cat "${{ inputs.output-path }}/latest-mac.yml"
+
+        elif [ -n "$intel_manifest" ]; then
+          echo "Only Intel manifest found - using as-is"
+          echo "merged=false" >> "$GITHUB_OUTPUT"
+          cp "$intel_manifest" "${{ inputs.output-path }}/latest-mac.yml"
+        elif [ -n "$arm64_manifest" ]; then
+          echo "Only ARM64 manifest found - using as-is"
+          echo "merged=false" >> "$GITHUB_OUTPUT"
+          cp "$arm64_manifest" "${{ inputs.output-path }}/latest-mac.yml"
+        else
+          echo "::error::No macOS manifests found - this will cause auto-update to fail"
+          exit 1
+        fi
+
+    - name: Validate merged manifest
+      id: validate
+      shell: bash
+      env:
+        # Single source of truth for yq checksum - must match merge step
+        YQ_SHA256: "a2c097180dd884a8d50c956ee16a9cec070f30a7947cf4ebf87d5f36213e9ed7"
+      run: |
+        manifest_file="${{ inputs.output-path }}/latest-mac.yml"
+
+        echo "=== Validating merged manifest ==="
+
+        # Check file exists
+        if [ ! -f "$manifest_file" ]; then
+          echo "::error::Merged manifest file not found at $manifest_file"
+          exit 1
+        fi
+
+        # Install yq if not already installed (for single-arch case)
+        if ! command -v yq &> /dev/null; then
+          YQ_VERSION="${{ inputs.yq-version }}"
+          YQ_URL="https://github.com/mikefarah/yq/releases/download/${YQ_VERSION}/yq_linux_amd64"
+
+          echo "Downloading yq ${YQ_VERSION}..."
+          wget -qO /tmp/yq "$YQ_URL"
+
+          # Verify checksum (YQ_SHA256 from env)
+          ACTUAL_SHA256=$(sha256sum /tmp/yq | cut -d' ' -f1)
+          if [ "$ACTUAL_SHA256" != "$YQ_SHA256" ]; then
+            echo "::error::yq checksum verification failed!"
+            echo "Expected: $YQ_SHA256"
+            echo "Actual:   $ACTUAL_SHA256"
+            exit 1
+          fi
+
+          sudo mv /tmp/yq /usr/local/bin/yq
+          sudo chmod +x /usr/local/bin/yq
+        fi
+
+        # Validate YAML is parseable
+        if ! yq eval '.' "$manifest_file" > /dev/null 2>&1; then
+          echo "::error::Merged manifest is not valid YAML"
+          cat "$manifest_file"
+          exit 1
+        fi
+        echo "YAML syntax is valid"
+
+        # Count files in manifest
+        file_count=$(yq eval '.files | length' "$manifest_file")
+        echo "file_count=$file_count" >> "$GITHUB_OUTPUT"
+        echo "Manifest contains $file_count file entries"
+
+        # Validate file count
+        if [ "$file_count" -eq 0 ]; then
+          echo "::error::Merged manifest contains no files"
+          exit 1
+        fi
+
+        # If we merged both architectures, expect at least 2 files (one per arch)
+        if [ "${{ steps.merge.outputs.merged }}" = "true" ] && [ "$file_count" -lt 2 ]; then
+          echo "::warning::Merged manifest has fewer than 2 files - merge may have failed"
+        fi
+
+        # Validate required fields exist
+        if ! yq eval '.version' "$manifest_file" | grep -q .; then
+          echo "::error::Manifest missing 'version' field"
+          exit 1
+        fi
+        echo "Version field present: $(yq eval '.version' "$manifest_file")"
+
+        echo "Manifest validation passed"
+
+    - name: Copy other manifests
+      if: inputs.copy-other-manifests == 'true'
+      shell: bash
+      run: |
+        echo "=== Copying other update manifests ==="
+
+        # Copy other manifests (Windows, Linux) - these don't have the duplicate issue
+        for manifest in latest.yml latest-linux.yml latest-linux-arm64.yml; do
+          found=$(find "${{ inputs.dist-path }}" -name "$manifest" -type f 2>/dev/null | head -1)
+          if [ -n "$found" ]; then
+            echo "Copying $manifest"
+            cp "$found" "${{ inputs.output-path }}/"
+          fi
+        done
+
+        echo ""
+        echo "=== Manifest files in ${{ inputs.output-path }} ==="
+        ls -la "${{ inputs.output-path }}"/*.yml 2>/dev/null || echo "No manifest files found"

.github/actions/setup-node-frontend/action.yml

@@ -0,0 +1,126 @@
+name: 'Setup Node.js Frontend'
+description: 'Set up Node.js with npm and cached dependencies for the frontend'
+
+inputs:
+  node-version:
+    description: 'Node.js version to use'
+    required: false
+    default: '24'
+  ignore-scripts:
+    description: 'Whether to use --ignore-scripts flag during npm ci'
+    required: false
+    default: 'false'
+
+outputs:
+  cache-hit:
+    description: 'Whether npm cache was hit'
+    value: ${{ steps.cache.outputs.cache-hit }}
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Setup Node.js ${{ inputs.node-version }}
+      uses: actions/setup-node@v4
+      with:
+        node-version: ${{ inputs.node-version }}
+
+    - name: Get npm cache directory
+      id: npm-cache-dir
+      shell: bash
+      run: echo "dir=$(npm config get cache)" >> "$GITHUB_OUTPUT"
+
+    - name: Cache npm dependencies
+      id: cache
+      uses: actions/cache@v4
+      with:
+        path: ${{ steps.npm-cache-dir.outputs.dir }}
+        key: ${{ runner.os }}-npm-${{ hashFiles('package-lock.json') }}
+        restore-keys: ${{ runner.os }}-npm-
+
+    - name: Install dependencies
+      shell: bash
+      # Run npm ci from root to properly handle workspace dependencies.
+      # With npm workspaces, the lock file is at root and dependencies are hoisted there.
+      # Running npm ci in apps/frontend would fail to populate node_modules correctly.
+      run: |
+        if [ "${{ inputs.ignore-scripts }}" == "true" ]; then
+          npm ci --ignore-scripts
+        else
+          npm ci
+        fi
+
+    - name: Link node_modules for electron-builder
+      shell: bash
+      # electron-builder expects node_modules in apps/frontend for native module rebuilding.
+      # With npm workspaces, packages are hoisted to root. Create a link so electron-builder
+      # can find the modules during packaging and code signing.
+      # Uses symlink on Unix, directory junction on Windows (works without admin privileges).
+      #
+      # IMPORTANT: npm workspaces may create a partial node_modules in apps/frontend for
+      # packages that couldn't be hoisted. We must remove it and create a proper link to root.
+      run: |
+        # Verify npm ci succeeded
+        if [ ! -d "node_modules" ]; then
+          echo "::error::Root node_modules does not exist. npm ci may have failed."
+          exit 1
+        fi
+
+        # Remove any existing node_modules in apps/frontend
+        # This handles: partial directories from npm workspaces, AND broken symlinks
+        if [ -e "apps/frontend/node_modules" ] || [ -L "apps/frontend/node_modules" ]; then
+          # Check if it's a valid symlink pointing to root node_modules
+          if [ -L "apps/frontend/node_modules" ]; then
+            target=$(readlink apps/frontend/node_modules 2>/dev/null || echo "")
+            if [ "$target" = "../../node_modules" ] && [ -d "apps/frontend/node_modules" ]; then
+              echo "Correct symlink already exists: apps/frontend/node_modules -> ../../node_modules"
+            else
+              echo "Removing incorrect/broken symlink (was: $target)..."
+              rm -f "apps/frontend/node_modules"
+            fi
+          else
+            echo "Removing partial node_modules directory created by npm workspaces..."
+            rm -rf "apps/frontend/node_modules"
+          fi
+        fi
+
+        # Create link if it doesn't exist or was removed
+        if [ ! -L "apps/frontend/node_modules" ]; then
+          if [ "$RUNNER_OS" == "Windows" ]; then
+            # Use directory junction on Windows (works without admin privileges)
+            # Use PowerShell's New-Item -ItemType Junction for reliable path handling
+            abs_target=$(cygpath -w "$(pwd)/node_modules")
+            link_path=$(cygpath -w "$(pwd)/apps/frontend/node_modules")
+            powershell -Command "New-Item -ItemType Junction -Path '$link_path' -Target '$abs_target'" > /dev/null
+            if [ $? -eq 0 ]; then
+              echo "Created junction: apps/frontend/node_modules -> $abs_target"
+            else
+              echo "::error::Failed to create directory junction on Windows"
+              exit 1
+            fi
+          else
+            # Use symlink on Unix (macOS/Linux)
+            if ln -s ../../node_modules apps/frontend/node_modules; then
+              echo "Created symlink: apps/frontend/node_modules -> ../../node_modules"
+            else
+              echo "::error::Failed to create symlink"
+              exit 1
+            fi
+          fi
+        fi
+
+        # Final verification - the link must exist and resolve correctly
+        # Note: On Windows, junctions don't show as symlinks (-L), so we check if the directory exists
+        # and can be listed. On Unix, we also verify it's a symlink.
+        if [ "$RUNNER_OS" != "Windows" ] && [ ! -L "apps/frontend/node_modules" ]; then
+          echo "::error::apps/frontend/node_modules symlink was not created"
+          exit 1
+        fi
+        # Verify the link resolves to a valid directory with content
+        if ! ls apps/frontend/node_modules/electron >/dev/null 2>&1; then
+          echo "::error::apps/frontend/node_modules does not resolve correctly (electron not found)"
+          ls -la apps/frontend/ || true
+          ls apps/frontend/node_modules 2>&1 | head -5 || true
+          exit 1
+        fi
+        count=$(ls apps/frontend/node_modules 2>/dev/null | wc -l)
+        echo "Verified: apps/frontend/node_modules resolves correctly ($count entries)"

.github/actions/setup-python-backend/action.yml

@@ -0,0 +1,52 @@
+name: 'Setup Python Backend'
+description: 'Set up Python with uv package manager and cached dependencies for the backend'
+
+inputs:
+  python-version:
+    description: 'Python version to use'
+    required: false
+    default: '3.12'
+  install-test-deps:
+    description: 'Whether to install test dependencies'
+    required: false
+    default: 'false'
+
+outputs:
+  cache-hit:
+    description: 'Whether cache was hit'
+    value: ${{ steps.cache.outputs.cache-hit }}
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Set up Python ${{ inputs.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv package manager
+      uses: astral-sh/setup-uv@v4
+      with:
+        version: "latest"
+
+    - name: Cache uv dependencies
+      id: cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/uv
+          ~/AppData/Local/uv/cache
+          ~/Library/Caches/uv
+        key: uv-${{ runner.os }}-${{ runner.arch }}-${{ inputs.python-version }}-${{ hashFiles('apps/backend/requirements.txt', 'tests/requirements-test.txt') }}
+        restore-keys: |
+          uv-${{ runner.os }}-${{ runner.arch }}-${{ inputs.python-version }}-
+
+    - name: Install dependencies
+      working-directory: apps/backend
+      shell: bash
+      run: |
+        uv venv
+        uv pip install -r requirements.txt
+        if [ "${{ inputs.install-test-deps }}" == "true" ]; then
+          uv pip install -r ../../tests/requirements-test.txt
+        fi

.github/actions/submit-macos-notarization/action.yml

@@ -0,0 +1,87 @@
+name: 'Submit macOS Notarization'
+description: 'Submit a macOS DMG file for Apple notarization asynchronously'
+
+inputs:
+  apple-id:
+    description: 'Apple ID for notarization'
+    required: true
+  apple-app-specific-password:
+    description: 'Apple app-specific password'
+    required: true
+  apple-team-id:
+    description: 'Apple Team ID'
+    required: true
+  dmg-path:
+    description: 'Path to the dist directory containing the DMG file'
+    required: false
+    default: 'apps/frontend/dist'
+
+outputs:
+  notarization-id:
+    description: 'The notarization request ID'
+    value: ${{ steps.submit.outputs.notarization_id }}
+  dmg-file:
+    description: 'The DMG filename that was submitted'
+    value: ${{ steps.submit.outputs.dmg_file }}
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Submit notarization (async)
+      id: submit
+      shell: bash
+      env:
+        APPLE_ID: ${{ inputs.apple-id }}
+        APPLE_APP_SPECIFIC_PASSWORD: ${{ inputs.apple-app-specific-password }}
+        APPLE_TEAM_ID: ${{ inputs.apple-team-id }}
+        DMG_PATH: ${{ inputs.dmg-path }}
+      run: |
+        if [ -z "$APPLE_ID" ]; then
+          echo "Skipping notarization: APPLE_ID not configured"
+          echo "notarization_id=" >> "$GITHUB_OUTPUT"
+          echo "dmg_file=" >> "$GITHUB_OUTPUT"
+          exit 0
+        fi
+
+        # Find the DMG file
+        DMG_FILE=$(find "$DMG_PATH" -name "*.dmg" -type f | head -1)
+        if [ -z "$DMG_FILE" ]; then
+          echo "::error::No DMG file found in $DMG_PATH"
+          exit 1
+        fi
+
+        echo "Submitting $DMG_FILE for notarization (async)..."
+
+        # Submit for notarization without waiting
+        # Capture both stdout and exit code
+        set +e
+        RESULT=$(xcrun notarytool submit "$DMG_FILE" \
+          --apple-id "$APPLE_ID" \
+          --password "$APPLE_APP_SPECIFIC_PASSWORD" \
+          --team-id "$APPLE_TEAM_ID" \
+          --no-wait \
+          --output-format json 2>&1)
+        SUBMIT_EXIT_CODE=$?
+        set -e
+
+        echo "$RESULT"
+
+        # Check if submission command itself failed (not just missing ID)
+        if [ $SUBMIT_EXIT_CODE -ne 0 ]; then
+          echo "::error::notarytool submit failed with exit code $SUBMIT_EXIT_CODE"
+          exit 1
+        fi
+
+        # Extract the notarization ID from JSON response
+        # jq is always available on macOS runners
+        NOTARIZATION_ID=$(echo "$RESULT" | jq -r '.id // empty' 2>/dev/null)
+
+        if [ -z "$NOTARIZATION_ID" ]; then
+          echo "::error::Failed to get notarization ID from response"
+          echo "Response was: $RESULT"
+          exit 1
+        fi
+
+        echo "Notarization submitted with ID: $NOTARIZATION_ID"
+        echo "notarization_id=$NOTARIZATION_ID" >> "$GITHUB_OUTPUT"
+        echo "dmg_file=$(basename "$DMG_FILE")" >> "$GITHUB_OUTPUT"

.github/dependabot.yml

@@ -0,0 +1,37 @@
+version: 2
+updates:
+  # Python dependencies
+  - package-ecosystem: pip
+    directory: /apps/backend
+    schedule:
+      interval: weekly
+    open-pull-requests-limit: 5
+    labels:
+      - dependencies
+      - python
+    commit-message:
+      prefix: "chore(deps)"
+
+  # npm dependencies
+  - package-ecosystem: npm
+    directory: /apps/frontend
+    schedule:
+      interval: weekly
+    open-pull-requests-limit: 5
+    labels:
+      - dependencies
+      - javascript
+    commit-message:
+      prefix: "chore(deps)"
+
+  # GitHub Actions
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    open-pull-requests-limit: 5
+    labels:
+      - dependencies
+      - ci
+    commit-message:
+      prefix: "ci(deps)"

.github/workflows/beta-release.yml

@@ -32,112 +32,101 @@ jobs:
 
           echo "Valid beta version: $VERSION"
 
-  update-version:
-    name: Update package.json version
+  create-tag:
+    name: Create beta tag
     needs: validate-version
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     outputs:
-      version: ${{ steps.version.outputs.version }}
+      version: ${{ github.event.inputs.version }}
     steps:
       - uses: actions/checkout@v4
         with:
           ref: develop
-          token: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
-        with:
-          node-version: '24'
-
-      - name: Update package.json version
-        id: version
-        run: |
-          VERSION="${{ github.event.inputs.version }}"
-
-          # Update frontend package.json
-          cd apps/frontend
-          npm version "$VERSION" --no-git-tag-version
-
-          echo "version=$VERSION" >> $GITHUB_OUTPUT
-          echo "Updated package.json to version $VERSION"
-
-      - name: Commit version bump
-        if: ${{ github.event.inputs.dry_run != 'true' }}
-        run: |
-          VERSION="${{ github.event.inputs.version }}"
-          git config user.name "github-actions[bot]"
-          git config user.email "github-actions[bot]@users.noreply.github.com"
-          # Stage all changed files in frontend directory (handles package-lock.json if it exists)
-          git add -A apps/frontend/
-          git commit -m "chore: bump version to $VERSION for beta release"
-          git push origin develop
 
       - name: Create and push tag
         if: ${{ github.event.inputs.dry_run != 'true' }}
         run: |
           VERSION="${{ github.event.inputs.version }}"
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
           git tag -a "v$VERSION" -m "Beta release v$VERSION"
           git push origin "v$VERSION"
           echo "Created tag v$VERSION"
 
+      - name: Create tag only (dry run)
+        if: ${{ github.event.inputs.dry_run == 'true' }}
+        run: |
+          VERSION="${{ github.event.inputs.version }}"
+          echo "DRY RUN: Would create tag v$VERSION"
+
   # Intel build on Intel runner for native compilation
   build-macos-intel:
-    needs: update-version
+    needs: create-tag
     runs-on: macos-15-intel
+    outputs:
+      notarization_id: ${{ steps.notarize.outputs.notarization-id }}
+      dmg_file: ${{ steps.notarize.outputs.dmg-file }}
     steps:
       - uses: actions/checkout@v4
         with:
-          ref: v${{ needs.update-version.outputs.version }}
+          # Use tag for real releases, develop branch for dry runs
+          ref: ${{ github.event.inputs.dry_run == 'true' && 'develop' || format('v{0}', needs.create-tag.outputs.version) }}
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
         with:
-          node-version: '24'
+          python-version: '3.11'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        run: echo "dir=$(npm config get cache)" >> $GITHUB_OUTPUT
+      - name: Setup Node.js and install dependencies
+        uses: ./.github/actions/setup-node-frontend
 
-      - uses: actions/cache@v4
+      - name: Install Rust toolchain (for building native Python packages)
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache pip wheel cache (for compiled packages like real_ladybug)
+        uses: actions/cache@v5
         with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
+          path: ~/Library/Caches/pip
+          key: pip-wheel-${{ runner.os }}-x64-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            pip-wheel-${{ runner.os }}-x64-
 
-      - name: Install dependencies
-        run: cd apps/frontend && npm ci
+      - name: Cache bundled Python
+        uses: actions/cache@v5
+        with:
+          path: apps/frontend/python-runtime
+          key: python-bundle-${{ runner.os }}-x64-3.12.8-rust-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            python-bundle-${{ runner.os }}-x64-3.12.8-rust-
 
       - name: Build application
         run: cd apps/frontend && npm run build
+        env:
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
       - name: Package macOS (Intel)
-        run: cd apps/frontend && npm run package:mac -- --arch=x64
+        run: |
+          VERSION="${{ needs.create-tag.outputs.version }}"
+          cd apps/frontend && npm run package:mac -- --x64 --config.extraMetadata.version="$VERSION"
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           CSC_LINK: ${{ secrets.MAC_CERTIFICATE }}
           CSC_KEY_PASSWORD: ${{ secrets.MAC_CERTIFICATE_PASSWORD }}
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
-      - name: Notarize macOS Intel app
-        env:
-          APPLE_ID: ${{ secrets.APPLE_ID }}
-          APPLE_APP_SPECIFIC_PASSWORD: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
-          APPLE_TEAM_ID: ${{ secrets.APPLE_TEAM_ID }}
-        run: |
-          if [ -z "$APPLE_ID" ]; then
-            echo "Skipping notarization: APPLE_ID not configured"
-            exit 0
-          fi
-          cd apps/frontend
-          for dmg in dist/*.dmg; do
-            echo "Notarizing $dmg..."
-            xcrun notarytool submit "$dmg" \
-              --apple-id "$APPLE_ID" \
-              --password "$APPLE_APP_SPECIFIC_PASSWORD" \
-              --team-id "$APPLE_TEAM_ID" \
-              --wait
-            xcrun stapler staple "$dmg"
-            echo "Successfully notarized and stapled $dmg"
-          done
+      - name: Submit notarization (async)
+        id: notarize
+        uses: ./.github/actions/submit-macos-notarization
+        with:
+          apple-id: ${{ secrets.APPLE_ID }}
+          apple-app-specific-password: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
+          apple-team-id: ${{ secrets.APPLE_TEAM_ID }}
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -146,65 +135,71 @@ jobs:
           path: |
             apps/frontend/dist/*.dmg
             apps/frontend/dist/*.zip
+            apps/frontend/dist/*.yml
 
   # Apple Silicon build on ARM64 runner for native compilation
   build-macos-arm64:
-    needs: update-version
+    needs: create-tag
     runs-on: macos-15
+    outputs:
+      notarization_id: ${{ steps.notarize.outputs.notarization-id }}
+      dmg_file: ${{ steps.notarize.outputs.dmg-file }}
     steps:
       - uses: actions/checkout@v4
         with:
-          ref: v${{ needs.update-version.outputs.version }}
+          # Use tag for real releases, develop branch for dry runs
+          ref: ${{ github.event.inputs.dry_run == 'true' && 'develop' || format('v{0}', needs.create-tag.outputs.version) }}
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
         with:
-          node-version: '24'
+          python-version: '3.11'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        run: echo "dir=$(npm config get cache)" >> $GITHUB_OUTPUT
+      - name: Setup Node.js and install dependencies
+        uses: ./.github/actions/setup-node-frontend
 
-      - uses: actions/cache@v4
+      - name: Cache pip wheel cache
+        uses: actions/cache@v5
         with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
+          path: ~/Library/Caches/pip
+          key: pip-wheel-${{ runner.os }}-arm64-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            pip-wheel-${{ runner.os }}-arm64-
 
-      - name: Install dependencies
-        run: cd apps/frontend && npm ci
+      - name: Cache bundled Python
+        uses: actions/cache@v5
+        with:
+          path: apps/frontend/python-runtime
+          key: python-bundle-${{ runner.os }}-arm64-3.12.8-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            python-bundle-${{ runner.os }}-arm64-3.12.8-
 
       - name: Build application
         run: cd apps/frontend && npm run build
+        env:
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
       - name: Package macOS (Apple Silicon)
-        run: cd apps/frontend && npm run package:mac -- --arch=arm64
+        run: |
+          VERSION="${{ needs.create-tag.outputs.version }}"
+          cd apps/frontend && npm run package:mac -- --arm64 --config.extraMetadata.version="$VERSION"
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           CSC_LINK: ${{ secrets.MAC_CERTIFICATE }}
           CSC_KEY_PASSWORD: ${{ secrets.MAC_CERTIFICATE_PASSWORD }}
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
-      - name: Notarize macOS ARM64 app
-        env:
-          APPLE_ID: ${{ secrets.APPLE_ID }}
-          APPLE_APP_SPECIFIC_PASSWORD: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
-          APPLE_TEAM_ID: ${{ secrets.APPLE_TEAM_ID }}
-        run: |
-          if [ -z "$APPLE_ID" ]; then
-            echo "Skipping notarization: APPLE_ID not configured"
-            exit 0
-          fi
-          cd apps/frontend
-          for dmg in dist/*.dmg; do
-            echo "Notarizing $dmg..."
-            xcrun notarytool submit "$dmg" \
-              --apple-id "$APPLE_ID" \
-              --password "$APPLE_APP_SPECIFIC_PASSWORD" \
-              --team-id "$APPLE_TEAM_ID" \
-              --wait
-            xcrun stapler staple "$dmg"
-            echo "Successfully notarized and stapled $dmg"
-          done
+      - name: Submit notarization (async)
+        id: notarize
+        uses: ./.github/actions/submit-macos-notarization
+        with:
+          apple-id: ${{ secrets.APPLE_ID }}
+          apple-app-specific-password: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
+          apple-team-id: ${{ secrets.APPLE_TEAM_ID }}
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -213,43 +208,177 @@ jobs:
           path: |
             apps/frontend/dist/*.dmg
             apps/frontend/dist/*.zip
+            apps/frontend/dist/*.yml
 
   build-windows:
-    needs: update-version
+    needs: create-tag
     runs-on: windows-latest
+    permissions:
+      id-token: write  # Required for OIDC authentication with Azure
+      contents: read
+    env:
+      # Job-level env so AZURE_CLIENT_ID is available for step-level if conditions
+      AZURE_CLIENT_ID: ${{ secrets.AZURE_CLIENT_ID }}
     steps:
       - uses: actions/checkout@v4
         with:
-          ref: v${{ needs.update-version.outputs.version }}
+          # Use tag for real releases, develop branch for dry runs
+          ref: ${{ github.event.inputs.dry_run == 'true' && 'develop' || format('v{0}', needs.create-tag.outputs.version) }}
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
         with:
-          node-version: '24'
+          python-version: '3.11'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        shell: bash
-        run: echo "dir=$(npm config get cache)" >> $GITHUB_OUTPUT
+      - name: Setup Node.js and install dependencies
+        uses: ./.github/actions/setup-node-frontend
 
-      - uses: actions/cache@v4
+      - name: Cache pip wheel cache
+        uses: actions/cache@v5
         with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
+          path: ~\AppData\Local\pip\Cache
+          key: pip-wheel-${{ runner.os }}-x64-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            pip-wheel-${{ runner.os }}-x64-
 
-      - name: Install dependencies
-        run: cd apps/frontend && npm ci
+      - name: Cache bundled Python
+        uses: actions/cache@v5
+        with:
+          path: apps/frontend/python-runtime
+          key: python-bundle-${{ runner.os }}-x64-3.12.8-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            python-bundle-${{ runner.os }}-x64-3.12.8-
 
       - name: Build application
         run: cd apps/frontend && npm run build
+        env:
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
       - name: Package Windows
-        run: cd apps/frontend && npm run package:win
+        shell: bash
+        run: |
+          VERSION="${{ needs.create-tag.outputs.version }}"
+          cd apps/frontend && npm run package:win -- --config.extraMetadata.version="$VERSION"
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          CSC_LINK: ${{ secrets.WIN_CERTIFICATE }}
-          CSC_KEY_PASSWORD: ${{ secrets.WIN_CERTIFICATE_PASSWORD }}
+          # Disable electron-builder's built-in signing (we use Azure Trusted Signing instead)
+          CSC_IDENTITY_AUTO_DISCOVERY: false
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
+
+      - name: Azure Login (OIDC)
+        if: env.AZURE_CLIENT_ID != ''
+        uses: azure/login@v2
+        with:
+          client-id: ${{ secrets.AZURE_CLIENT_ID }}
+          tenant-id: ${{ secrets.AZURE_TENANT_ID }}
+          subscription-id: ${{ secrets.AZURE_SUBSCRIPTION_ID }}
+
+      - name: Sign Windows executable with Azure Trusted Signing
+        if: env.AZURE_CLIENT_ID != ''
+        uses: azure/trusted-signing-action@v0.5.11
+        with:
+          endpoint: https://neu.codesigning.azure.net/
+          trusted-signing-account-name: ${{ secrets.AZURE_SIGNING_ACCOUNT }}
+          certificate-profile-name: ${{ secrets.AZURE_CERTIFICATE_PROFILE }}
+          files-folder: apps/frontend/dist
+          files-folder-filter: exe
+          file-digest: SHA256
+          timestamp-rfc3161: http://timestamp.acs.microsoft.com
+          timestamp-digest: SHA256
+
+      - name: Verify Windows executable is signed
+        if: env.AZURE_CLIENT_ID != ''
+        shell: pwsh
+        run: |
+          cd apps/frontend/dist
+          $exeFile = Get-ChildItem -Filter "*.exe" | Select-Object -First 1
+          if ($exeFile) {
+            Write-Host "Verifying signature on $($exeFile.Name)..."
+            $sig = Get-AuthenticodeSignature -FilePath $exeFile.FullName
+            if ($sig.Status -ne 'Valid') {
+              Write-Host "::error::Signature verification failed: $($sig.Status)"
+              Write-Host "::error::Status Message: $($sig.StatusMessage)"
+              exit 1
+            }
+            Write-Host "✅ Signature verified successfully"
+            Write-Host "  Subject: $($sig.SignerCertificate.Subject)"
+            Write-Host "  Issuer: $($sig.SignerCertificate.Issuer)"
+            Write-Host "  Thumbprint: $($sig.SignerCertificate.Thumbprint)"
+          } else {
+            Write-Host "::error::No .exe file found to verify"
+            exit 1
+          }
+
+      - name: Regenerate checksums after signing
+        if: env.AZURE_CLIENT_ID != ''
+        shell: pwsh
+        run: |
+          $ErrorActionPreference = "Stop"
+          cd apps/frontend/dist
+
+          # Find the installer exe (electron-builder names it with "Setup" or just the app name)
+          # electron-builder produces one installer exe per build
+          $exeFiles = Get-ChildItem -Filter "*.exe"
+          if ($exeFiles.Count -eq 0) {
+            Write-Host "::error::No .exe files found in dist folder"
+            exit 1
+          }
+
+          Write-Host "Found $($exeFiles.Count) exe file(s): $($exeFiles.Name -join ', ')"
+
+          $ymlFile = "latest.yml"
+          if (-not (Test-Path $ymlFile)) {
+            Write-Host "::error::$ymlFile not found - cannot update checksums"
+            exit 1
+          }
+
+          $content = Get-Content $ymlFile -Raw
+          $originalContent = $content
+
+          # Process each exe file and update its hash in latest.yml
+          foreach ($exeFile in $exeFiles) {
+            Write-Host "Processing $($exeFile.Name)..."
+
+            # Compute SHA512 hash and convert to base64 (electron-builder format)
+            $bytes = [System.IO.File]::ReadAllBytes($exeFile.FullName)
+            $sha512 = [System.Security.Cryptography.SHA512]::Create()
+            $hashBytes = $sha512.ComputeHash($bytes)
+            $hash = [System.Convert]::ToBase64String($hashBytes)
+            $size = $exeFile.Length
+
+            Write-Host "  Hash: $hash"
+            Write-Host "  Size: $size"
+          }
+
+          # For electron-builder, latest.yml has a single file entry for the installer
+          # Update the sha512 and size for the primary exe (first one, typically the installer)
+          $primaryExe = $exeFiles | Select-Object -First 1
+          $bytes = [System.IO.File]::ReadAllBytes($primaryExe.FullName)
+          $sha512 = [System.Security.Cryptography.SHA512]::Create()
+          $hashBytes = $sha512.ComputeHash($bytes)
+          $hash = [System.Convert]::ToBase64String($hashBytes)
+          $size = $primaryExe.Length
+
+          # Update sha512 hash (base64 pattern: alphanumeric, +, /, =)
+          $content = $content -replace 'sha512: [A-Za-z0-9+/=]+', "sha512: $hash"
+          # Update size
+          $content = $content -replace 'size: \d+', "size: $size"
+
+          if ($content -eq $originalContent) {
+            Write-Host "::error::Checksum replacement failed - content unchanged. Check if latest.yml format has changed."
+            exit 1
+          }
+
+          Set-Content -Path $ymlFile -Value $content -NoNewline
+          Write-Host "✅ Updated $ymlFile with new base64 hash and size for $($primaryExe.Name)"
+
+      - name: Skip signing notice
+        if: env.AZURE_CLIENT_ID == ''
+        run: echo "::warning::Windows signing skipped - AZURE_CLIENT_ID not configured. The .exe will be unsigned."
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -257,40 +386,69 @@ jobs:
           name: windows-builds
           path: |
             apps/frontend/dist/*.exe
+            apps/frontend/dist/*.yml
 
   build-linux:
-    needs: update-version
+    needs: create-tag
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
-          ref: v${{ needs.update-version.outputs.version }}
+          # Use tag for real releases, develop branch for dry runs
+          ref: ${{ github.event.inputs.dry_run == 'true' && 'develop' || format('v{0}', needs.create-tag.outputs.version) }}
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
         with:
-          node-version: '24'
+          python-version: '3.11'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        run: echo "dir=$(npm config get cache)" >> $GITHUB_OUTPUT
+      - name: Setup Node.js and install dependencies
+        uses: ./.github/actions/setup-node-frontend
 
-      - uses: actions/cache@v4
+      - name: Setup Flatpak and verification tools
+        run: |
+          set -e
+          sudo apt-get update
+          sudo apt-get install -y flatpak flatpak-builder libarchive-tools
+          flatpak remote-add --user --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
+          flatpak install -y --user flathub org.freedesktop.Platform//25.08 org.freedesktop.Sdk//25.08
+          flatpak install -y --user flathub org.electronjs.Electron2.BaseApp//25.08
+
+      - name: Cache pip wheel cache
+        uses: actions/cache@v5
         with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
+          path: ~/.cache/pip
+          key: pip-wheel-${{ runner.os }}-x64-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            pip-wheel-${{ runner.os }}-x64-
 
-      - name: Install dependencies
-        run: cd apps/frontend && npm ci
+      - name: Cache bundled Python
+        uses: actions/cache@v5
+        with:
+          path: apps/frontend/python-runtime
+          key: python-bundle-${{ runner.os }}-x64-3.12.8-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            python-bundle-${{ runner.os }}-x64-3.12.8-
 
       - name: Build application
         run: cd apps/frontend && npm run build
+        env:
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
       - name: Package Linux
-        run: cd apps/frontend && npm run package:linux
+        run: |
+          VERSION="${{ needs.create-tag.outputs.version }}"
+          cd apps/frontend && npm run package:linux -- --config.extraMetadata.version="$VERSION"
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
+
+      - name: Verify Linux packages
+        run: cd apps/frontend && npm run verify:linux
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -299,9 +457,53 @@ jobs:
           path: |
             apps/frontend/dist/*.AppImage
             apps/frontend/dist/*.deb
+            apps/frontend/dist/*.flatpak
+            apps/frontend/dist/*.yml
+
+  # Finalize macOS notarization (runs in parallel with Windows/Linux builds)
+  finalize-notarization:
+    needs: [build-macos-intel, build-macos-arm64]
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download Intel DMG
+        uses: actions/download-artifact@v7
+        with:
+          name: macos-intel-builds
+          path: intel
+
+      - name: Download ARM64 DMG
+        uses: actions/download-artifact@v7
+        with:
+          name: macos-arm64-builds
+          path: arm64
+
+      - name: Wait for notarization and staple
+        uses: ./.github/actions/finalize-macos-notarization
+        with:
+          apple-id: ${{ secrets.APPLE_ID }}
+          apple-app-specific-password: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
+          apple-team-id: ${{ secrets.APPLE_TEAM_ID }}
+          intel-notarization-id: ${{ needs.build-macos-intel.outputs.notarization_id }}
+          arm64-notarization-id: ${{ needs.build-macos-arm64.outputs.notarization_id }}
+          intel-dmg-file: ${{ needs.build-macos-intel.outputs.dmg_file }}
+          arm64-dmg-file: ${{ needs.build-macos-arm64.outputs.dmg_file }}
+
+      - name: Upload stapled Intel DMG
+        uses: actions/upload-artifact@v4
+        with:
+          name: macos-intel-stapled
+          path: intel/*.dmg
+
+      - name: Upload stapled ARM64 DMG
+        uses: actions/upload-artifact@v4
+        with:
+          name: macos-arm64-stapled
+          path: arm64/*.dmg
 
   create-release:
-    needs: [update-version, build-macos-intel, build-macos-arm64, build-windows, build-linux]
+    needs: [create-tag, finalize-notarization, build-windows, build-linux]
     runs-on: ubuntu-latest
     if: ${{ github.event.inputs.dry_run != 'true' }}
     permissions:
@@ -309,29 +511,118 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          ref: v${{ needs.update-version.outputs.version }}
+          ref: v${{ needs.create-tag.outputs.version }}
           fetch-depth: 0
 
       - name: Download all artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           path: dist
 
-      - name: Flatten and validate artifacts
+      - name: Flatten binary artifacts
         run: |
           mkdir -p release-assets
-          find dist -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" \) -exec cp {} release-assets/ \;
+
+          # Copy stapled macOS DMGs (from finalize-notarization job)
+          # Validate that stapled DMGs exist before copying
+          if ! find dist/macos-intel-stapled dist/macos-arm64-stapled -type f -name "*.dmg" 2>/dev/null | grep -q .; then
+            echo "::warning::No stapled DMGs found. Using un-stapled DMGs from build artifacts."
+            find dist/macos-intel-builds dist/macos-arm64-builds -type f -name "*.dmg" -exec cp {} release-assets/ \; 2>/dev/null || true
+          else
+            find dist/macos-intel-stapled dist/macos-arm64-stapled -type f -name "*.dmg" -exec cp {} release-assets/ \; 2>/dev/null || true
+          fi
+
+          # Copy other macOS artifacts (zip, yml, blockmap for delta updates) from original build
+          find dist/macos-intel-builds dist/macos-arm64-builds -type f \( -name "*.zip" -o -name "*.yml" -o -name "*.blockmap" \) -exec cp {} release-assets/ \; 2>/dev/null || true
+
+          # Copy Windows and Linux artifacts (including blockmap for delta updates)
+          find dist/windows-builds dist/linux-builds -type f \( -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" -o -name "*.flatpak" -o -name "*.yml" -o -name "*.blockmap" \) -exec cp {} release-assets/ \; 2>/dev/null || true
 
           # Validate that at least one artifact was copied
-          artifact_count=$(find release-assets -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" \) | wc -l)
+          artifact_count=$(find release-assets -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" -o -name "*.flatpak" \) | wc -l)
           if [ "$artifact_count" -eq 0 ]; then
-            echo "::error::No build artifacts found! Expected .dmg, .zip, .exe, .AppImage, or .deb files."
+            echo "::error::No build artifacts found! Expected .dmg, .zip, .exe, .AppImage, .deb, or .flatpak files."
             exit 1
           fi
 
-          echo "Found $artifact_count artifact(s):"
+          echo "Found $artifact_count binary artifact(s):"
           ls -la release-assets/
 
+      # Merge macOS manifests from Intel and ARM64 builds
+      # See: https://github.com/electron-userland/electron-builder/issues/5592
+      - name: Merge macOS manifests
+        uses: ./.github/actions/merge-macos-manifests
+        with:
+          dist-path: dist
+          output-path: release-assets
+          copy-other-manifests: 'true'
+
+      - name: Rename and validate beta manifests
+        run: |
+          cd release-assets
+
+          echo "=== Current manifest files ==="
+          ls -la *.yml 2>/dev/null || echo "No yml files found yet"
+
+          # electron-builder generates latest*.yml files by default
+          # For beta channel, electron-updater expects beta*.yml files
+          # Rename: latest.yml -> beta.yml, latest-mac.yml -> beta-mac.yml, latest-linux.yml -> beta-linux.yml
+
+          # Windows: latest.yml -> beta.yml
+          if [ -f "latest.yml" ]; then
+            echo "Renaming latest.yml -> beta.yml (Windows)"
+            mv latest.yml beta.yml
+          fi
+
+          # macOS: latest-mac.yml -> beta-mac.yml
+          if [ -f "latest-mac.yml" ]; then
+            echo "Renaming latest-mac.yml -> beta-mac.yml (macOS)"
+            mv latest-mac.yml beta-mac.yml
+          fi
+
+          # Linux: latest-linux.yml -> beta-linux.yml
+          if [ -f "latest-linux.yml" ]; then
+            echo "Renaming latest-linux.yml -> beta-linux.yml (Linux)"
+            mv latest-linux.yml beta-linux.yml
+          fi
+
+          # Linux ARM64: latest-linux-arm64.yml -> beta-linux-arm64.yml (if exists)
+          if [ -f "latest-linux-arm64.yml" ]; then
+            echo "Renaming latest-linux-arm64.yml -> beta-linux-arm64.yml (Linux ARM64)"
+            mv latest-linux-arm64.yml beta-linux-arm64.yml
+          fi
+
+          echo ""
+          echo "=== Beta manifest files after rename ==="
+          ls -la *.yml 2>/dev/null || echo "No yml files found"
+
+          # Validate required beta manifests exist
+          missing_manifests=""
+
+          if [ ! -f "beta-mac.yml" ]; then
+            missing_manifests="$missing_manifests beta-mac.yml"
+          fi
+
+          if [ ! -f "beta.yml" ]; then
+            missing_manifests="$missing_manifests beta.yml"
+          fi
+
+          if [ ! -f "beta-linux.yml" ]; then
+            missing_manifests="$missing_manifests beta-linux.yml"
+          fi
+
+          if [ -n "$missing_manifests" ]; then
+            echo "::error::Missing required beta manifests:$missing_manifests"
+            echo "::error::Auto-update will fail on affected platforms without these files!"
+            exit 1
+          fi
+
+          echo ""
+          echo "All required beta manifests present:"
+          echo "  - beta-mac.yml (macOS)"
+          echo "  - beta.yml (Windows)"
+          echo "  - beta-linux.yml (Linux)"
+
       - name: Generate checksums
         run: |
           cd release-assets
@@ -341,10 +632,10 @@ jobs:
       - name: Create Beta Release
         uses: softprops/action-gh-release@v2
         with:
-          tag_name: v${{ needs.update-version.outputs.version }}
-          name: v${{ needs.update-version.outputs.version }} (Beta)
+          tag_name: v${{ needs.create-tag.outputs.version }}
+          name: v${{ needs.create-tag.outputs.version }} (Beta)
           body: |
-            ## Beta Release v${{ needs.update-version.outputs.version }}
+            ## Beta Release v${{ needs.create-tag.outputs.version }}
 
             This is a **beta release** for testing new features. It may contain bugs or incomplete functionality.
 
@@ -358,7 +649,7 @@ jobs:
 
             ---
 
-            **Full Changelog**: https://github.com/${{ github.repository }}/compare/main...v${{ needs.update-version.outputs.version }}
+            **Full Changelog**: https://github.com/${{ github.repository }}/compare/main...v${{ needs.create-tag.outputs.version }}
           files: release-assets/*
           draft: false
           prerelease: true
@@ -366,24 +657,89 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   dry-run-summary:
-    needs: [update-version, build-macos-intel, build-macos-arm64, build-windows, build-linux]
+    needs: [create-tag, finalize-notarization, build-windows, build-linux]
     runs-on: ubuntu-latest
     if: ${{ github.event.inputs.dry_run == 'true' }}
     steps:
+      - uses: actions/checkout@v4
+
       - name: Download all artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           path: dist
 
+      - name: Flatten binary artifacts
+        run: |
+          mkdir -p release-assets
+
+          # Copy stapled macOS DMGs (from finalize-notarization job)
+          find dist/macos-intel-stapled dist/macos-arm64-stapled -type f -name "*.dmg" -exec cp {} release-assets/ \; 2>/dev/null || true
+
+          # Copy other macOS artifacts (zip, yml, blockmap for delta updates) from original build
+          find dist/macos-intel-builds dist/macos-arm64-builds -type f \( -name "*.zip" -o -name "*.yml" -o -name "*.blockmap" \) -exec cp {} release-assets/ \; 2>/dev/null || true
+
+          # Copy Windows and Linux artifacts (including blockmap for delta updates)
+          find dist/windows-builds dist/linux-builds -type f \( -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" -o -name "*.flatpak" -o -name "*.yml" -o -name "*.blockmap" \) -exec cp {} release-assets/ \; 2>/dev/null || true
+
+      # Merge macOS manifests (same logic as real release)
+      - name: Merge macOS manifests
+        uses: ./.github/actions/merge-macos-manifests
+        with:
+          dist-path: dist
+          output-path: release-assets
+          copy-other-manifests: 'true'
+
+      - name: Validate and rename beta manifests
+        run: |
+          cd release-assets
+
+          # Rename latest*.yml to beta*.yml
+          [ -f "latest.yml" ] && mv latest.yml beta.yml
+          [ -f "latest-mac.yml" ] && mv latest-mac.yml beta-mac.yml
+          [ -f "latest-linux.yml" ] && mv latest-linux.yml beta-linux.yml
+          [ -f "latest-linux-arm64.yml" ] && mv latest-linux-arm64.yml beta-linux-arm64.yml
+
+          # Validate required manifests
+          missing=""
+          [ ! -f "beta-mac.yml" ] && missing="$missing beta-mac.yml"
+          [ ! -f "beta.yml" ] && missing="$missing beta.yml"
+          [ ! -f "beta-linux.yml" ] && missing="$missing beta-linux.yml"
+
+          if [ -n "$missing" ]; then
+            echo "::warning::DRY RUN: Missing required beta manifests:$missing"
+            echo "MANIFEST_STATUS=FAILED" >> $GITHUB_ENV
+          else
+            echo "MANIFEST_STATUS=PASSED" >> $GITHUB_ENV
+
+            # Show merged manifest content for verification
+            echo ""
+            echo "=== beta-mac.yml content (should have both architectures) ==="
+            cat beta-mac.yml
+          fi
+
       - name: Dry run summary
         run: |
           echo "## Beta Release Dry Run Complete" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "**Version:** ${{ needs.update-version.outputs.version }}" >> $GITHUB_STEP_SUMMARY
+          echo "**Version:** ${{ needs.create-tag.outputs.version }}" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "Build artifacts created successfully:" >> $GITHUB_STEP_SUMMARY
+
+          echo "### Build Artifacts" >> $GITHUB_STEP_SUMMARY
           echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
-          find dist -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" \) >> $GITHUB_STEP_SUMMARY
+          find dist -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" -o -name "*.flatpak" \) >> $GITHUB_STEP_SUMMARY
           echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
+
+          echo "### Update Manifests (Required for Auto-Update)" >> $GITHUB_STEP_SUMMARY
+          if [ "$MANIFEST_STATUS" = "PASSED" ]; then
+            echo "All required beta manifests present:" >> $GITHUB_STEP_SUMMARY
+            echo "- beta-mac.yml (macOS)" >> $GITHUB_STEP_SUMMARY
+            echo "- beta.yml (Windows)" >> $GITHUB_STEP_SUMMARY
+            echo "- beta-linux.yml (Linux)" >> $GITHUB_STEP_SUMMARY
+          else
+            echo "**WARNING: Missing required manifests! Auto-update will fail.**" >> $GITHUB_STEP_SUMMARY
+            echo "Check build logs for details." >> $GITHUB_STEP_SUMMARY
+          fi
+          echo "" >> $GITHUB_STEP_SUMMARY
+
           echo "To create a real release, run this workflow again with dry_run unchecked." >> $GITHUB_STEP_SUMMARY

.github/workflows/build-prebuilds.yml

@@ -10,11 +10,11 @@ on:
       electron_version:
         description: 'Electron version to build for'
         required: false
-        default: '39.2.6'
+        default: '40.0.0'
 
 env:
   # Default Electron version - update when upgrading Electron in package.json
-  ELECTRON_VERSION: ${{ github.event.inputs.electron_version || '39.2.6' }}
+  ELECTRON_VERSION: ${{ github.event.inputs.electron_version || '40.0.0' }}
 
 jobs:
   build-windows:
@@ -30,7 +30,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Node.js
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: '24'
 
@@ -110,7 +110,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download all artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           path: artifacts
 

.github/workflows/ci.yml

@@ -1,59 +1,105 @@
+# Cross-Platform CI Pipeline
+#
+# Tests on all target platforms (Linux, Windows, macOS) to catch
+# platform-specific bugs before they merge. ALL platforms must pass.
+#
+# Optimized: Reduced matrix (4 jobs vs 6), merged integration tests,
+# coverage on Linux only, path filters to skip on docs-only changes.
+
 name: CI
 
 on:
   push:
     branches: [main, develop]
+    paths:
+      - 'apps/**'
+      - 'tests/**'
+      - 'package*.json'
+      - 'requirements*.txt'
+      - 'pyproject.toml'
+      - 'tsconfig*.json'
+      - 'biome.jsonc'
+      - '.github/workflows/ci.yml'
+      - '.github/actions/**'
   pull_request:
     branches: [main, develop]
+    paths:
+      - 'apps/**'
+      - 'tests/**'
+      - 'package*.json'
+      - 'requirements*.txt'
+      - 'pyproject.toml'
+      - 'tsconfig*.json'
+      - 'biome.jsonc'
+      - '.github/workflows/ci.yml'
+      - '.github/actions/**'
+
+concurrency:
+  group: ci-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  actions: read
 
 jobs:
-  # Python tests
+  # --------------------------------------------------------------------------
+  # Python Backend Tests - Optimized Matrix (4 jobs instead of 6)
+  # --------------------------------------------------------------------------
   test-python:
-    runs-on: ubuntu-latest
+    name: test-python (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.12', '3.13']
+        # 3.12 on all OS for cross-platform coverage
+        # 3.13 on Linux only for compatibility check (saves 2 jobs)
+        include:
+          - os: ubuntu-latest
+            python-version: '3.12'
+          - os: ubuntu-latest
+            python-version: '3.13'
+          - os: windows-latest
+            python-version: '3.12'
+          - os: macos-latest
+            python-version: '3.12'
 
     steps:
-      - name: Checkout
+      - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - name: Setup Python backend
+        uses: ./.github/actions/setup-python-backend
         with:
           python-version: ${{ matrix.python-version }}
+          install-test-deps: 'true'
 
-      - name: Install uv
-        uses: astral-sh/setup-uv@v4
-        with:
-          version: "latest"
-
-      - name: Install dependencies
-        working-directory: apps/backend
-        run: |
-          uv venv
-          uv pip install -r requirements.txt
-          uv pip install -r ../../tests/requirements-test.txt
-
-      - name: Run tests
+      - name: Run all tests (including platform-specific)
         working-directory: apps/backend
+        shell: bash
         env:
           PYTHONPATH: ${{ github.workspace }}/apps/backend
         run: |
-          source .venv/bin/activate
+          if [ "$RUNNER_OS" == "Windows" ]; then
+            source .venv/Scripts/activate
+          else
+            source .venv/bin/activate
+          fi
           pytest ../../tests/ -v --tb=short -x
 
-      - name: Run tests with coverage
-        if: matrix.python-version == '3.12'
+      - name: Run coverage (Linux + Python 3.12 only)
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
         working-directory: apps/backend
+        shell: bash
         env:
           PYTHONPATH: ${{ github.workspace }}/apps/backend
         run: |
           source .venv/bin/activate
-          pytest ../../tests/ -v --cov=. --cov-report=xml --cov-report=term-missing
+          pytest ../../tests/ -v --cov=. --cov-report=xml --cov-report=term-missing --cov-fail-under=10
 
-      - name: Upload coverage reports
-        if: matrix.python-version == '3.12'
+      - name: Upload coverage to Codecov
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
         uses: codecov/codecov-action@v4
         with:
           file: ./apps/backend/coverage.xml
@@ -61,44 +107,59 @@ jobs:
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-  # Frontend lint, typecheck, test, and build
+  # --------------------------------------------------------------------------
+  # Frontend Tests - All Platforms
+  # --------------------------------------------------------------------------
   test-frontend:
-    runs-on: ubuntu-latest
+    name: test-frontend (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
     steps:
-      - name: Checkout
+      - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Node.js frontend
+        uses: ./.github/actions/setup-node-frontend
         with:
-          node-version: '24'
+          ignore-scripts: 'true'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        run: echo "dir=$(npm config get cache)" >> "$GITHUB_OUTPUT"
-
-      - uses: actions/cache@v4
-        with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
-
-      - name: Install dependencies
-        working-directory: apps/frontend
-        run: npm ci --ignore-scripts
-
-      - name: Lint
-        working-directory: apps/frontend
-        run: npm run lint
-
-      - name: Type check
+      - name: Run TypeScript type check
         working-directory: apps/frontend
         run: npm run typecheck
 
-      - name: Run tests
+      - name: Run unit tests
         working-directory: apps/frontend
         run: npm run test
 
-      - name: Build
+      - name: Build application
         working-directory: apps/frontend
         run: npm run build
+
+  # --------------------------------------------------------------------------
+  # Gate Job - Single check for branch protection
+  # --------------------------------------------------------------------------
+  ci-complete:
+    name: CI Complete
+    runs-on: ubuntu-latest
+    needs: [test-python, test-frontend]
+    if: always()
+    steps:
+      - name: Check all CI jobs passed
+        run: |
+          echo "CI Job Results:"
+          echo "  test-python:   ${{ needs.test-python.result }}"
+          echo "  test-frontend: ${{ needs.test-frontend.result }}"
+          echo ""
+
+          if [[ "${{ needs.test-python.result }}" != "success" ]] || \
+             [[ "${{ needs.test-frontend.result }}" != "success" ]]; then
+            echo "❌ One or more CI jobs failed"
+            exit 1
+          fi
+
+          echo "✅ All CI checks passed"

.github/workflows/issue-auto-label.yml

@@ -1,4 +1,4 @@
-name: Auto Label
+name: Issue Auto Label
 
 on:
   issues:
@@ -11,7 +11,7 @@ jobs:
       issues: write
     steps:
       - name: Add area label from form
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         with:
           script: |
             const issue = context.payload.issue;

.github/workflows/lint.yml

@@ -3,24 +3,44 @@ name: Lint
 on:
   push:
     branches: [main, develop]
+    paths:
+      - 'apps/**'
+      - 'tests/**'
+      - '.github/workflows/lint.yml'
+      - '.github/actions/**'
+      - 'apps/frontend/biome.jsonc'
+      - '.pre-commit-config.yaml'
   pull_request:
     branches: [main, develop]
+    paths:
+      - 'apps/**'
+      - 'tests/**'
+      - '.github/workflows/lint.yml'
+      - '.github/actions/**'
+      - 'apps/frontend/biome.jsonc'
+      - '.pre-commit-config.yaml'
+
+concurrency:
+  group: lint-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  # Python linting
+  # Python linting (Ruff) - already fast, no changes needed
   python:
+    name: Python (Ruff)
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.12'
 
+      # Pin ruff version to match .pre-commit-config.yaml
       - name: Install ruff
-        run: pip install ruff
+        run: pip install ruff==0.14.10
 
       - name: Run ruff check
         run: ruff check apps/backend/ --output-format=github
@@ -28,26 +48,42 @@ jobs:
       - name: Run ruff format check
         run: ruff format apps/backend/ --check --diff
 
-  # TypeScript/React linting
-  frontend:
+  # TypeScript/JavaScript linting (Biome) - 15-25x faster than ESLint
+  typescript:
+    name: TypeScript (Biome)
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      # Pin version to match package.json for consistent behavior
+      - name: Setup Biome
+        uses: biomejs/setup-biome@v2
         with:
-          node-version: '24'
+          version: 2.3.11
 
-      - name: Install dependencies
+      - name: Run Biome
         working-directory: apps/frontend
-        run: npm ci --ignore-scripts
+        # biome ci fails on errors by default; warnings are reported but don't block
+        # Use --error-on-warnings when ready to enforce all rules
+        run: biome ci .
 
-      - name: Run ESLint
-        working-directory: apps/frontend
-        run: npm run lint
-
-      - name: Run TypeScript check
-        working-directory: apps/frontend
-        run: npm run typecheck
+  # --------------------------------------------------------------------------
+  # Gate Job - Single check for branch protection
+  # --------------------------------------------------------------------------
+  lint-complete:
+    name: Lint Complete
+    runs-on: ubuntu-latest
+    needs: [python, typescript]
+    if: always()
+    steps:
+      - name: Check lint results
+        run: |
+          if [[ "${{ needs.python.result }}" != "success" ]] || \
+             [[ "${{ needs.typescript.result }}" != "success" ]]; then
+            echo "❌ Linting failed"
+            echo "  Python:     ${{ needs.python.result }}"
+            echo "  TypeScript: ${{ needs.typescript.result }}"
+            exit 1
+          fi
+          echo "✅ All linting passed"

.github/workflows/pr-labeler.yml

@@ -0,0 +1,299 @@
+name: PR Labeler
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+concurrency:
+  group: pr-labeler-${{ github.event.pull_request.number }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  label:
+    name: Auto Label PR
+    runs-on: ubuntu-latest
+    # Security: Prevent fork PRs from modifying labels (they don't have write access)
+    if: github.event.pull_request.head.repo.full_name == github.repository
+    timeout-minutes: 5
+
+    steps:
+      - name: Label PR
+        uses: actions/github-script@v8
+        with:
+          retries: 3
+          retry-exempt-status-codes: 400,401,403,404,422
+          script: |
+            // ═══════════════════════════════════════════════════════════════
+            // CONFIGURATION - Single source of truth for all settings
+            // ═══════════════════════════════════════════════════════════════
+
+            const CONFIG = {
+              // Size thresholds (lines changed)
+              SIZE_THRESHOLDS: {
+                XS: 10,
+                S: 100,
+                M: 500,
+                L: 1000
+              },
+
+              // Conventional commit type mappings
+              TYPE_MAP: Object.freeze({
+                'feat': 'feature',
+                'fix': 'bug',
+                'docs': 'documentation',
+                'refactor': 'refactor',
+                'test': 'test',
+                'ci': 'ci',
+                'chore': 'chore',
+                'perf': 'performance',
+                'style': 'style',
+                'build': 'build'
+              }),
+
+              // Area detection paths
+              AREA_PATHS: Object.freeze({
+                frontend: 'apps/frontend/',
+                backend: 'apps/backend/',
+                ci: '.github/'
+              }),
+
+              // Label definitions
+              LABELS: Object.freeze({
+                SIZE: ['size/XS', 'size/S', 'size/M', 'size/L', 'size/XL'],
+                AREA: ['area/frontend', 'area/backend', 'area/fullstack', 'area/ci']
+              }),
+
+              // Pagination
+              MAX_FILES_PER_PAGE: 100
+            };
+
+            // ═══════════════════════════════════════════════════════════════
+            // HELPER FUNCTIONS - Small, focused, single responsibility
+            // ═══════════════════════════════════════════════════════════════
+
+            /**
+             * Safely parse conventional commit type from PR title
+             * @param {string} title - PR title
+             * @returns {{type: string|null, isBreaking: boolean}}
+             */
+            function parseConventionalCommit(title) {
+              if (!title || typeof title !== 'string') {
+                return { type: null, isBreaking: false };
+              }
+
+              // Limit input length to prevent ReDoS attacks
+              const safeTitle = title.slice(0, 200);
+              const match = safeTitle.match(/^(\w{1,20})(\([^)]{0,50}\))?(!)?:/);
+
+              if (!match) {
+                return { type: null, isBreaking: false };
+              }
+
+              return {
+                type: match[1].toLowerCase(),
+                isBreaking: match[3] === '!'
+              };
+            }
+
+            /**
+             * Determine size label based on lines changed
+             * @param {number} totalLines - Total lines changed
+             * @returns {string} Size label
+             */
+            function determineSizeLabel(totalLines) {
+              const { SIZE_THRESHOLDS } = CONFIG;
+
+              if (totalLines < SIZE_THRESHOLDS.XS) return 'size/XS';
+              if (totalLines < SIZE_THRESHOLDS.S) return 'size/S';
+              if (totalLines < SIZE_THRESHOLDS.M) return 'size/M';
+              if (totalLines < SIZE_THRESHOLDS.L) return 'size/L';
+              return 'size/XL';
+            }
+
+            /**
+             * Detect areas affected by file changes
+             * @param {Array} files - List of changed files
+             * @returns {{frontend: boolean, backend: boolean, ci: boolean}}
+             */
+            function detectAreas(files) {
+              const areas = { frontend: false, backend: false, ci: false };
+              const { AREA_PATHS } = CONFIG;
+
+              for (const file of files) {
+                const path = file.filename || '';
+                if (path.startsWith(AREA_PATHS.frontend)) areas.frontend = true;
+                if (path.startsWith(AREA_PATHS.backend)) areas.backend = true;
+                if (path.startsWith(AREA_PATHS.ci)) areas.ci = true;
+              }
+
+              return areas;
+            }
+
+            /**
+             * Determine area label based on detected areas
+             * @param {{frontend: boolean, backend: boolean, ci: boolean}} areas
+             * @returns {string|null} Area label or null
+             */
+            function determineAreaLabel(areas) {
+              if (areas.frontend && areas.backend) return 'area/fullstack';
+              if (areas.frontend) return 'area/frontend';
+              if (areas.backend) return 'area/backend';
+              if (areas.ci) return 'area/ci';
+              return null;
+            }
+
+            /**
+             * Remove labels from PR (with error handling)
+             * @param {Array} labels - Labels to remove
+             * @param {number} prNumber - PR number
+             */
+            async function removeLabels(labels, prNumber) {
+              const { owner, repo } = context.repo;
+
+              await Promise.allSettled(labels.map(async (label) => {
+                try {
+                  await github.rest.issues.removeLabel({
+                    owner,
+                    repo,
+                    issue_number: prNumber,
+                    name: label
+                  });
+                  console.log(`  ✓ Removed: ${label}`);
+                } catch (e) {
+                  // 404 means label wasn't present - that's fine
+                  if (e.status !== 404) {
+                    console.log(`  ⚠ Failed to remove ${label}: ${e.message}`);
+                  }
+                }
+              }));
+            }
+
+            /**
+             * Add labels to PR (with error handling)
+             * @param {Array} labels - Labels to add
+             * @param {number} prNumber - PR number
+             */
+            async function addLabels(labels, prNumber) {
+              if (labels.length === 0) return;
+
+              const { owner, repo } = context.repo;
+
+              try {
+                await github.rest.issues.addLabels({
+                  owner,
+                  repo,
+                  issue_number: prNumber,
+                  labels
+                });
+                console.log(`  ✓ Added: ${labels.join(', ')}`);
+              } catch (e) {
+                if (e.status === 404) {
+                  core.warning(`One or more labels do not exist. Create them in repository settings.`);
+                } else {
+                  throw e;
+                }
+              }
+            }
+
+            /**
+             * Fetch PR files with full pagination support
+             * @param {number} prNumber - PR number
+             * @returns {Array} List of all files (paginated)
+             */
+            async function fetchPRFiles(prNumber) {
+              const { owner, repo } = context.repo;
+
+              try {
+                // Use paginate to fetch ALL files, not just first 100
+                const files = await github.paginate(
+                  github.rest.pulls.listFiles,
+                  { owner, repo, pull_number: prNumber, per_page: CONFIG.MAX_FILES_PER_PAGE }
+                );
+                return files;
+              } catch (e) {
+                console.log(`  ⚠ Could not fetch files: ${e.message}`);
+                return [];
+              }
+            }
+
+            // ═══════════════════════════════════════════════════════════════
+            // MAIN LOGIC - Orchestrates the labeling process
+            // ═══════════════════════════════════════════════════════════════
+
+            const { owner, repo } = context.repo;
+            const pr = context.payload.pull_request;
+            const prNumber = pr.number;
+            const title = pr.title || '';
+
+            console.log(`::group::PR #${prNumber} - Auto-labeling`);
+            console.log(`Title: ${title.slice(0, 100)}${title.length > 100 ? '...' : ''}`);
+            console.log(`Action: ${context.payload.action}`);
+
+            const labelsToAdd = new Set();
+            const labelsToRemove = new Set();
+
+            // 1. Parse conventional commit type
+            const { type, isBreaking } = parseConventionalCommit(title);
+            if (type && CONFIG.TYPE_MAP[type]) {
+              labelsToAdd.add(CONFIG.TYPE_MAP[type]);
+              console.log(`  📝 Type: ${type} → ${CONFIG.TYPE_MAP[type]}`);
+            } else {
+              console.log(`  ℹ️ No conventional commit prefix detected`);
+            }
+
+            if (isBreaking) {
+              labelsToAdd.add('breaking-change');
+              console.log(`  ⚠️ Breaking change detected`);
+            }
+
+            // 2. Detect areas from changed files
+            const files = await fetchPRFiles(prNumber);
+            const areas = detectAreas(files);
+            const areaLabel = determineAreaLabel(areas);
+
+            if (areaLabel) {
+              labelsToAdd.add(areaLabel);
+              CONFIG.LABELS.AREA.filter(l => l !== areaLabel).forEach(l => labelsToRemove.add(l));
+              console.log(`  📁 Area: ${areaLabel.replace('area/', '')}`);
+            }
+
+            // 3. Calculate size label
+            const totalLines = (pr.additions || 0) + (pr.deletions || 0);
+            const sizeLabel = determineSizeLabel(totalLines);
+            labelsToAdd.add(sizeLabel);
+            CONFIG.LABELS.SIZE.filter(l => l !== sizeLabel).forEach(l => labelsToRemove.add(l));
+            console.log(`  📏 Size: ${sizeLabel} (${totalLines} lines)`);
+
+            console.log('::endgroup::');
+
+            // 4. Apply label changes
+            console.log(`::group::Applying labels`);
+
+            // Remove labels that should be replaced (exclude ones we're adding)
+            const removeList = [...labelsToRemove].filter(l => !labelsToAdd.has(l));
+            await removeLabels(removeList, prNumber);
+
+            // Add new labels
+            await addLabels([...labelsToAdd], prNumber);
+
+            console.log('::endgroup::');
+            console.log(`✅ PR #${prNumber} labeled successfully`);
+
+            // 5. Write job summary
+            const summaryType = type ? CONFIG.TYPE_MAP[type] || 'unknown' : 'none';
+            const summaryArea = areaLabel ? areaLabel.replace('area/', '') : 'other';
+
+            await core.summary
+              .addHeading(`PR #${prNumber} Auto-Labels`, 3)
+              .addTable([
+                [{ data: 'Category', header: true }, { data: 'Label', header: true }],
+                ['Type', summaryType],
+                ['Area', summaryArea],
+                ['Size', sizeLabel]
+              ])
+              .addRaw(`\n**Files:** ${files.length} | **Lines:** +${pr.additions || 0} / -${pr.deletions || 0}\n`)
+              .write();

.github/workflows/prepare-release.yml

@@ -1,8 +1,10 @@
 name: Prepare Release
 
 # Triggers when code is pushed to main (e.g., merging develop → main)
-# If package.json version is newer than the latest tag, creates a new tag
-# which then triggers the release.yml workflow
+# If package.json version is newer than the latest tag:
+# 1. Validates CHANGELOG.md has an entry for this version (FAILS if missing)
+# 2. Extracts release notes from CHANGELOG.md
+# 3. Creates a new tag which triggers release.yml
 
 on:
   push:
@@ -10,6 +12,13 @@ on:
     paths:
       - 'apps/frontend/package.json'
       - 'package.json'
+  workflow_dispatch:
+    inputs:
+      force:
+        description: 'Force release even if version check fails (use with caution)'
+        required: false
+        default: false
+        type: boolean
 
 jobs:
   check-and-tag:
@@ -20,10 +29,23 @@ jobs:
       should_release: ${{ steps.check.outputs.should_release }}
       new_version: ${{ steps.check.outputs.new_version }}
     steps:
+      # Fail fast with clear error if PAT_TOKEN is not configured
+      - name: Validate PAT_TOKEN is configured
+        run: |
+          if [ -z "${{ secrets.PAT_TOKEN }}" ]; then
+            echo "::error::PAT_TOKEN secret is not configured."
+            echo "::error::This secret is required for automatic release triggering."
+            echo "::error::See https://github.com/AndyMik90/Auto-Claude/pull/1043 for setup instructions."
+            exit 1
+          fi
+
+      # IMPORTANT: Use PAT_TOKEN instead of GITHUB_TOKEN
+      # When GITHUB_TOKEN pushes a tag, it does NOT trigger other workflows (GitHub security feature)
+      # PAT_TOKEN allows the tag push to trigger release.yml automatically
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ secrets.PAT_TOKEN }}
 
       - name: Get package version
         id: package
@@ -52,23 +74,141 @@ jobs:
         run: |
           PACKAGE_VERSION="${{ steps.package.outputs.version }}"
           LATEST_VERSION="${{ steps.latest_tag.outputs.version }}"
+          FORCE="${{ github.event.inputs.force }}"
 
           echo "Comparing: package=$PACKAGE_VERSION vs latest_tag=$LATEST_VERSION"
 
-          # Use sort -V for version comparison
-          HIGHER=$(printf '%s\n%s' "$PACKAGE_VERSION" "$LATEST_VERSION" | sort -V | tail -n1)
-
-          if [ "$HIGHER" = "$PACKAGE_VERSION" ] && [ "$PACKAGE_VERSION" != "$LATEST_VERSION" ]; then
+          # Use npx semver for proper semantic version comparison
+          # This correctly handles pre-release versions (2.7.3 > 2.7.3-beta.1)
+          if npx -y semver "$PACKAGE_VERSION" -r ">$LATEST_VERSION" > /dev/null 2>&1; then
             echo "should_release=true" >> $GITHUB_OUTPUT
             echo "new_version=$PACKAGE_VERSION" >> $GITHUB_OUTPUT
             echo "✅ New release needed: v$PACKAGE_VERSION"
+          elif [ "$FORCE" = "true" ]; then
+            echo "should_release=true" >> $GITHUB_OUTPUT
+            echo "new_version=$PACKAGE_VERSION" >> $GITHUB_OUTPUT
+            echo "⚠️ Force release enabled: v$PACKAGE_VERSION"
           else
             echo "should_release=false" >> $GITHUB_OUTPUT
             echo "⏭️ No release needed (package version not newer than latest tag)"
           fi
 
-      - name: Create and push tag
+      # CRITICAL: Validate CHANGELOG.md has entry for this version BEFORE creating tag
+      - name: Validate and extract changelog
         if: steps.check.outputs.should_release == 'true'
+        id: changelog
+        run: |
+          VERSION="${{ steps.check.outputs.new_version }}"
+          CHANGELOG_FILE="CHANGELOG.md"
+
+          echo "🔍 Validating CHANGELOG.md for version $VERSION..."
+
+          if [ ! -f "$CHANGELOG_FILE" ]; then
+            echo "::error::CHANGELOG.md not found! Please create CHANGELOG.md with release notes."
+            exit 1
+          fi
+
+          # Extract changelog section for this version
+          # Looks for "## X.Y.Z" header and captures until next "## " or "---" or end
+          CHANGELOG_CONTENT=$(awk -v ver="$VERSION" '
+            BEGIN { found=0; content="" }
+            /^## / {
+              if (found) exit
+              # Match version at start of header (e.g., "## 2.7.3 -" or "## 2.7.3")
+              if ($2 == ver || $2 ~ "^"ver"[[:space:]]*-") {
+                found=1
+                # Skip the header line itself, we will add our own
+                next
+              }
+            }
+            /^---$/ { if (found) exit }
+            found { content = content $0 "\n" }
+            END {
+              if (!found) {
+                print "NOT_FOUND"
+                exit 1
+              }
+              # Trim leading/trailing whitespace
+              gsub(/^[[:space:]]+|[[:space:]]+$/, "", content)
+              print content
+            }
+          ' "$CHANGELOG_FILE")
+
+          if [ "$CHANGELOG_CONTENT" = "NOT_FOUND" ] || [ -z "$CHANGELOG_CONTENT" ]; then
+            echo ""
+            echo "::error::═══════════════════════════════════════════════════════════════════════"
+            echo "::error::  CHANGELOG VALIDATION FAILED"
+            echo "::error::═══════════════════════════════════════════════════════════════════════"
+            echo "::error::"
+            echo "::error::  Version $VERSION not found in CHANGELOG.md!"
+            echo "::error::"
+            echo "::error::  Before releasing, please update CHANGELOG.md with an entry like:"
+            echo "::error::"
+            echo "::error::    ## $VERSION - Your Release Title"
+            echo "::error::"
+            echo "::error::    ### ✨ New Features"
+            echo "::error::    - Feature description"
+            echo "::error::"
+            echo "::error::    ### 🐛 Bug Fixes"
+            echo "::error::    - Fix description"
+            echo "::error::"
+            echo "::error::═══════════════════════════════════════════════════════════════════════"
+            echo ""
+
+            # Also add to job summary for visibility
+            echo "## ❌ Release Blocked: Missing Changelog" >> $GITHUB_STEP_SUMMARY
+            echo "" >> $GITHUB_STEP_SUMMARY
+            echo "Version **$VERSION** was not found in CHANGELOG.md." >> $GITHUB_STEP_SUMMARY
+            echo "" >> $GITHUB_STEP_SUMMARY
+            echo "### How to fix:" >> $GITHUB_STEP_SUMMARY
+            echo "1. Update CHANGELOG.md with release notes for version $VERSION" >> $GITHUB_STEP_SUMMARY
+            echo "2. Commit and push the changes" >> $GITHUB_STEP_SUMMARY
+            echo "3. The release will automatically retry" >> $GITHUB_STEP_SUMMARY
+            echo "" >> $GITHUB_STEP_SUMMARY
+            echo "### Expected format:" >> $GITHUB_STEP_SUMMARY
+            echo "\`\`\`markdown" >> $GITHUB_STEP_SUMMARY
+            echo "## $VERSION - Release Title" >> $GITHUB_STEP_SUMMARY
+            echo "" >> $GITHUB_STEP_SUMMARY
+            echo "### ✨ New Features" >> $GITHUB_STEP_SUMMARY
+            echo "- Feature description" >> $GITHUB_STEP_SUMMARY
+            echo "" >> $GITHUB_STEP_SUMMARY
+            echo "### 🐛 Bug Fixes" >> $GITHUB_STEP_SUMMARY
+            echo "- Fix description" >> $GITHUB_STEP_SUMMARY
+            echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
+
+            exit 1
+          fi
+
+          echo "✅ Found changelog entry for version $VERSION"
+          echo ""
+          echo "--- Extracted Release Notes ---"
+          echo "$CHANGELOG_CONTENT"
+          echo "--- End Release Notes ---"
+
+          # Save changelog to file for artifact upload
+          echo "$CHANGELOG_CONTENT" > changelog-extract.md
+
+          # Also save to output (for short changelogs)
+          # Using heredoc for multiline output
+          {
+            echo "content<<CHANGELOG_EOF"
+            echo "$CHANGELOG_CONTENT"
+            echo "CHANGELOG_EOF"
+          } >> $GITHUB_OUTPUT
+
+          echo "changelog_valid=true" >> $GITHUB_OUTPUT
+
+      # Upload changelog as artifact for release.yml to use
+      - name: Upload changelog artifact
+        if: steps.check.outputs.should_release == 'true' && steps.changelog.outputs.changelog_valid == 'true'
+        uses: actions/upload-artifact@v4
+        with:
+          name: changelog-${{ steps.check.outputs.new_version }}
+          path: changelog-extract.md
+          retention-days: 1
+
+      - name: Create and push tag
+        if: steps.check.outputs.should_release == 'true' && steps.changelog.outputs.changelog_valid == 'true'
         run: |
           VERSION="${{ steps.check.outputs.new_version }}"
           TAG="v$VERSION"
@@ -85,17 +225,19 @@ jobs:
 
       - name: Summary
         run: |
-          if [ "${{ steps.check.outputs.should_release }}" = "true" ]; then
+          if [ "${{ steps.check.outputs.should_release }}" = "true" ] && [ "${{ steps.changelog.outputs.changelog_valid }}" = "true" ]; then
             echo "## 🚀 Release Triggered" >> $GITHUB_STEP_SUMMARY
             echo "" >> $GITHUB_STEP_SUMMARY
             echo "**Version:** v${{ steps.check.outputs.new_version }}" >> $GITHUB_STEP_SUMMARY
             echo "" >> $GITHUB_STEP_SUMMARY
+            echo "✅ Changelog validated and extracted from CHANGELOG.md" >> $GITHUB_STEP_SUMMARY
+            echo "" >> $GITHUB_STEP_SUMMARY
             echo "The release workflow has been triggered and will:" >> $GITHUB_STEP_SUMMARY
             echo "1. Build binaries for all platforms" >> $GITHUB_STEP_SUMMARY
-            echo "2. Generate changelog from PRs" >> $GITHUB_STEP_SUMMARY
+            echo "2. Use changelog from CHANGELOG.md" >> $GITHUB_STEP_SUMMARY
             echo "3. Create GitHub release" >> $GITHUB_STEP_SUMMARY
             echo "4. Update README with new version" >> $GITHUB_STEP_SUMMARY
-          else
+          elif [ "${{ steps.check.outputs.should_release }}" = "false" ]; then
             echo "## ⏭️ No Release Needed" >> $GITHUB_STEP_SUMMARY
             echo "" >> $GITHUB_STEP_SUMMARY
             echo "**Package version:** ${{ steps.package.outputs.version }}" >> $GITHUB_STEP_SUMMARY

.github/workflows/quality-security.yml

@@ -0,0 +1,177 @@
+name: Quality Security
+
+# CodeQL runs on all PRs, pushes to main, and weekly schedule
+# Note: CodeQL takes 20-30 min per language (40-60 min total)
+# Bandit is fast (5-10 min)
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'apps/**'
+      - 'tests/**'
+      - 'pyproject.toml'
+      - 'package.json'
+      - '.github/workflows/quality-security.yml'
+  pull_request:
+    branches: [main, develop]
+    paths:
+      - 'apps/**'
+      - 'tests/**'
+      - 'pyproject.toml'
+      - 'package.json'
+      - '.github/workflows/quality-security.yml'
+  schedule:
+    - cron: '0 0 * * 1' # Weekly on Monday at midnight UTC
+
+concurrency:
+  group: security-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  security-events: write
+  actions: read
+
+jobs:
+  codeql:
+    name: CodeQL (${{ matrix.language }})
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [python, javascript-typescript]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-extended,security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v3
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:${{ matrix.language }}"
+
+  # Bandit runs on all PRs - it's fast (5-10 min)
+  python-security:
+    name: Python Security (Bandit)
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+
+      - name: Install Bandit
+        run: pip install bandit
+
+      - name: Run Bandit security scan
+        id: bandit
+        run: |
+          echo "::group::Running Bandit security scan"
+          bandit -r apps/backend/ -ll -ii -f json -o bandit-report.json || BANDIT_EXIT=$?
+          if [ "${BANDIT_EXIT:-0}" -gt 1 ]; then
+            echo "::error::Bandit scan failed with exit code $BANDIT_EXIT"
+            exit 1
+          fi
+          echo "::endgroup::"
+
+      - name: Analyze Bandit results
+        uses: actions/github-script@v8
+        with:
+          script: |
+            const fs = require('fs');
+
+            if (!fs.existsSync('bandit-report.json')) {
+              core.setFailed('Bandit report not found - scan may have failed');
+              return;
+            }
+
+            const report = JSON.parse(fs.readFileSync('bandit-report.json', 'utf8'));
+            const results = report.results || [];
+
+            const high = results.filter(r => r.issue_severity === 'HIGH');
+            const medium = results.filter(r => r.issue_severity === 'MEDIUM');
+            const low = results.filter(r => r.issue_severity === 'LOW');
+
+            console.log(`::group::Bandit Security Scan Results`);
+            console.log(`Found ${results.length} issues:`);
+            console.log(`  HIGH:   ${high.length}`);
+            console.log(`  MEDIUM: ${medium.length}`);
+            console.log(`  LOW:    ${low.length}`);
+            console.log('::endgroup::');
+
+            let summary = `## Python Security Scan (Bandit)\n\n`;
+            summary += `| Severity | Count |\n`;
+            summary += `|----------|-------|\n`;
+            summary += `| High | ${high.length} |\n`;
+            summary += `| Medium | ${medium.length} |\n`;
+            summary += `| Low | ${low.length} |\n\n`;
+
+            if (high.length > 0) {
+              summary += `### High Severity Issues\n\n`;
+              for (const issue of high) {
+                summary += `- **${issue.filename}:${issue.line_number}**\n`;
+                summary += `  - ${issue.issue_text}\n`;
+                summary += `  - Test: \`${issue.test_id}\` (${issue.test_name})\n\n`;
+              }
+            }
+
+            core.summary.addRaw(summary);
+            await core.summary.write();
+
+            if (high.length > 0) {
+              core.setFailed(`Found ${high.length} high severity security issue(s)`);
+            } else {
+              console.log('No high severity security issues found');
+            }
+
+  # --------------------------------------------------------------------------
+  # Gate Job - Single check for branch protection
+  # --------------------------------------------------------------------------
+  security-summary:
+    name: Security Summary
+    runs-on: ubuntu-latest
+    needs: [codeql, python-security]
+    if: always()
+    timeout-minutes: 5
+    steps:
+      - name: Check security results
+        uses: actions/github-script@v8
+        with:
+          script: |
+            const codeql = '${{ needs.codeql.result }}';
+            const bandit = '${{ needs.python-security.result }}';
+
+            console.log('Security Check Results:');
+            console.log(`  CodeQL:        ${codeql}`);
+            console.log(`  Bandit:        ${bandit}`);
+
+            // Only 'failure' is a real failure; 'skipped' is acceptable (e.g., path filters, PR skipping CodeQL)
+            const acceptable = ['success', 'skipped'];
+            const codeqlOk = acceptable.includes(codeql);
+            const banditOk = acceptable.includes(bandit);
+            const allPassed = codeqlOk && banditOk;
+
+            if (allPassed) {
+              console.log('\n✅ All security checks passed');
+              core.summary.addRaw('## ✅ Security Checks Passed\n\nAll security scans completed successfully.');
+            } else {
+              console.log('\n❌ Some security checks failed');
+              core.summary.addRaw('## ❌ Security Checks Failed\n\nOne or more security scans found issues.');
+              core.setFailed('Security checks failed');
+            }
+
+            await core.summary.write();

.github/workflows/release.yml

@@ -1,4 +1,10 @@
 name: Release
+# Triggers on version tags (v*) to build and publish releases
+#
+# IMPORTANT: If branch protection is enabled on 'main', the update-readme job
+# requires a PAT or GitHub App token with bypass permissions to push directly.
+# Currently uses GITHUB_TOKEN which works if "Allow GitHub Actions to create
+# and approve pull requests" is enabled OR branch protection is not configured.
 
 on:
   push:
@@ -9,7 +15,7 @@ on:
       dry_run:
         description: 'Test build without creating release'
         required: false
-        default: true
+        default: false
         type: boolean
 
 jobs:
@@ -17,58 +23,63 @@ jobs:
   # Note: macos-15-intel is the last Intel runner, supported until Fall 2027
   build-macos-intel:
     runs-on: macos-15-intel
+    outputs:
+      notarization_id: ${{ steps.notarize.outputs.notarization-id }}
+      dmg_file: ${{ steps.notarize.outputs.dmg-file }}
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
         with:
-          node-version: '24'
+          python-version: '3.11'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        run: echo "dir=$(npm config get cache)" >> $GITHUB_OUTPUT
+      - name: Setup Node.js and install dependencies
+        uses: ./.github/actions/setup-node-frontend
 
-      - uses: actions/cache@v4
+      - name: Install Rust toolchain (for building native Python packages)
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache pip wheel cache (for compiled packages like real_ladybug)
+        uses: actions/cache@v5
         with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
+          path: ~/Library/Caches/pip
+          key: pip-wheel-${{ runner.os }}-x64-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            pip-wheel-${{ runner.os }}-x64-
 
-      - name: Install dependencies
-        run: cd apps/frontend && npm ci
+      - name: Cache bundled Python
+        uses: actions/cache@v5
+        with:
+          path: apps/frontend/python-runtime
+          key: python-bundle-${{ runner.os }}-x64-3.12.8-rust-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            python-bundle-${{ runner.os }}-x64-3.12.8-rust-
 
       - name: Build application
         run: cd apps/frontend && npm run build
+        env:
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
       - name: Package macOS (Intel)
-        run: cd apps/frontend && npm run package:mac -- --arch=x64
+        run: cd apps/frontend && npm run package:mac -- --x64
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           CSC_LINK: ${{ secrets.MAC_CERTIFICATE }}
           CSC_KEY_PASSWORD: ${{ secrets.MAC_CERTIFICATE_PASSWORD }}
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
-      - name: Notarize macOS Intel app
-        env:
-          APPLE_ID: ${{ secrets.APPLE_ID }}
-          APPLE_APP_SPECIFIC_PASSWORD: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
-          APPLE_TEAM_ID: ${{ secrets.APPLE_TEAM_ID }}
-        run: |
-          if [ -z "$APPLE_ID" ]; then
-            echo "Skipping notarization: APPLE_ID not configured"
-            exit 0
-          fi
-          cd apps/frontend
-          for dmg in dist/*.dmg; do
-            echo "Notarizing $dmg..."
-            xcrun notarytool submit "$dmg" \
-              --apple-id "$APPLE_ID" \
-              --password "$APPLE_APP_SPECIFIC_PASSWORD" \
-              --team-id "$APPLE_TEAM_ID" \
-              --wait
-            xcrun stapler staple "$dmg"
-            echo "Successfully notarized and stapled $dmg"
-          done
+      - name: Submit notarization (async)
+        id: notarize
+        uses: ./.github/actions/submit-macos-notarization
+        with:
+          apple-id: ${{ secrets.APPLE_ID }}
+          apple-app-specific-password: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
+          apple-team-id: ${{ secrets.APPLE_TEAM_ID }}
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -77,62 +88,66 @@ jobs:
           path: |
             apps/frontend/dist/*.dmg
             apps/frontend/dist/*.zip
+            apps/frontend/dist/*.yml
+            apps/frontend/dist/*.blockmap
 
   # Apple Silicon build on ARM64 runner for native compilation
   build-macos-arm64:
     runs-on: macos-15
+    outputs:
+      notarization_id: ${{ steps.notarize.outputs.notarization-id }}
+      dmg_file: ${{ steps.notarize.outputs.dmg-file }}
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
         with:
-          node-version: '24'
+          python-version: '3.11'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        run: echo "dir=$(npm config get cache)" >> $GITHUB_OUTPUT
+      - name: Setup Node.js and install dependencies
+        uses: ./.github/actions/setup-node-frontend
 
-      - uses: actions/cache@v4
+      - name: Cache pip wheel cache
+        uses: actions/cache@v5
         with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
+          path: ~/Library/Caches/pip
+          key: pip-wheel-${{ runner.os }}-arm64-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            pip-wheel-${{ runner.os }}-arm64-
 
-      - name: Install dependencies
-        run: cd apps/frontend && npm ci
+      - name: Cache bundled Python
+        uses: actions/cache@v5
+        with:
+          path: apps/frontend/python-runtime
+          key: python-bundle-${{ runner.os }}-arm64-3.12.8-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            python-bundle-${{ runner.os }}-arm64-3.12.8-
 
       - name: Build application
         run: cd apps/frontend && npm run build
+        env:
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
       - name: Package macOS (Apple Silicon)
-        run: cd apps/frontend && npm run package:mac -- --arch=arm64
+        run: cd apps/frontend && npm run package:mac -- --arm64
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           CSC_LINK: ${{ secrets.MAC_CERTIFICATE }}
           CSC_KEY_PASSWORD: ${{ secrets.MAC_CERTIFICATE_PASSWORD }}
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
-      - name: Notarize macOS ARM64 app
-        env:
-          APPLE_ID: ${{ secrets.APPLE_ID }}
-          APPLE_APP_SPECIFIC_PASSWORD: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
-          APPLE_TEAM_ID: ${{ secrets.APPLE_TEAM_ID }}
-        run: |
-          if [ -z "$APPLE_ID" ]; then
-            echo "Skipping notarization: APPLE_ID not configured"
-            exit 0
-          fi
-          cd apps/frontend
-          for dmg in dist/*.dmg; do
-            echo "Notarizing $dmg..."
-            xcrun notarytool submit "$dmg" \
-              --apple-id "$APPLE_ID" \
-              --password "$APPLE_APP_SPECIFIC_PASSWORD" \
-              --team-id "$APPLE_TEAM_ID" \
-              --wait
-            xcrun stapler staple "$dmg"
-            echo "Successfully notarized and stapled $dmg"
-          done
+      - name: Submit notarization (async)
+        id: notarize
+        uses: ./.github/actions/submit-macos-notarization
+        with:
+          apple-id: ${{ secrets.APPLE_ID }}
+          apple-app-specific-password: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
+          apple-team-id: ${{ secrets.APPLE_TEAM_ID }}
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -141,40 +156,171 @@ jobs:
           path: |
             apps/frontend/dist/*.dmg
             apps/frontend/dist/*.zip
+            apps/frontend/dist/*.yml
+            apps/frontend/dist/*.blockmap
 
   build-windows:
     runs-on: windows-latest
+    permissions:
+      id-token: write  # Required for OIDC authentication with Azure
+      contents: read
+    env:
+      # Job-level env so AZURE_CLIENT_ID is available for step-level if conditions
+      AZURE_CLIENT_ID: ${{ secrets.AZURE_CLIENT_ID }}
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
         with:
-          node-version: '24'
+          python-version: '3.11'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        shell: bash
-        run: echo "dir=$(npm config get cache)" >> $GITHUB_OUTPUT
+      - name: Setup Node.js and install dependencies
+        uses: ./.github/actions/setup-node-frontend
 
-      - uses: actions/cache@v4
+      - name: Cache pip wheel cache
+        uses: actions/cache@v5
         with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
+          path: ~\AppData\Local\pip\Cache
+          key: pip-wheel-${{ runner.os }}-x64-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            pip-wheel-${{ runner.os }}-x64-
 
-      - name: Install dependencies
-        run: cd apps/frontend && npm ci
+      - name: Cache bundled Python
+        uses: actions/cache@v5
+        with:
+          path: apps/frontend/python-runtime
+          key: python-bundle-${{ runner.os }}-x64-3.12.8-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            python-bundle-${{ runner.os }}-x64-3.12.8-
 
       - name: Build application
         run: cd apps/frontend && npm run build
+        env:
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
       - name: Package Windows
         run: cd apps/frontend && npm run package:win
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          CSC_LINK: ${{ secrets.WIN_CERTIFICATE }}
-          CSC_KEY_PASSWORD: ${{ secrets.WIN_CERTIFICATE_PASSWORD }}
+          # Disable electron-builder's built-in signing (we use Azure Trusted Signing instead)
+          CSC_IDENTITY_AUTO_DISCOVERY: false
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
+
+      - name: Azure Login (OIDC)
+        if: env.AZURE_CLIENT_ID != ''
+        uses: azure/login@v2
+        with:
+          client-id: ${{ secrets.AZURE_CLIENT_ID }}
+          tenant-id: ${{ secrets.AZURE_TENANT_ID }}
+          subscription-id: ${{ secrets.AZURE_SUBSCRIPTION_ID }}
+
+      - name: Sign Windows executable with Azure Trusted Signing
+        if: env.AZURE_CLIENT_ID != ''
+        uses: azure/trusted-signing-action@v0.5.11
+        with:
+          endpoint: https://neu.codesigning.azure.net/
+          trusted-signing-account-name: ${{ secrets.AZURE_SIGNING_ACCOUNT }}
+          certificate-profile-name: ${{ secrets.AZURE_CERTIFICATE_PROFILE }}
+          files-folder: apps/frontend/dist
+          files-folder-filter: exe
+          file-digest: SHA256
+          timestamp-rfc3161: http://timestamp.acs.microsoft.com
+          timestamp-digest: SHA256
+
+      - name: Verify Windows executable is signed
+        if: env.AZURE_CLIENT_ID != ''
+        shell: pwsh
+        run: |
+          cd apps/frontend/dist
+          $exeFile = Get-ChildItem -Filter "*.exe" | Select-Object -First 1
+          if ($exeFile) {
+            Write-Host "Verifying signature on $($exeFile.Name)..."
+            $sig = Get-AuthenticodeSignature -FilePath $exeFile.FullName
+            if ($sig.Status -ne 'Valid') {
+              Write-Host "::error::Signature verification failed: $($sig.Status)"
+              Write-Host "::error::Status Message: $($sig.StatusMessage)"
+              exit 1
+            }
+            Write-Host "✅ Signature verified successfully"
+            Write-Host "  Subject: $($sig.SignerCertificate.Subject)"
+            Write-Host "  Issuer: $($sig.SignerCertificate.Issuer)"
+            Write-Host "  Thumbprint: $($sig.SignerCertificate.Thumbprint)"
+          } else {
+            Write-Host "::error::No .exe file found to verify"
+            exit 1
+          }
+
+      - name: Regenerate checksums after signing
+        if: env.AZURE_CLIENT_ID != ''
+        shell: pwsh
+        run: |
+          $ErrorActionPreference = "Stop"
+          cd apps/frontend/dist
+
+          # Find the installer exe (electron-builder names it with "Setup" or just the app name)
+          # electron-builder produces one installer exe per build
+          $exeFiles = Get-ChildItem -Filter "*.exe"
+          if ($exeFiles.Count -eq 0) {
+            Write-Host "::error::No .exe files found in dist folder"
+            exit 1
+          }
+
+          Write-Host "Found $($exeFiles.Count) exe file(s): $($exeFiles.Name -join ', ')"
+
+          $ymlFile = "latest.yml"
+          if (-not (Test-Path $ymlFile)) {
+            Write-Host "::error::$ymlFile not found - cannot update checksums"
+            exit 1
+          }
+
+          $content = Get-Content $ymlFile -Raw
+          $originalContent = $content
+
+          # Process each exe file and update its hash in latest.yml
+          foreach ($exeFile in $exeFiles) {
+            Write-Host "Processing $($exeFile.Name)..."
+
+            # Compute SHA512 hash and convert to base64 (electron-builder format)
+            $bytes = [System.IO.File]::ReadAllBytes($exeFile.FullName)
+            $sha512 = [System.Security.Cryptography.SHA512]::Create()
+            $hashBytes = $sha512.ComputeHash($bytes)
+            $hash = [System.Convert]::ToBase64String($hashBytes)
+            $size = $exeFile.Length
+
+            Write-Host "  Hash: $hash"
+            Write-Host "  Size: $size"
+          }
+
+          # For electron-builder, latest.yml has a single file entry for the installer
+          # Update the sha512 and size for the primary exe (first one, typically the installer)
+          $primaryExe = $exeFiles | Select-Object -First 1
+          $bytes = [System.IO.File]::ReadAllBytes($primaryExe.FullName)
+          $sha512 = [System.Security.Cryptography.SHA512]::Create()
+          $hashBytes = $sha512.ComputeHash($bytes)
+          $hash = [System.Convert]::ToBase64String($hashBytes)
+          $size = $primaryExe.Length
+
+          # Update sha512 hash (base64 pattern: alphanumeric, +, /, =)
+          $content = $content -replace 'sha512: [A-Za-z0-9+/=]+', "sha512: $hash"
+          # Update size
+          $content = $content -replace 'size: \d+', "size: $size"
+
+          if ($content -eq $originalContent) {
+            Write-Host "::error::Checksum replacement failed - content unchanged. Check if latest.yml format has changed."
+            exit 1
+          }
+
+          Set-Content -Path $ymlFile -Value $content -NoNewline
+          Write-Host "✅ Updated $ymlFile with new base64 hash and size for $($primaryExe.Name)"
+
+      - name: Skip signing notice
+        if: env.AZURE_CLIENT_ID == ''
+        run: echo "::warning::Windows signing skipped - AZURE_CLIENT_ID not configured. The .exe will be unsigned."
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -182,37 +328,63 @@ jobs:
           name: windows-builds
           path: |
             apps/frontend/dist/*.exe
+            apps/frontend/dist/*.yml
+            apps/frontend/dist/*.blockmap
 
   build-linux:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      - name: Setup Python
+        uses: actions/setup-python@v6
         with:
-          node-version: '24'
+          python-version: '3.11'
 
-      - name: Get npm cache directory
-        id: npm-cache
-        run: echo "dir=$(npm config get cache)" >> $GITHUB_OUTPUT
+      - name: Setup Node.js and install dependencies
+        uses: ./.github/actions/setup-node-frontend
 
-      - uses: actions/cache@v4
+      - name: Setup Flatpak and verification tools
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y flatpak flatpak-builder libarchive-tools
+          flatpak remote-add --user --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
+          flatpak install -y --user flathub org.freedesktop.Platform//25.08 org.freedesktop.Sdk//25.08
+          flatpak install -y --user flathub org.electronjs.Electron2.BaseApp//25.08
+
+      - name: Cache pip wheel cache
+        uses: actions/cache@v5
         with:
-          path: ${{ steps.npm-cache.outputs.dir }}
-          key: ${{ runner.os }}-npm-${{ hashFiles('**/package-lock.json') }}
-          restore-keys: ${{ runner.os }}-npm-
+          path: ~/.cache/pip
+          key: pip-wheel-${{ runner.os }}-x64-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            pip-wheel-${{ runner.os }}-x64-
 
-      - name: Install dependencies
-        run: cd apps/frontend && npm ci
+      - name: Cache bundled Python
+        uses: actions/cache@v5
+        with:
+          path: apps/frontend/python-runtime
+          key: python-bundle-${{ runner.os }}-x64-3.12.8-${{ hashFiles('apps/backend/requirements.txt') }}
+          restore-keys: |
+            python-bundle-${{ runner.os }}-x64-3.12.8-
 
       - name: Build application
         run: cd apps/frontend && npm run build
+        env:
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
 
       - name: Package Linux
         run: cd apps/frontend && npm run package:linux
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
+          SENTRY_TRACES_SAMPLE_RATE: ${{ secrets.SENTRY_TRACES_SAMPLE_RATE }}
+          SENTRY_PROFILES_SAMPLE_RATE: ${{ secrets.SENTRY_PROFILES_SAMPLE_RATE }}
+
+      - name: Verify Linux packages
+        run: cd apps/frontend && npm run verify:linux
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
@@ -221,9 +393,54 @@ jobs:
           path: |
             apps/frontend/dist/*.AppImage
             apps/frontend/dist/*.deb
+            apps/frontend/dist/*.flatpak
+            apps/frontend/dist/*.yml
+            apps/frontend/dist/*.blockmap
+
+  # Finalize macOS notarization (runs in parallel with Windows/Linux builds)
+  finalize-notarization:
+    needs: [build-macos-intel, build-macos-arm64]
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download Intel DMG
+        uses: actions/download-artifact@v7
+        with:
+          name: macos-intel-builds
+          path: intel
+
+      - name: Download ARM64 DMG
+        uses: actions/download-artifact@v7
+        with:
+          name: macos-arm64-builds
+          path: arm64
+
+      - name: Wait for notarization and staple
+        uses: ./.github/actions/finalize-macos-notarization
+        with:
+          apple-id: ${{ secrets.APPLE_ID }}
+          apple-app-specific-password: ${{ secrets.APPLE_APP_SPECIFIC_PASSWORD }}
+          apple-team-id: ${{ secrets.APPLE_TEAM_ID }}
+          intel-notarization-id: ${{ needs.build-macos-intel.outputs.notarization_id }}
+          arm64-notarization-id: ${{ needs.build-macos-arm64.outputs.notarization_id }}
+          intel-dmg-file: ${{ needs.build-macos-intel.outputs.dmg_file }}
+          arm64-dmg-file: ${{ needs.build-macos-arm64.outputs.dmg_file }}
+
+      - name: Upload stapled Intel DMG
+        uses: actions/upload-artifact@v4
+        with:
+          name: macos-intel-stapled
+          path: intel/*.dmg
+
+      - name: Upload stapled ARM64 DMG
+        uses: actions/upload-artifact@v4
+        with:
+          name: macos-arm64-stapled
+          path: arm64/*.dmg
 
   create-release:
-    needs: [build-macos-intel, build-macos-arm64, build-windows, build-linux]
+    needs: [build-macos-intel, build-macos-arm64, finalize-notarization, build-windows, build-linux]
     runs-on: ubuntu-latest
     permissions:
       contents: write
@@ -233,23 +450,80 @@ jobs:
           fetch-depth: 0
 
       - name: Download all artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           path: dist
 
-      - name: Flatten and validate artifacts
+      - name: Flatten binary artifacts
         run: |
           mkdir -p release-assets
-          find dist -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" \) -exec cp {} release-assets/ \;
 
-          # Validate that at least one artifact was copied
-          artifact_count=$(find release-assets -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" \) | wc -l)
-          if [ "$artifact_count" -eq 0 ]; then
-            echo "::error::No build artifacts found! Expected .dmg, .zip, .exe, .AppImage, or .deb files."
+          # Copy stapled macOS DMGs (from finalize-notarization job)
+          # Validate that stapled DMGs exist before copying
+          if ! find dist/macos-intel-stapled dist/macos-arm64-stapled -type f -name "*.dmg" 2>/dev/null | grep -q .; then
+            echo "::warning::No stapled DMGs found. Using un-stapled DMGs from build artifacts."
+            find dist/macos-intel-builds dist/macos-arm64-builds -type f -name "*.dmg" -exec cp {} release-assets/ \; 2>/dev/null || true
+          else
+            find dist/macos-intel-stapled dist/macos-arm64-stapled -type f -name "*.dmg" -exec cp {} release-assets/ \; 2>/dev/null || true
+          fi
+
+          # Copy other macOS artifacts (zip, yml, blockmap) from original build
+          find dist/macos-intel-builds dist/macos-arm64-builds -type f \( -name "*.zip" -o -name "*.yml" -o -name "*.blockmap" \) -exec cp {} release-assets/ \; 2>/dev/null || true
+
+          # Copy Windows and Linux artifacts
+          find dist/windows-builds dist/linux-builds -type f \( -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" -o -name "*.flatpak" -o -name "*.yml" -o -name "*.blockmap" \) -exec cp {} release-assets/ \; 2>/dev/null || true
+
+          # Validate that installer files exist
+          installer_count=$(find release-assets -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" -o -name "*.flatpak" \) | wc -l)
+          if [ "$installer_count" -eq 0 ]; then
+            echo "::error::No installer artifacts found! Expected .dmg, .zip, .exe, .AppImage, .deb, or .flatpak files."
             exit 1
           fi
 
-          echo "Found $artifact_count artifact(s):"
+          echo "Found $installer_count binary artifact(s):"
+          find release-assets -type f \( -name "*.dmg" -o -name "*.zip" -o -name "*.exe" -o -name "*.AppImage" -o -name "*.deb" -o -name "*.flatpak" \) -exec basename {} \;
+
+      # Merge macOS manifests from Intel and ARM64 builds
+      # See: https://github.com/electron-userland/electron-builder/issues/5592
+      - name: Merge macOS manifests
+        uses: ./.github/actions/merge-macos-manifests
+        with:
+          dist-path: dist
+          output-path: release-assets
+          copy-other-manifests: 'true'
+
+      - name: Validate manifests
+        run: |
+          # Validate that electron-updater manifest files are present (required for auto-updates)
+          yml_count=$(find release-assets -type f -name "*.yml" | wc -l)
+          if [ "$yml_count" -eq 0 ]; then
+            echo "::error::No update manifest (.yml) files found! Auto-update will not work."
+            exit 1
+          fi
+
+          echo "Found $yml_count manifest file(s):"
+          find release-assets -type f -name "*.yml" -exec basename {} \;
+
+          # Validate required manifests exist
+          missing=""
+          [ ! -f "release-assets/latest-mac.yml" ] && missing="$missing latest-mac.yml"
+          [ ! -f "release-assets/latest.yml" ] && missing="$missing latest.yml"
+          [ ! -f "release-assets/latest-linux.yml" ] && missing="$missing latest-linux.yml"
+
+          if [ -n "$missing" ]; then
+            echo "::error::Missing required manifests:$missing"
+            echo "::error::Auto-update will fail on affected platforms!"
+            exit 1
+          fi
+
+          echo ""
+          echo "All required manifests present:"
+          echo "  - latest-mac.yml (macOS)"
+          echo "  - latest.yml (Windows)"
+          echo "  - latest-linux.yml (Linux)"
+
+          echo ""
+          echo "All release assets:"
           ls -la release-assets/
 
       - name: Generate checksums
@@ -258,144 +532,6 @@ jobs:
           sha256sum ./* > checksums.sha256
           cat checksums.sha256
 
-      - name: Scan with VirusTotal
-        id: virustotal
-        continue-on-error: true
-        if: ${{ github.event_name == 'push' || (github.event_name == 'workflow_dispatch' && inputs.dry_run != true) }}
-        env:
-          VT_API_KEY: ${{ secrets.VIRUSTOTAL_API_KEY }}
-        run: |
-          if [ -z "$VT_API_KEY" ]; then
-            echo "::warning::VIRUSTOTAL_API_KEY not configured, skipping scan"
-            echo "vt_results=" >> $GITHUB_OUTPUT
-            exit 0
-          fi
-
-          echo "## VirusTotal Scan Results" > vt_results.md
-          echo "" >> vt_results.md
-
-          for file in release-assets/*.{exe,dmg,AppImage,deb}; do
-            [ -f "$file" ] || continue
-            filename=$(basename "$file")
-            filesize=$(stat -c%s "$file" 2>/dev/null || stat -f%z "$file")
-            echo "Scanning $filename (${filesize} bytes)..."
-
-            # For files > 32MB, get a special upload URL first
-            if [ "$filesize" -gt 33554432 ]; then
-              echo "  Large file detected, requesting upload URL..."
-              upload_url_response=$(curl -s --request GET \
-                --url "https://www.virustotal.com/api/v3/files/upload_url" \
-                --header "x-apikey: $VT_API_KEY")
-
-              upload_url=$(echo "$upload_url_response" | jq -r '.data // empty')
-              if [ -z "$upload_url" ]; then
-                echo "::warning::Failed to get upload URL for large file $filename"
-                echo "Response: $upload_url_response"
-                echo "- $filename - ⚠️ Upload failed (large file)" >> vt_results.md
-                continue
-              fi
-              api_url="$upload_url"
-            else
-              api_url="https://www.virustotal.com/api/v3/files"
-            fi
-
-            # Upload file to VirusTotal
-            response=$(curl -s --request POST \
-              --url "$api_url" \
-              --header "x-apikey: $VT_API_KEY" \
-              --form "file=@$file")
-
-            # Check if response is valid JSON before parsing
-            if ! echo "$response" | jq -e . >/dev/null 2>&1; then
-              echo "::warning::VirusTotal returned invalid JSON for $filename"
-              echo "Response (first 500 chars): ${response:0:500}"
-              echo "- $filename - ⚠️ Scan failed (invalid response)" >> vt_results.md
-              continue
-            fi
-
-            # Check for API error response
-            error_code=$(echo "$response" | jq -r '.error.code // empty')
-            if [ -n "$error_code" ]; then
-              error_msg=$(echo "$response" | jq -r '.error.message // "Unknown error"')
-              echo "::warning::VirusTotal API error for $filename: $error_code - $error_msg"
-              echo "- $filename - ⚠️ Scan failed ($error_code)" >> vt_results.md
-              continue
-            fi
-
-            # Extract analysis ID
-            analysis_id=$(echo "$response" | jq -r '.data.id // empty')
-
-            if [ -z "$analysis_id" ]; then
-              echo "::warning::Failed to upload $filename to VirusTotal"
-              echo "Response: $response"
-              echo "- $filename - ⚠️ Upload failed" >> vt_results.md
-              continue
-            fi
-
-            echo "Uploaded $filename, analysis ID: $analysis_id"
-
-            # Wait for analysis to complete (max 5 minutes per file)
-            analysis=""
-            for i in {1..30}; do
-              sleep 10
-              analysis=$(curl -s --request GET \
-                --url "https://www.virustotal.com/api/v3/analyses/$analysis_id" \
-                --header "x-apikey: $VT_API_KEY")
-
-              # Validate JSON response
-              if ! echo "$analysis" | jq -e . >/dev/null 2>&1; then
-                echo "  Warning: Invalid JSON response on attempt $i, retrying..."
-                continue
-              fi
-
-              status=$(echo "$analysis" | jq -r '.data.attributes.status // "unknown"')
-              echo "  Status: $status (attempt $i/30)"
-
-              if [ "$status" = "completed" ]; then
-                break
-              fi
-            done
-
-            # Final validation that we have valid analysis data
-            if ! echo "$analysis" | jq -e '.data.attributes.stats' >/dev/null 2>&1; then
-              echo "::warning::Could not get complete analysis for $filename, using local hash"
-              file_hash=$(sha256sum "$file" | cut -d' ' -f1)
-              echo "- [$filename](https://www.virustotal.com/gui/file/$file_hash) - ⚠️ Analysis incomplete" >> vt_results.md
-              continue
-            fi
-
-            # Get file hash for permanent URL
-            file_hash=$(echo "$analysis" | jq -r '.meta.file_info.sha256 // empty')
-
-            if [ -z "$file_hash" ]; then
-              # Fallback: calculate hash locally
-              file_hash=$(sha256sum "$file" | cut -d' ' -f1)
-            fi
-
-            # Get detection stats
-            malicious=$(echo "$analysis" | jq -r '.data.attributes.stats.malicious // 0')
-            suspicious=$(echo "$analysis" | jq -r '.data.attributes.stats.suspicious // 0')
-            undetected=$(echo "$analysis" | jq -r '.data.attributes.stats.undetected // 0')
-
-            vt_url="https://www.virustotal.com/gui/file/$file_hash"
-
-            if [ "$malicious" -gt 0 ] || [ "$suspicious" -gt 0 ]; then
-              echo "::warning::$filename has $malicious malicious and $suspicious suspicious detections (likely false positives)"
-              echo "- [$filename]($vt_url) - ⚠️ **$malicious malicious, $suspicious suspicious** detections (review recommended)" >> vt_results.md
-            else
-              echo "$filename is clean ($undetected engines, 0 detections)"
-              echo "- [$filename]($vt_url) - ✅ Clean ($undetected engines, 0 detections)" >> vt_results.md
-            fi
-          done
-
-          echo "" >> vt_results.md
-
-          # Save results for release notes
-          cat vt_results.md
-          echo "vt_results<<EOF" >> $GITHUB_OUTPUT
-          cat vt_results.md >> $GITHUB_OUTPUT
-          echo "EOF" >> $GITHUB_OUTPUT
-
       - name: Dry run summary
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.dry_run == true }}
         run: |
@@ -409,23 +545,77 @@ jobs:
           cat release-assets/checksums.sha256 >> $GITHUB_STEP_SUMMARY
           echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
 
-      - name: Generate changelog
-        if: ${{ github.event_name == 'push' || (github.event_name == 'workflow_dispatch' && inputs.dry_run != true) }}
+      - name: Extract changelog from CHANGELOG.md
+        if: ${{ github.event_name == 'push' }}
         id: changelog
-        uses: release-drafter/release-drafter@v6
-        with:
-          config-name: release-drafter.yml
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          # Extract version from tag (v2.7.2 -> 2.7.2)
+          VERSION=${GITHUB_REF_NAME#v}
+          CHANGELOG_FILE="CHANGELOG.md"
+
+          echo "📋 Extracting release notes for version $VERSION from CHANGELOG.md..."
+
+          if [ ! -f "$CHANGELOG_FILE" ]; then
+            echo "::warning::CHANGELOG.md not found, using minimal release notes"
+            echo "body=Release v$VERSION" >> $GITHUB_OUTPUT
+            exit 0
+          fi
+
+          # Extract changelog section for this version
+          # Looks for "## X.Y.Z" header and captures until next "## " or "---"
+          CHANGELOG_CONTENT=$(awk -v ver="$VERSION" '
+            BEGIN { found=0; content="" }
+            /^## / {
+              if (found) exit
+              # Match version at start of header (e.g., "## 2.7.3 -" or "## 2.7.3")
+              if ($2 == ver || $2 ~ "^"ver"[[:space:]]*-") {
+                found=1
+                next
+              }
+            }
+            /^---$/ { if (found) exit }
+            found { content = content $0 "\n" }
+            END {
+              if (!found) {
+                print "NOT_FOUND"
+                exit 0
+              }
+              # Trim leading/trailing whitespace
+              gsub(/^[[:space:]]+|[[:space:]]+$/, "", content)
+              print content
+            }
+          ' "$CHANGELOG_FILE")
+
+          if [ "$CHANGELOG_CONTENT" = "NOT_FOUND" ] || [ -z "$CHANGELOG_CONTENT" ]; then
+            echo "::warning::Version $VERSION not found in CHANGELOG.md, using minimal release notes"
+            REPO="${{ github.repository }}"
+            CHANGELOG_CONTENT="Release v$VERSION"$'\n\n'"See [CHANGELOG.md](https://github.com/${REPO}/blob/main/CHANGELOG.md) for details."
+          fi
+
+          echo "✅ Extracted changelog content"
+
+          # Save to file first (more reliable for multiline)
+          echo "$CHANGELOG_CONTENT" > changelog-body.md
+
+          # Use file-based output for multiline content
+          {
+            echo "body<<CHANGELOG_EOF"
+            cat changelog-body.md
+            echo "CHANGELOG_EOF"
+          } >> $GITHUB_OUTPUT
 
       - name: Create Release
-        if: ${{ github.event_name == 'push' || (github.event_name == 'workflow_dispatch' && inputs.dry_run != true) }}
+        if: ${{ github.event_name == 'push' }}
         uses: softprops/action-gh-release@v2
         with:
           body: |
             ${{ steps.changelog.outputs.body }}
 
-            ${{ steps.virustotal.outputs.vt_results }}
+            ---
+
+            **Full Changelog**: https://github.com/${{ github.repository }}/blob/main/CHANGELOG.md
+
+            _VirusTotal scan results will be added automatically after release._
           files: release-assets/*
           draft: false
           prerelease: ${{ contains(github.ref, 'beta') || contains(github.ref, 'alpha') }}
@@ -436,35 +626,46 @@ jobs:
   update-readme:
     needs: [create-release]
     runs-on: ubuntu-latest
-    if: ${{ github.event_name == 'push' || (github.event_name == 'workflow_dispatch' && inputs.dry_run != true) }}
+    # Only update README on actual releases (tag push), not dry runs
+    if: ${{ github.event_name == 'push' }}
     permissions:
       contents: write
     steps:
       - uses: actions/checkout@v4
         with:
           ref: main
-          token: ${{ secrets.GITHUB_TOKEN }}
+          # Use PAT_TOKEN to bypass branch protection rules on main
+          token: ${{ secrets.PAT_TOKEN }}
 
-      - name: Extract version from tag
+      - name: Extract version and detect release type
         id: version
         run: |
           # Extract version from tag (v2.7.2 -> 2.7.2)
           VERSION=${GITHUB_REF_NAME#v}
           echo "version=$VERSION" >> $GITHUB_OUTPUT
-          echo "Updating README to version: $VERSION"
+
+          # Detect if this is a prerelease (contains - after version, e.g., 2.7.2-beta.10)
+          if [[ "$VERSION" == *-* ]]; then
+            echo "is_prerelease=true" >> $GITHUB_OUTPUT
+            echo "Detected PRERELEASE: $VERSION"
+          else
+            echo "is_prerelease=false" >> $GITHUB_OUTPUT
+            echo "Detected STABLE release: $VERSION"
+          fi
 
       - name: Update README.md
         run: |
           VERSION="${{ steps.version.outputs.version }}"
+          IS_PRERELEASE="${{ steps.version.outputs.is_prerelease }}"
 
-          # Update version badge: version-X.Y.Z-blue
-          sed -i "s/version-[0-9]*\.[0-9]*\.[0-9]*-blue/version-${VERSION}-blue/g" README.md
+          if [ "$IS_PRERELEASE" = "true" ]; then
+            python3 scripts/update-readme.py "$VERSION" --prerelease
+          else
+            python3 scripts/update-readme.py "$VERSION"
+          fi
 
-          # Update download links: Auto-Claude-X.Y.Z
-          sed -i "s/Auto-Claude-[0-9]*\.[0-9]*\.[0-9]*/Auto-Claude-${VERSION}/g" README.md
-
-          echo "README.md updated to version $VERSION"
-          grep -E "(version-|Auto-Claude-)" README.md | head -10
+          echo "--- Verifying update ---"
+          grep -E "(stable-|beta-|version-)[0-9]" README.md | head -5
 
       - name: Commit and push README update
         run: |

.github/workflows/stale.yml

@@ -15,7 +15,7 @@ jobs:
         with:
           stale-issue-message: |
             This issue has been inactive for 60 days. It will be closed in 14 days if there's no activity.
-            
+
             - If this is still relevant, please comment or update the issue
             - If you're working on this, add the `in-progress` label
           close-issue-message: 'Closed due to inactivity. Feel free to reopen if still relevant.'

.github/workflows/test-azure-auth.yml

@@ -0,0 +1,21 @@
+name: Test Azure Auth
+
+on:
+  workflow_dispatch:
+
+jobs:
+  test-auth:
+    runs-on: windows-latest
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Azure Login (OIDC)
+        uses: azure/login@v2
+        with:
+          client-id: ${{ secrets.AZURE_CLIENT_ID }}
+          tenant-id: ${{ secrets.AZURE_TENANT_ID }}
+          subscription-id: ${{ secrets.AZURE_SUBSCRIPTION_ID }}
+
+      - name: Success
+        run: echo "Azure authentication successful!"

.github/workflows/test-on-tag.yml

@@ -1,63 +0,0 @@
-name: Test on Tag
-
-on:
-  push:
-    tags:
-      - 'v*'
-
-jobs:
-  # Python tests
-  test-python:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.12', '3.13']
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@v4
-        with:
-          version: "latest"
-
-      - name: Install dependencies
-        working-directory: apps/backend
-        run: |
-          uv venv
-          uv pip install -r requirements.txt
-          uv pip install -r ../../tests/requirements-test.txt
-
-      - name: Run tests
-        working-directory: apps/backend
-        env:
-          PYTHONPATH: ${{ github.workspace }}/apps/backend
-        run: |
-          source .venv/bin/activate
-          pytest ../../tests/ -v --tb=short
-
-  # Frontend tests
-  test-frontend:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
-        with:
-          node-version: '24'
-
-      - name: Install dependencies
-        working-directory: apps/frontend
-        run: npm ci --ignore-scripts
-
-      - name: Run tests
-        working-directory: apps/frontend
-        run: npm run test

.github/workflows/validate-version.yml

@@ -1,71 +0,0 @@
-name: Validate Version
-
-on:
-  push:
-    tags:
-      - 'v*'
-
-jobs:
-  validate-version:
-    name: Validate package.json version matches tag
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Extract version from tag
-        id: tag_version
-        run: |
-          # Extract version from tag (e.g., v2.5.5 -> 2.5.5)
-          TAG_VERSION=${GITHUB_REF#refs/tags/v}
-          echo "version=$TAG_VERSION" >> $GITHUB_OUTPUT
-          echo "Tag version: $TAG_VERSION"
-
-      - name: Extract version from package.json
-        id: package_version
-        run: |
-          # Read version from package.json
-          PACKAGE_VERSION=$(node -p "require('./apps/frontend/package.json').version")
-          echo "version=$PACKAGE_VERSION" >> $GITHUB_OUTPUT
-          echo "Package.json version: $PACKAGE_VERSION"
-
-      - name: Compare versions
-        run: |
-          TAG_VERSION="${{ steps.tag_version.outputs.version }}"
-          PACKAGE_VERSION="${{ steps.package_version.outputs.version }}"
-
-          echo "=========================================="
-          echo "Version Validation"
-          echo "=========================================="
-          echo "Git tag version:      v$TAG_VERSION"
-          echo "package.json version: $PACKAGE_VERSION"
-          echo "=========================================="
-
-          if [ "$TAG_VERSION" != "$PACKAGE_VERSION" ]; then
-            echo ""
-            echo "❌ ERROR: Version mismatch detected!"
-            echo ""
-            echo "The version in package.json ($PACKAGE_VERSION) does not match"
-            echo "the git tag version ($TAG_VERSION)."
-            echo ""
-            echo "To fix this:"
-            echo "  1. Delete this tag: git tag -d v$TAG_VERSION"
-            echo "  2. Update package.json version to $TAG_VERSION"
-            echo "  3. Commit the change"
-            echo "  4. Recreate the tag: git tag -a v$TAG_VERSION -m 'Release v$TAG_VERSION'"
-            echo ""
-            echo "Or use the automated script:"
-            echo "  node scripts/bump-version.js $TAG_VERSION"
-            echo ""
-            exit 1
-          fi
-
-          echo ""
-          echo "✅ SUCCESS: Versions match!"
-          echo ""
-
-      - name: Version validation result
-        if: success()
-        run: |
-          echo "::notice::Version validation passed - package.json version matches tag v${{ steps.tag_version.outputs.version }}"

.github/workflows/virustotal-scan.yml

@@ -0,0 +1,343 @@
+name: VirusTotal Scan
+
+# Runs AFTER release is published to avoid blocking release creation
+# VirusTotal scans can take 5+ minutes per file, which delays releases
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Release tag to scan (e.g., v2.8.0)'
+        required: true
+        type: string
+
+# Prevent TOCTOU race condition when updating release notes
+# If two runs target the same tag, queue them instead of running in parallel
+concurrency:
+  group: virustotal-${{ github.event.inputs.tag || github.event.release.tag_name }}
+  cancel-in-progress: false
+
+jobs:
+  scan:
+    name: Scan release assets
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write  # Required to update release notes
+    steps:
+      - name: Determine release tag
+        id: tag
+        run: |
+          if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
+            echo "tag=${{ github.event.inputs.tag }}" >> $GITHUB_OUTPUT
+          else
+            echo "tag=${{ github.event.release.tag_name }}" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Check for API key
+        id: check-key
+        env:
+          VT_KEY: ${{ secrets.VIRUSTOTAL_API_KEY }}
+        run: |
+          if [ -z "$VT_KEY" ]; then
+            echo "::warning::VIRUSTOTAL_API_KEY not configured, skipping scan"
+            echo "has_key=false" >> $GITHUB_OUTPUT
+          else
+            echo "has_key=true" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Download release assets
+        if: steps.check-key.outputs.has_key == 'true'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          TAG="${{ steps.tag.outputs.tag }}"
+          echo "Downloading assets for release $TAG..."
+
+          mkdir -p release-assets
+
+          # First verify the release exists
+          if ! gh release view "$TAG" --repo "${{ github.repository }}" >/dev/null 2>&1; then
+            echo "::error::Release $TAG not found"
+            exit 1
+          fi
+
+          # Download assets, distinguishing between "no matching assets" and real errors
+          set +e
+          gh release download "$TAG" \
+            --repo "${{ github.repository }}" \
+            --pattern "*.exe" \
+            --pattern "*.dmg" \
+            --pattern "*.AppImage" \
+            --pattern "*.deb" \
+            --pattern "*.flatpak" \
+            --dir release-assets 2>&1
+          exit_code=$?
+          set -e
+
+          if [ $exit_code -ne 0 ]; then
+            # Check if it's just "no assets matched" vs a real error
+            asset_count=$(gh release view "$TAG" --repo "${{ github.repository }}" --json assets -q '.assets | length')
+            if [ "$asset_count" -eq 0 ]; then
+              echo "Release has no assets yet (this is OK for new releases)"
+            else
+              # Check if any scannable assets exist that should have been downloaded
+              scannable_assets=$(gh release view "$TAG" --repo "${{ github.repository }}" --json assets \
+                -q '.assets[].name | select(test("\\.(exe|dmg|AppImage|deb|flatpak)$"))' | wc -l)
+              if [ "$scannable_assets" -gt 0 ]; then
+                echo "::error::Download failed - $scannable_assets scannable asset(s) exist but download failed"
+                exit 1
+              fi
+              echo "No assets matched the patterns (exe, dmg, AppImage, deb, flatpak)"
+            fi
+          fi
+
+          echo "Downloaded assets:"
+          ls -la release-assets/ || echo "No assets found"
+
+      - name: Scan with VirusTotal
+        if: steps.check-key.outputs.has_key == 'true'
+        id: virustotal
+        env:
+          VT_API_KEY: ${{ secrets.VIRUSTOTAL_API_KEY }}
+        run: |
+          echo "## VirusTotal Scan Results" > vt_results.md
+          echo "" >> vt_results.md
+
+          # Check if there are any files to scan
+          shopt -s nullglob
+          files=(release-assets/*.{exe,dmg,AppImage,deb,flatpak})
+          if [ ${#files[@]} -eq 0 ]; then
+            echo "No scannable files found in release assets"
+            echo "- No executable files found in release" >> vt_results.md
+            echo "vt_results<<EOF" >> $GITHUB_OUTPUT
+            cat vt_results.md >> $GITHUB_OUTPUT
+            echo "EOF" >> $GITHUB_OUTPUT
+            exit 0
+          fi
+
+          for file in "${files[@]}"; do
+            [ -f "$file" ] || continue
+            filename=$(basename "$file")
+            filesize=$(stat -c%s "$file" 2>/dev/null || stat -f%z "$file")
+            echo "Scanning $filename (${filesize} bytes)..."
+
+            # VirusTotal requires special upload URL for files > 32MB
+            LARGE_FILE_THRESHOLD=33554432  # 32 MB in bytes
+            if [ "$filesize" -gt "$LARGE_FILE_THRESHOLD" ]; then
+              echo "  Large file detected, requesting upload URL..."
+              upload_http_response=$(curl -s -w '\n%{http_code}' --request GET \
+                --url "https://www.virustotal.com/api/v3/files/upload_url" \
+                --header "x-apikey: $VT_API_KEY")
+              upload_http_code=$(echo "$upload_http_response" | tail -1)
+              upload_url_response=$(echo "$upload_http_response" | sed '$d')
+
+              if [ "$upload_http_code" != "200" ]; then
+                echo "::warning::Failed to get upload URL for large file $filename (HTTP $upload_http_code)"
+                echo "- $filename - ⚠️ Upload failed (large file, HTTP $upload_http_code)" >> vt_results.md
+                continue
+              fi
+
+              upload_url=$(echo "$upload_url_response" | jq -r '.data // empty')
+              if [ -z "$upload_url" ]; then
+                echo "::warning::Failed to get upload URL for large file $filename"
+                echo "Response: $upload_url_response"
+                echo "- $filename - ⚠️ Upload failed (large file)" >> vt_results.md
+                continue
+              fi
+              api_url="$upload_url"
+            else
+              api_url="https://www.virustotal.com/api/v3/files"
+            fi
+
+            # Upload file to VirusTotal (capture HTTP status code)
+            http_response=$(curl -s -w '\n%{http_code}' --request POST \
+              --url "$api_url" \
+              --header "x-apikey: $VT_API_KEY" \
+              --form "file=@$file")
+            http_code=$(echo "$http_response" | tail -1)
+            response=$(echo "$http_response" | sed '$d')
+
+            # Check HTTP status code first
+            if [ "$http_code" != "200" ]; then
+              echo "::warning::VirusTotal returned HTTP $http_code for $filename"
+              if [ "$http_code" = "429" ]; then
+                echo "- $filename - ⚠️ Scan failed (rate limited)" >> vt_results.md
+              elif [ "$http_code" = "403" ]; then
+                echo "- $filename - ⚠️ Scan failed (forbidden - check API key)" >> vt_results.md
+              else
+                echo "- $filename - ⚠️ Scan failed (HTTP $http_code)" >> vt_results.md
+              fi
+              continue
+            fi
+
+            # Check if response is valid JSON before parsing
+            if ! echo "$response" | jq -e . >/dev/null 2>&1; then
+              echo "::warning::VirusTotal returned invalid JSON for $filename"
+              echo "Response (first 500 chars): ${response:0:500}"
+              echo "- $filename - ⚠️ Scan failed (invalid response)" >> vt_results.md
+              continue
+            fi
+
+            # Check for API error response
+            error_code=$(echo "$response" | jq -r '.error.code // empty')
+            if [ -n "$error_code" ]; then
+              error_msg=$(echo "$response" | jq -r '.error.message // "Unknown error"')
+              echo "::warning::VirusTotal API error for $filename: $error_code - $error_msg"
+              echo "- $filename - ⚠️ Scan failed ($error_code)" >> vt_results.md
+              continue
+            fi
+
+            # Extract analysis ID
+            analysis_id=$(echo "$response" | jq -r '.data.id // empty')
+
+            if [ -z "$analysis_id" ]; then
+              echo "::warning::Failed to upload $filename to VirusTotal"
+              echo "Response: $response"
+              echo "- $filename - ⚠️ Upload failed" >> vt_results.md
+              continue
+            fi
+
+            echo "Uploaded $filename, analysis ID: $analysis_id"
+
+            # Wait for analysis to complete (max 5 minutes per file)
+            analysis=""
+            for i in {1..30}; do
+              sleep 10
+              analysis_http_response=$(curl -s -w '\n%{http_code}' --request GET \
+                --url "https://www.virustotal.com/api/v3/analyses/$analysis_id" \
+                --header "x-apikey: $VT_API_KEY")
+              analysis_http_code=$(echo "$analysis_http_response" | tail -1)
+              analysis=$(echo "$analysis_http_response" | sed '$d')
+
+              # Check HTTP status code
+              if [ "$analysis_http_code" != "200" ]; then
+                echo "  Warning: HTTP $analysis_http_code on attempt $i, retrying..."
+                if [ "$analysis_http_code" = "429" ]; then
+                  echo "  Rate limited, waiting longer..."
+                  sleep 30
+                fi
+                continue
+              fi
+
+              # Validate JSON response
+              if ! echo "$analysis" | jq -e . >/dev/null 2>&1; then
+                echo "  Warning: Invalid JSON response on attempt $i, retrying..."
+                continue
+              fi
+
+              status=$(echo "$analysis" | jq -r '.data.attributes.status // "unknown"')
+              echo "  Status: $status (attempt $i/30)"
+
+              if [ "$status" = "completed" ]; then
+                break
+              fi
+            done
+
+            # Handle analysis timeout - if loop completed without status=completed
+            if [ "$status" != "completed" ]; then
+              echo "::warning::Analysis timed out for $filename (status: $status after 5 minutes)"
+              file_hash=$(sha256sum "$file" | cut -d' ' -f1)
+              echo "- [$filename](https://www.virustotal.com/gui/file/$file_hash) - ⚠️ Analysis timed out" >> vt_results.md
+              continue
+            fi
+
+            # Final validation that we have valid analysis data
+            if ! echo "$analysis" | jq -e '.data.attributes.stats' >/dev/null 2>&1; then
+              echo "::warning::Could not get complete analysis for $filename, using local hash"
+              file_hash=$(sha256sum "$file" | cut -d' ' -f1)
+              echo "- [$filename](https://www.virustotal.com/gui/file/$file_hash) - ⚠️ Analysis incomplete" >> vt_results.md
+              continue
+            fi
+
+            # Get file hash for permanent URL
+            file_hash=$(echo "$analysis" | jq -r '.meta.file_info.sha256 // empty')
+
+            if [ -z "$file_hash" ]; then
+              # Fallback: calculate hash locally
+              file_hash=$(sha256sum "$file" | cut -d' ' -f1)
+            fi
+
+            # Get detection stats
+            malicious=$(echo "$analysis" | jq -r '.data.attributes.stats.malicious // 0')
+            suspicious=$(echo "$analysis" | jq -r '.data.attributes.stats.suspicious // 0')
+            undetected=$(echo "$analysis" | jq -r '.data.attributes.stats.undetected // 0')
+
+            vt_url="https://www.virustotal.com/gui/file/$file_hash"
+
+            if [ "$malicious" -gt 0 ] || [ "$suspicious" -gt 0 ]; then
+              echo "::warning::$filename has $malicious malicious and $suspicious suspicious detections (likely false positives)"
+              echo "- [$filename]($vt_url) - ⚠️ **$malicious malicious, $suspicious suspicious** detections (review recommended)" >> vt_results.md
+            else
+              echo "$filename is clean ($undetected engines, 0 detections)"
+              echo "- [$filename]($vt_url) - ✅ Clean ($undetected engines, 0 detections)" >> vt_results.md
+            fi
+          done
+
+          echo "" >> vt_results.md
+
+          # Save results for next step
+          cat vt_results.md
+          echo "vt_results<<EOF" >> $GITHUB_OUTPUT
+          cat vt_results.md >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+      - name: Update release notes with scan results
+        if: steps.check-key.outputs.has_key == 'true' && steps.virustotal.outputs.vt_results != ''
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          TAG="${{ steps.tag.outputs.tag }}"
+
+          # Get current release body with error checking
+          if ! current_body=$(gh release view "$TAG" --repo "${{ github.repository }}" --json body -q '.body'); then
+            echo "::error::Failed to fetch current release body for $TAG"
+            exit 1
+          fi
+
+          # Additional safeguard for empty body
+          if [ -z "$current_body" ]; then
+            echo "::warning::Release body is empty, this may indicate a problem"
+          fi
+
+          # Check if VirusTotal results already exist in the body
+          if echo "$current_body" | grep -q "## VirusTotal Scan Results"; then
+            echo "VirusTotal results already in release notes, skipping update"
+            exit 0
+          fi
+
+          # Use file-based approach to avoid shell expansion issues
+          # First, write current body to file
+          echo "$current_body" > release-body.md
+
+          # Remove placeholder text if present (portable sed approach)
+          sed '/_VirusTotal scan results will be added automatically after release\./d' release-body.md > release-body.tmp && mv release-body.tmp release-body.md
+
+          # Append separator and VT results
+          echo "" >> release-body.md
+          echo "---" >> release-body.md
+          echo "" >> release-body.md
+          cat vt_results.md >> release-body.md
+
+          # Update release using --notes-file to avoid shell quoting issues
+          gh release edit "$TAG" \
+            --repo "${{ github.repository }}" \
+            --notes-file release-body.md
+
+          echo "✅ Updated release notes with VirusTotal scan results"
+
+      - name: Summary
+        if: always()
+        run: |
+          echo "## VirusTotal Scan Summary" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "**Release:** ${{ steps.tag.outputs.tag }}" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          if [ "${{ steps.check-key.outputs.has_key }}" = "false" ]; then
+            echo "⚠️ Scan skipped: VIRUSTOTAL_API_KEY not configured" >> $GITHUB_STEP_SUMMARY
+          elif [ -f vt_results.md ]; then
+            cat vt_results.md >> $GITHUB_STEP_SUMMARY
+          else
+            echo "No scan results available" >> $GITHUB_STEP_SUMMARY
+          fi

.github/workflows/welcome.yml

@@ -18,16 +18,16 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           issue-message: |
             👋 Thanks for opening your first issue!
-            
+
             A maintainer will triage this soon. In the meantime:
             - Make sure you've provided all the requested info
-            - Join our [Discord](https://discord.gg/KCXaPBr4Dj) for faster help
+            - Join our [Discord](https://discord.gg/QhRnz9m5HE) for faster help
           pr-message: |
             🎉 Thanks for your first PR!
-            
+
             A maintainer will review it soon. Please make sure:
-            - Your branch is synced with `main`
+            - Your branch is synced with `develop`
             - CI checks pass
-            - You've followed our [contribution guide](CONTRIBUTING.md)
-            
-            Welcome to the Auto-Claude community!
+            - You've followed our [contribution guide](https://github.com/AndyMik90/Auto-Claude/blob/develop/CONTRIBUTING.md)
+
+            Welcome to the Auto Claude community!

.gitignore

@@ -7,6 +7,7 @@
 Thumbs.db
 ehthumbs.db
 Desktop.ini
+nul
 
 # ===========================
 # Security - Environment & Secrets
@@ -14,6 +15,7 @@ Desktop.ini
 .env
 .env.*
 !.env.example
+/config.json
 *.pem
 *.key
 *.crt
@@ -55,6 +57,8 @@ lerna-debug.log*
 # Auto Claude Generated
 # ===========================
 .auto-claude/
+.planning/
+.planning-archive/
 .auto-build-security.json
 .auto-claude-security.json
 .auto-claude-status
@@ -106,7 +110,8 @@ dmypy.json
 # ===========================
 # Node.js (apps/frontend)
 # ===========================
-node_modules/
+node_modules
+apps/frontend/node_modules
 .npm
 .yarn/
 .pnp.*
@@ -115,6 +120,7 @@ node_modules/
 dist/
 out/
 *.tsbuildinfo
+apps/frontend/python-runtime/
 
 # Cache
 .cache/
@@ -162,3 +168,10 @@ _bmad-output/
 .claude/
 /docs
 OPUS_ANALYSIS_AND_IDEAS.md
+/.github/agents
+
+# Auto Claude generated files
+.security-key
+/shared_docs
+logs/security/
+Agents.md

.husky/commit-msg

@@ -1,12 +1,16 @@
 #!/bin/sh
 
 # Commit message validation
-# Enforces conventional commit format: type(scope): description
+# Enforces conventional commit format: type(scope)!?: description
 #
 # Valid types: feat, fix, docs, style, refactor, perf, test, build, ci, chore, revert
+# Scope allows: letters, numbers, hyphens, underscores, slashes, dots
+# Optional ! for breaking changes
 # Examples:
 #   feat(tasks): add drag and drop support
 #   fix(terminal): resolve scroll position issue
+#   feat!: breaking change without scope
+#   feat(api)!: breaking change with scope
 #   docs: update README with setup instructions
 #   chore: update dependencies
 
@@ -14,8 +18,10 @@ commit_msg_file=$1
 commit_msg=$(cat "$commit_msg_file")
 
 # Regex for conventional commits
-# Format: type(optional-scope): description
-pattern="^(feat|fix|docs|style|refactor|perf|test|build|ci|chore|revert)(\([a-z0-9-]+\))?: .{1,100}$"
+# Format: type(optional-scope)!?: description
+# Scope allows: letters, numbers, hyphens, underscores, slashes, dots (consistent with GitHub workflow)
+# Optional ! for breaking changes: feat!: or feat(scope)!:
+pattern="^(feat|fix|docs|style|refactor|perf|test|build|ci|chore|revert)(\([a-zA-Z0-9_/.-]+\))?!?: .{1,100}$"
 
 # Allow merge commits
 if echo "$commit_msg" | grep -qE "^Merge "; then
@@ -36,7 +42,7 @@ if ! echo "$first_line" | grep -qE "$pattern"; then
   echo ""
   echo "Your message: $first_line"
   echo ""
-  echo "Expected format: type(scope): description"
+  echo "Expected format: type(scope)!?: description"
   echo ""
   echo "Valid types:"
   echo "  feat     - A new feature"
@@ -54,6 +60,8 @@ if ! echo "$first_line" | grep -qE "$pattern"; then
   echo "Examples:"
   echo "  feat(tasks): add drag and drop support"
   echo "  fix(terminal): resolve scroll position issue"
+  echo "  feat!: breaking change without scope"
+  echo "  feat(api)!: breaking change with scope"
   echo "  docs: update README"
   echo "  chore: update dependencies"
   echo ""

.husky/pre-commit

@@ -1,5 +1,39 @@
 #!/bin/sh
 
+# =============================================================================
+# GIT WORKTREE ENVIRONMENT CLEANUP
+# =============================================================================
+# Git automatically sets GIT_DIR (and CWD to the working tree root) before
+# running hooks -- even in worktrees. We do NOT need to manually parse .git
+# files or export GIT_DIR/GIT_WORK_TREE.
+#
+# However, external tools (IDEs, agents, parent shells) may leave stale
+# GIT_DIR/GIT_WORK_TREE values in the environment. If these point to a
+# different repo or worktree, git commands in this hook would target the
+# wrong repository. Unsetting them lets git re-resolve the correct values
+# from the working directory.
+# =============================================================================
+unset GIT_DIR
+unset GIT_WORK_TREE
+
+# =============================================================================
+# SAFETY CHECK: Detect and fix corrupted core.worktree configuration
+# =============================================================================
+# core.worktree lives in the SHARED .git/config (not per-worktree). If any
+# process accidentally writes it (e.g., running `git init` with a leaked
+# GIT_WORK_TREE), ALL repos and worktrees see the wrong working tree root,
+# causing files from one worktree to "leak" into others.
+#
+# This check runs from both main repo and worktree contexts since the config
+# is shared and corruption can happen from either.
+CORE_WORKTREE=$(git config --get core.worktree 2>/dev/null || true)
+if [ -n "$CORE_WORKTREE" ]; then
+  echo "Warning: Detected corrupted core.worktree setting ('$CORE_WORKTREE'), removing it..."
+  if ! git config --unset core.worktree 2>/dev/null; then
+    echo "Warning: Failed to unset core.worktree. Manual intervention may be needed."
+  fi
+fi
+
 echo "Running pre-commit checks..."
 
 # =============================================================================
@@ -36,12 +70,46 @@ if git diff --cached --name-only | grep -q "^package.json$"; then
       echo "  Updated apps/backend/__init__.py to $VERSION"
     fi
 
-    # Sync to README.md
+    # Sync to README.md - section-aware updates (stable vs beta)
     if [ -f "README.md" ]; then
-      # Update version badge
-      sed -i.bak "s/version-[0-9]*\.[0-9]*\.[0-9]*-blue/version-$VERSION-blue/g" README.md
-      # Update download links
-      sed -i.bak "s/Auto-Claude-[0-9]*\.[0-9]*\.[0-9]*/Auto-Claude-$VERSION/g" README.md
+      # Escape hyphens for shields.io badge format (shields.io uses -- for literal hyphens)
+      ESCAPED_VERSION=$(echo "$VERSION" | sed 's/-/--/g')
+
+      # Detect if this is a prerelease (contains - after base version, e.g., 2.7.2-beta.10)
+      if echo "$VERSION" | grep -q '-'; then
+        # PRERELEASE: Update only beta sections
+        echo "  Detected PRERELEASE version: $VERSION"
+
+        # Update beta version badge (orange)
+        sed -i.bak "s/beta-[0-9]*\.[0-9]*\.[0-9]*\(--[a-z]*\.[0-9]*\)*-orange/beta-$ESCAPED_VERSION-orange/g" README.md
+
+        # Update beta version badge link (within BETA_VERSION_BADGE section)
+        sed -i.bak '/<!-- BETA_VERSION_BADGE -->/,/<!-- BETA_VERSION_BADGE_END -->/s|releases/tag/v[0-9.a-z-]*)|releases/tag/v'"$VERSION"')|g' README.md
+
+        # Update beta download links (within BETA_DOWNLOADS section only)
+        # Use perl for cross-platform compatibility (BSD sed doesn't support {block} syntax)
+        for SUFFIX in "win32-x64.exe" "darwin-arm64.dmg" "darwin-x64.dmg" "linux-x86_64.AppImage" "linux-amd64.deb" "linux-x86_64.flatpak"; do
+          perl -i -pe 'if (/<!-- BETA_DOWNLOADS -->/ .. /<!-- BETA_DOWNLOADS_END -->/) { s|Auto-Claude-[0-9.a-z-]*-'"$SUFFIX"'\]\(https://github.com/AndyMik90/Auto-Claude/releases/download/v[^/]*/Auto-Claude-[^)]*-'"$SUFFIX"'\)|Auto-Claude-'"$VERSION"'-'"$SUFFIX"'](https://github.com/AndyMik90/Auto-Claude/releases/download/v'"$VERSION"'/Auto-Claude-'"$VERSION"'-'"$SUFFIX"')|g }' README.md
+        done
+      else
+        # STABLE: Update stable sections and top badge
+        echo "  Detected STABLE version: $VERSION"
+
+        # Update top version badge (blue) - within TOP_VERSION_BADGE section
+        sed -i.bak '/<!-- TOP_VERSION_BADGE -->/,/<!-- TOP_VERSION_BADGE_END -->/s/version-[0-9]*\.[0-9]*\.[0-9]*\(--[a-z]*\.[0-9]*\)*-blue/version-'"$ESCAPED_VERSION"'-blue/g' README.md
+        sed -i.bak '/<!-- TOP_VERSION_BADGE -->/,/<!-- TOP_VERSION_BADGE_END -->/s|releases/tag/v[0-9.a-z-]*)|releases/tag/v'"$VERSION"')|g' README.md
+
+        # Update stable version badge (blue) - within STABLE_VERSION_BADGE section
+        sed -i.bak '/<!-- STABLE_VERSION_BADGE -->/,/<!-- STABLE_VERSION_BADGE_END -->/s/stable-[0-9]*\.[0-9]*\.[0-9]*\(--[a-z]*\.[0-9]*\)*-blue/stable-'"$ESCAPED_VERSION"'-blue/g' README.md
+        sed -i.bak '/<!-- STABLE_VERSION_BADGE -->/,/<!-- STABLE_VERSION_BADGE_END -->/s|releases/tag/v[0-9.a-z-]*)|releases/tag/v'"$VERSION"')|g' README.md
+
+        # Update stable download links (within STABLE_DOWNLOADS section only)
+        # Use perl for cross-platform compatibility (BSD sed doesn't support {block} syntax)
+        for SUFFIX in "win32-x64.exe" "darwin-arm64.dmg" "darwin-x64.dmg" "linux-x86_64.AppImage" "linux-amd64.deb"; do
+          perl -i -pe 'if (/<!-- STABLE_DOWNLOADS -->/ .. /<!-- STABLE_DOWNLOADS_END -->/) { s|Auto-Claude-[0-9.a-z-]*-'"$SUFFIX"'\]\(https://github.com/AndyMik90/Auto-Claude/releases/download/v[^/]*/Auto-Claude-[^)]*-'"$SUFFIX"'\)|Auto-Claude-'"$VERSION"'-'"$SUFFIX"'](https://github.com/AndyMik90/Auto-Claude/releases/download/v'"$VERSION"'/Auto-Claude-'"$VERSION"'-'"$SUFFIX"')|g }' README.md
+        done
+      fi
+
       rm -f README.md.bak
       git add README.md
       echo "  Updated README.md to $VERSION"
@@ -59,6 +127,13 @@ fi
 if git diff --cached --name-only | grep -q "^apps/backend/.*\.py$"; then
   echo "Python changes detected, running backend checks..."
 
+  # Detect if we're in a worktree
+  IS_WORKTREE=false
+  if [ -f ".git" ]; then
+    # .git is a file (not directory) in worktrees
+    IS_WORKTREE=true
+  fi
+
   # Determine ruff command (venv or global)
   RUFF=""
   if [ -f "apps/backend/.venv/bin/ruff" ]; then
@@ -70,49 +145,91 @@ if git diff --cached --name-only | grep -q "^apps/backend/.*\.py$"; then
   fi
 
   if [ -n "$RUFF" ]; then
-    # Run ruff linting (auto-fix)
-    echo "Running ruff lint..."
-    $RUFF check apps/backend/ --fix
-    if [ $? -ne 0 ]; then
-      echo "Ruff lint failed. Please fix Python linting errors before committing."
-      exit 1
+    # Get only staged Python files in apps/backend (process only what's being committed)
+    STAGED_PY_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep "^apps/backend/.*\.py$" || true)
+
+    if [ -n "$STAGED_PY_FILES" ]; then
+      # Run ruff linting (auto-fix) only on staged files
+      echo "Running ruff lint on staged files..."
+      echo "$STAGED_PY_FILES" | xargs $RUFF check --fix
+      if [ $? -ne 0 ]; then
+        echo "Ruff lint failed. Please fix Python linting errors before committing."
+        exit 1
+      fi
+
+      # Run ruff format (auto-fix) only on staged files
+      echo "Running ruff format on staged files..."
+      echo "$STAGED_PY_FILES" | xargs $RUFF format
+
+      # Re-stage only the files that were originally staged (in case ruff modified them)
+      echo "$STAGED_PY_FILES" | xargs git add
     fi
-
-    # Run ruff format (auto-fix)
-    echo "Running ruff format..."
-    $RUFF format apps/backend/
-
-    # Stage any files that were auto-fixed by ruff (POSIX-compliant)
-    find apps/backend -name "*.py" -type f -exec git add {} + 2>/dev/null || true
   else
-    echo "Warning: ruff not found, skipping Python linting. Install with: uv pip install ruff"
+    if [ "$IS_WORKTREE" = true ]; then
+      echo ""
+      echo "⚠️  WARNING: ruff not available in this worktree."
+      echo "   Python linting checks will be skipped."
+      echo "   This is expected for auto-claude worktrees."
+      echo "   Full validation will occur when PR is created/merged."
+      echo ""
+    else
+      echo "Warning: ruff not found, skipping Python linting. Install with: uv pip install ruff"
+    fi
   fi
 
   # Run pytest (skip slow/integration tests and Windows-incompatible tests for pre-commit speed)
+  # Run from repo root (not apps/backend) so tests that use Path.resolve() get correct CWD.
+  # PYTHONPATH includes apps/backend so imports resolve correctly.
   echo "Running Python tests..."
-  cd apps/backend
-  # Tests to skip: graphiti (external deps), merge_file_tracker/service_orchestrator/worktree/workspace (Windows path/git issues)
-  IGNORE_TESTS="--ignore=../../tests/test_graphiti.py --ignore=../../tests/test_merge_file_tracker.py --ignore=../../tests/test_service_orchestrator.py --ignore=../../tests/test_worktree.py --ignore=../../tests/test_workspace.py"
-  if [ -d ".venv" ]; then
-    # Use venv if it exists
-    if [ -f ".venv/bin/pytest" ]; then
-      PYTHONPATH=. .venv/bin/pytest ../../tests/ -v --tb=short -x -m "not slow and not integration" $IGNORE_TESTS
-    elif [ -f ".venv/Scripts/pytest.exe" ]; then
-      # Windows
-      PYTHONPATH=. .venv/Scripts/pytest.exe ../../tests/ -v --tb=short -x -m "not slow and not integration" $IGNORE_TESTS
-    else
-      PYTHONPATH=. python -m pytest ../../tests/ -v --tb=short -x -m "not slow and not integration" $IGNORE_TESTS
+  (
+    # Tests to skip: graphiti (external deps), merge_file_tracker/service_orchestrator/worktree/workspace (Windows path/git issues)
+    # Also skip tests that require optional dependencies (pydantic structured outputs)
+    # Also skip gitlab_e2e (e2e test sensitive to test-ordering env contamination, validated by CI)
+    IGNORE_TESTS="--ignore=tests/test_graphiti.py --ignore=tests/test_merge_file_tracker.py --ignore=tests/test_service_orchestrator.py --ignore=tests/test_worktree.py --ignore=tests/test_workspace.py --ignore=tests/test_finding_validation.py --ignore=tests/test_sdk_structured_output.py --ignore=tests/test_structured_outputs.py --ignore=tests/test_gitlab_e2e.py"
+    # Determine Python executable from venv
+    VENV_PYTHON=""
+    if [ -f "apps/backend/.venv/bin/python" ]; then
+      VENV_PYTHON="apps/backend/.venv/bin/python"
+    elif [ -f "apps/backend/.venv/Scripts/python.exe" ]; then
+      VENV_PYTHON="apps/backend/.venv/Scripts/python.exe"
     fi
-  else
-    PYTHONPATH=. python -m pytest ../../tests/ -v --tb=short -x -m "not slow and not integration" $IGNORE_TESTS
-  fi
-  if [ $? -ne 0 ]; then
+
+    # -k "not windows_path": skip tests using fake Windows paths that break
+    # Path.resolve() on macOS/Linux. These are validated by CI on all platforms.
+    if [ -n "$VENV_PYTHON" ]; then
+      # Check if pytest is installed in venv
+      if $VENV_PYTHON -c "import pytest" 2>/dev/null; then
+        PYTHONPATH=apps/backend $VENV_PYTHON -m pytest tests/ -v --tb=short -x -m "not slow and not integration" -k "not windows_path" $IGNORE_TESTS
+      else
+        echo "Warning: pytest not installed in venv. Installing test dependencies..."
+        $VENV_PYTHON -m pip install -q -r tests/requirements-test.txt
+        PYTHONPATH=apps/backend $VENV_PYTHON -m pytest tests/ -v --tb=short -x -m "not slow and not integration" -k "not windows_path" $IGNORE_TESTS
+      fi
+    elif [ -d "apps/backend/.venv" ]; then
+      echo "Warning: venv exists but Python not found in it, using system Python"
+      PYTHONPATH=apps/backend python -m pytest tests/ -v --tb=short -x -m "not slow and not integration" -k "not windows_path" $IGNORE_TESTS
+    elif [ "$IS_WORKTREE" = true ]; then
+      echo ""
+      echo "⚠️  WARNING: Python venv not available in this worktree."
+      echo "   Python tests will be skipped."
+      echo "   This is expected for auto-claude worktrees."
+      echo "   Full validation will occur when PR is created/merged."
+      echo ""
+      exit 77  # GNU convention for 'test skipped' (avoids pytest exit-code collision)
+    else
+      echo "Warning: No .venv found in apps/backend, using system Python"
+      PYTHONPATH=apps/backend python -m pytest tests/ -v --tb=short -x -m "not slow and not integration" -k "not windows_path" $IGNORE_TESTS
+    fi
+  )
+  PYTHON_EXIT=$?
+  if [ $PYTHON_EXIT -eq 77 ]; then
+    echo "Backend checks passed! (Python tests skipped — worktree)"
+  elif [ $PYTHON_EXIT -ne 0 ]; then
     echo "Python tests failed. Please fix failing tests before committing."
     exit 1
+  else
+    echo "Backend checks passed!"
   fi
-  cd ../..
-  
-  echo "Backend checks passed!"
 fi
 
 # =============================================================================
@@ -122,37 +239,86 @@ fi
 # Check if there are staged files in apps/frontend
 if git diff --cached --name-only | grep -q "^apps/frontend/"; then
   echo "Frontend changes detected, running frontend checks..."
-  cd apps/frontend
-  
-  # Run lint-staged (handles staged .ts/.tsx files)
-  npm exec lint-staged
-  
-  # Run TypeScript type check
-  echo "Running type check..."
-  npm run typecheck
-  if [ $? -ne 0 ]; then
-    echo "Type check failed. Please fix TypeScript errors before committing."
-    exit 1
+
+  # Detect if we're in a worktree and check if dependencies are available
+  IS_WORKTREE=false
+  DEPS_AVAILABLE=true
+
+  if [ -f ".git" ]; then
+    # .git is a file (not directory) in worktrees
+    IS_WORKTREE=true
+    echo "Detected git worktree environment"
   fi
-  
-  # Run linting
-  echo "Running lint..."
-  npm run lint
-  if [ $? -ne 0 ]; then
-    echo "Lint failed. Run 'npm run lint:fix' to auto-fix issues."
-    exit 1
+
+  # Check if node_modules has actual dependencies by looking for a known package
+  # @lydell/node-pty is required for terminal code and is a common source of TypeScript errors
+  # It may be in root node_modules (hoisted) or apps/frontend/node_modules
+  # Note: -d follows symlinks automatically, so this works for both real dirs and symlinks
+  # We check for the full package path (@lydell/node-pty) rather than just the namespace
+  # for precise detection - ensures the actual dependency is installed, not just any @lydell package
+  if [ ! -d "node_modules/@lydell/node-pty" ] && [ ! -d "apps/frontend/node_modules/@lydell/node-pty" ]; then
+    DEPS_AVAILABLE=false
   fi
-  
-  # Check for vulnerabilities (only high severity)
-  echo "Checking for vulnerabilities..."
-  npm audit --audit-level=high
-  if [ $? -ne 0 ]; then
-    echo "High severity vulnerabilities found. Run 'npm audit fix' to resolve."
-    exit 1
+
+  if [ "$DEPS_AVAILABLE" = false ]; then
+    if [ "$IS_WORKTREE" = true ]; then
+      # In worktree without dependencies - warn but allow commit
+      echo ""
+      echo "⚠️  WARNING: node_modules not available in this worktree."
+      echo "   TypeScript and lint checks will be skipped."
+      echo "   This is expected for auto-claude worktrees."
+      echo "   Full validation will occur when PR is created/merged."
+      echo ""
+    else
+      # Main repo without dependencies - this is an error
+      echo "Error: node_modules not found. Run 'npm install' first."
+      exit 1
+    fi
+  else
+    # Dependencies available - run full frontend checks
+    # Use subshell to isolate directory changes and prevent worktree corruption
+    (
+      cd apps/frontend
+
+      # Run lint-staged (handles staged .ts/.tsx files)
+      npm exec lint-staged
+      if [ $? -ne 0 ]; then
+        echo "lint-staged failed. Please fix linting errors before committing."
+        exit 1
+      fi
+
+      # Run TypeScript type check
+      echo "Running type check..."
+      npm run typecheck
+      if [ $? -ne 0 ]; then
+        echo "Type check failed. Please fix TypeScript errors before committing."
+        exit 1
+      fi
+
+      # Run linting
+      echo "Running lint..."
+      npm run lint
+      if [ $? -ne 0 ]; then
+        echo "Lint failed. Run 'npm run lint:fix' to auto-fix issues."
+        exit 1
+      fi
+
+      # Check for vulnerabilities (only critical severity)
+      # Note: Using critical level because electron-builder has a known high-severity
+      # tar vulnerability (CVE-2026-23745) that cannot be fixed until electron-builder
+      # releases an update with tar@7.x support. This is a build dependency, not runtime.
+      echo "Checking for vulnerabilities..."
+      npm audit --audit-level=critical
+      if [ $? -ne 0 ]; then
+        echo "Critical severity vulnerabilities found. Run 'npm audit fix' to resolve."
+        exit 1
+      fi
+    )
+    if [ $? -ne 0 ]; then
+      exit 1
+    fi
+    echo "Frontend checks passed!"
   fi
-  
-  cd ../..
-  echo "Frontend checks passed!"
 fi
 
 echo "All pre-commit checks passed!"

.pre-commit-config.yaml

@@ -1,29 +1,95 @@
 repos:
   # Version sync - propagate root package.json version to all files
+  # NOTE: Skip in worktrees - version sync modifies root files which don't exist in worktree
   - repo: local
     hooks:
       - id: version-sync
         name: Version Sync
-        entry: bash -c '
-          VERSION=$(node -p "require(\"./package.json\").version");
-          if [ -n "$VERSION" ]; then
-            # Sync to apps/frontend/package.json
-            node -e "const fs=require(\"fs\");const p=require(\"./apps/frontend/package.json\");if(p.version!==\"$VERSION\"){p.version=\"$VERSION\";fs.writeFileSync(\"./apps/frontend/package.json\",JSON.stringify(p,null,2)+\"\n\");}";
-            # Sync to apps/backend/__init__.py
-            sed -i.bak "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" apps/backend/__init__.py && rm -f apps/backend/__init__.py.bak;
-            # Sync to README.md
-            sed -i.bak "s/version-[0-9]*\.[0-9]*\.[0-9]*-blue/version-$VERSION-blue/g" README.md;
-            sed -i.bak "s/Auto-Claude-[0-9]*\.[0-9]*\.[0-9]*/Auto-Claude-$VERSION/g" README.md && rm -f README.md.bak;
-            git add apps/frontend/package.json apps/backend/__init__.py README.md 2>/dev/null || true;
-          fi
-        '
+        entry: bash
+        args:
+          - -c
+          - |
+            # Skip in worktrees - .git is a file pointing to main repo, not a directory
+            # Version sync modifies root-level files that may not exist in worktree context
+            if [ -f ".git" ]; then
+              echo "Skipping version-sync in worktree (root files not accessible)"
+              exit 0
+            fi
+            VERSION=$(node -p "require('./package.json').version")
+            if [ -n "$VERSION" ]; then
+
+              # Sync to apps/frontend/package.json
+              node -e "
+                const fs = require('fs');
+                const p = require('./apps/frontend/package.json');
+                const v = process.argv[1];
+                if (p.version !== v) {
+                  p.version = v;
+                  fs.writeFileSync('./apps/frontend/package.json', JSON.stringify(p, null, 2) + '\n');
+                }
+              " "$VERSION"
+
+              # Sync to apps/backend/__init__.py
+              sed -i.bak "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" apps/backend/__init__.py && rm -f apps/backend/__init__.py.bak
+
+              # Sync to README.md - section-aware updates (stable vs beta)
+              ESCAPED_VERSION=$(echo "$VERSION" | sed 's/-/--/g')
+
+              # Detect if this is a prerelease (contains - after base version)
+              if echo "$VERSION" | grep -q '-'; then
+                # PRERELEASE: Update only beta sections
+                echo "  Detected PRERELEASE version: $VERSION"
+
+                # Update beta version badge (orange)
+                sed -i.bak "s/beta-[0-9]*\.[0-9]*\.[0-9]*\(--[a-z]*\.[0-9]*\)*-orange/beta-$ESCAPED_VERSION-orange/g" README.md
+
+                # Update beta version badge link
+                sed -i.bak '/<!-- BETA_VERSION_BADGE -->/,/<!-- BETA_VERSION_BADGE_END -->/s|releases/tag/v[0-9.a-z-]*)|releases/tag/v'"$VERSION"')|g' README.md
+
+                # Update beta download links (within BETA_DOWNLOADS section only)
+                for SUFFIX in "win32-x64.exe" "darwin-arm64.dmg" "darwin-x64.dmg" "linux-x86_64.AppImage" "linux-amd64.deb" "linux-x86_64.flatpak"; do
+                  sed -i.bak '/<!-- BETA_DOWNLOADS -->/,/<!-- BETA_DOWNLOADS_END -->/{s|Auto-Claude-[0-9.a-z-]*-'"$SUFFIX"'](https://github.com/AndyMik90/Auto-Claude/releases/download/v[^/]*/Auto-Claude-[^)]*-'"$SUFFIX"')|Auto-Claude-'"$VERSION"'-'"$SUFFIX"'](https://github.com/AndyMik90/Auto-Claude/releases/download/v'"$VERSION"'/Auto-Claude-'"$VERSION"'-'"$SUFFIX"')|g}' README.md
+                done
+              else
+                # STABLE: Update stable sections and top badge
+                echo "  Detected STABLE version: $VERSION"
+
+                # Update top version badge (blue)
+                sed -i.bak '/<!-- TOP_VERSION_BADGE -->/,/<!-- TOP_VERSION_BADGE_END -->/s/version-[0-9]*\.[0-9]*\.[0-9]*\(--[a-z]*\.[0-9]*\)*-blue/version-'"$ESCAPED_VERSION"'-blue/g' README.md
+                sed -i.bak '/<!-- TOP_VERSION_BADGE -->/,/<!-- TOP_VERSION_BADGE_END -->/s|releases/tag/v[0-9.a-z-]*)|releases/tag/v'"$VERSION"')|g' README.md
+
+                # Update stable version badge (blue)
+                sed -i.bak '/<!-- STABLE_VERSION_BADGE -->/,/<!-- STABLE_VERSION_BADGE_END -->/s/stable-[0-9]*\.[0-9]*\.[0-9]*\(--[a-z]*\.[0-9]*\)*-blue/stable-'"$ESCAPED_VERSION"'-blue/g' README.md
+                sed -i.bak '/<!-- STABLE_VERSION_BADGE -->/,/<!-- STABLE_VERSION_BADGE_END -->/s|releases/tag/v[0-9.a-z-]*)|releases/tag/v'"$VERSION"')|g' README.md
+
+                # Update stable download links (within STABLE_DOWNLOADS section only)
+                for SUFFIX in "win32-x64.exe" "darwin-arm64.dmg" "darwin-x64.dmg" "linux-x86_64.AppImage" "linux-amd64.deb"; do
+                  sed -i.bak '/<!-- STABLE_DOWNLOADS -->/,/<!-- STABLE_DOWNLOADS_END -->/{s|Auto-Claude-[0-9.a-z-]*-'"$SUFFIX"'](https://github.com/AndyMik90/Auto-Claude/releases/download/v[^/]*/Auto-Claude-[^)]*-'"$SUFFIX"')|Auto-Claude-'"$VERSION"'-'"$SUFFIX"'](https://github.com/AndyMik90/Auto-Claude/releases/download/v'"$VERSION"'/Auto-Claude-'"$VERSION"'-'"$SUFFIX"')|g}' README.md
+                done
+              fi
+              rm -f README.md.bak
+
+              # Stage changes
+              git add apps/frontend/package.json apps/backend/__init__.py README.md 2>/dev/null || true
+            fi
         language: system
         files: ^package\.json$
         pass_filenames: false
 
+  # Python encoding check - prevent regression of UTF-8 encoding fixes (PR #782)
+  - repo: local
+    hooks:
+      - id: check-file-encoding
+        name: Check file encoding parameters
+        entry: python scripts/check_encoding.py
+        language: system
+        types: [python]
+        files: ^apps/backend/
+        description: Ensures all file operations specify encoding="utf-8"
+
   # Python linting (apps/backend/)
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.3
+    rev: v0.14.10
     hooks:
       - id: ruff
         args: [--fix]
@@ -31,37 +97,77 @@ repos:
       - id: ruff-format
         files: ^apps/backend/
 
-  # Python tests (apps/backend/) - skip slow/integration tests for pre-commit speed
+  # Python tests (apps/backend/) - run full test suite from project root
   # Tests to skip: graphiti (external deps), merge_file_tracker/service_orchestrator/worktree/workspace (Windows path/git issues)
   - repo: local
     hooks:
       - id: pytest
         name: Python Tests
-        entry: bash -c 'cd apps/backend && PYTHONPATH=. python -m pytest ../../tests/ -v --tb=short -x -m "not slow and not integration" --ignore=../../tests/test_graphiti.py --ignore=../../tests/test_merge_file_tracker.py --ignore=../../tests/test_service_orchestrator.py --ignore=../../tests/test_worktree.py --ignore=../../tests/test_workspace.py'
+        entry: bash
+        args:
+          - -c
+          - |
+            # Run pytest directly from project root
+            if [ -f "apps/backend/.venv/bin/pytest" ]; then
+              PYTEST_CMD="apps/backend/.venv/bin/pytest"
+            elif [ -f "apps/backend/.venv/Scripts/pytest.exe" ]; then
+              PYTEST_CMD="apps/backend/.venv/Scripts/pytest.exe"
+            else
+              PYTEST_CMD="python -m pytest"
+            fi
+            $PYTEST_CMD tests/ \
+              -v \
+              --tb=short \
+              -x \
+              -m "not slow and not integration" \
+              --ignore=tests/test_graphiti.py \
+              --ignore=tests/test_merge_file_tracker.py \
+              --ignore=tests/test_service_orchestrator.py \
+              --ignore=tests/test_worktree.py \
+              --ignore=tests/test_workspace.py
         language: system
         files: ^(apps/backend/.*\.py$|tests/.*\.py$)
         pass_filenames: false
 
-  # Frontend linting (apps/frontend/)
+  # Frontend linting (apps/frontend/) - Biome is 15-25x faster than ESLint
+  # NOTE: These hooks check for worktree context to avoid npm/node_modules issues
   - repo: local
     hooks:
-      - id: eslint
-        name: ESLint
-        entry: bash -c 'cd apps/frontend && npm run lint'
+      - id: biome
+        name: Biome (lint + format)
+        entry: bash
+        args:
+          - -c
+          - |
+            # Skip in worktrees if node_modules doesn't exist (Biome not installed)
+            if [ -f ".git" ] && [ ! -d "apps/frontend/node_modules" ]; then
+              echo "Skipping Biome in worktree (node_modules not found)"
+              exit 0
+            fi
+            cd apps/frontend && npx biome check --write --no-errors-on-unmatched .
         language: system
-        files: ^apps/frontend/.*\.(ts|tsx|js|jsx)$
+        files: ^apps/frontend/.*\.(ts|tsx|js|jsx|json)$
         pass_filenames: false
 
       - id: typecheck
         name: TypeScript Check
-        entry: bash -c 'cd apps/frontend && npm run typecheck'
+        entry: bash
+        args:
+          - -c
+          - |
+            # Skip in worktrees if node_modules doesn't exist (dependencies not installed)
+            if [ -f ".git" ] && [ ! -d "apps/frontend/node_modules" ]; then
+              echo "Skipping TypeScript check in worktree (node_modules not found)"
+              exit 0
+            fi
+            cd apps/frontend && npm run typecheck
         language: system
         files: ^apps/frontend/.*\.(ts|tsx)$
         pass_filenames: false
 
   # General checks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

2025-02-16-github-issues-documentation-design.md

@@ -0,0 +1,240 @@
+# GitHub Issues Documentation Design
+
+**Date:** 2025-02-16
+**Status:** Approved
+**Author:** Claude (Superpowers Brainstorming)
+
+## Overview
+
+Create comprehensive, user-friendly documentation for Auto Claude's GitHub Issues integration. The documentation will serve a mixed audience (new and existing users) with progressive depth across three documents.
+
+## Target Audience
+
+**Mixed audience with progressive depth:**
+- **End users** - New to Auto Claude, want to understand features and get started quickly
+- **Technical users** - Existing users wanting to optimize AI configuration and manage costs
+- **Pro users/developers** - Want to customize prompts, context injection, and extend the system
+
+## Document Structure
+
+### New Directory: `guides/github-issues/`
+
+```
+guides/
+└── github-issues/
+    ├── README.md                                    # Navigation index
+    ├── github-issues-user-guide.md                  # Document 1
+    ├── github-issues-advanced-ai-configuration.md   # Document 2
+    └── github-issues-customization-guide.md         # Document 3
+```
+
+### Document 1: User Guide
+
+**Audience:** End users (non-technical)
+**Focus:** Features, workflows, getting started
+
+**Sections:**
+1. **Overview** - What is GitHub Issues integration? Why use it?
+2. **Quick Start (5 minutes)** - Get your first issue investigated end-to-end
+3. **Key Features** - Bullet points of main capabilities
+4. **Integration Workflow** - Import → Investigate → Create Task → Implement (EMPHASIS)
+5. **Setup & Configuration** - GitHub authentication, connecting repos
+6. **Using the Features**
+   - Importing & browsing issues
+   - Running AI investigations
+   - Creating tasks from results
+   - Posting findings back to GitHub
+7. **FAQ** - Common questions
+
+**Tone:** Friendly, encouraging, approachable. Plain English with minimal jargon.
+
+### Document 2: Advanced AI Configuration
+
+**Audience:** Technical users, team leads
+**Focus:** AI tuning, performance, cost management
+
+**Sections:**
+1. **Overview** - Who this guide is for
+2. **Opus 4.6 Features** - Fast Mode, 128K tokens, adaptive thinking
+3. **The 4 Specialist Agents** - Deep dive into each agent's role
+4. **Pricing & Cost Management** - Token limits, cost optimization strategies
+5. **Advanced Configuration** - Per-specialist settings, performance tuning
+6. **Technical Architecture** - How investigation works under the hood
+
+**Tone:** Professional, technical but clear. Explains technical concepts in context.
+
+### Document 3: Customization Guide
+
+**Audience:** Developers, pro users extending Auto Claude
+**Focus:** System customization, prompts, context injection
+
+**Sections:**
+1. **Overview** - Who this is for (developers extending Auto Claude)
+2. **Prompt System Architecture** - How agent prompts are structured
+3. **Context Injection System** - How context is built and passed to agents
+4. **Customizing Agent Prompts** - Modifying XML prompt files
+   - Finding the prompt files
+   - Prompt structure and variables
+   - Creating custom investigation specialists
+5. **Context Configuration** - Customizing what data is included
+   - File selection patterns
+   - Context window management
+   - Repository context settings
+6. **Adding Custom Specialists** - Creating new investigation agents
+7. **Extending the Integration** - Hooks, custom providers
+8. **Examples & Recipes** - Common customizations
+
+**Tone:** Developer-to-developer, technical, code-heavy, minimal hand-holding.
+
+## Content Approach
+
+### Progressive Disclosure
+- Each document builds on the previous one
+- Clear navigation links between documents
+- Users can enter at their appropriate level
+
+### Writing Style Guidelines
+
+| Document | Tone | Language | Example Style |
+|----------|------|----------|---------------|
+| User Guide | Friendly, encouraging | Plain English | "Think of AI investigation as having a senior developer analyze the issue for you" |
+| Advanced Config | Professional, technical | Terms explained in context | "Fast Mode uses optimized token generation to reduce investigation time by 2.5x" |
+| Customization | Developer-to-developer | Technical, code-heavy | "Modify the `<system_context>` variable in `prompts/github/root_cause.xml`" |
+
+### Code & Configuration Examples
+- **Doc 1:** Simple copy-paste examples, UI navigation
+- **Doc 2:** Configuration snippets, environment variables
+- **Doc 3:** Full XML/Python examples, file paths, code blocks
+
+## Visual Elements
+
+### Screenshots (Hybrid Approach)
+
+**User Guide:**
+1. GitHub Issues main UI (issue list, filters, actions)
+2. Issue detail view (comments, labels, "Investigate" button)
+3. Investigation in progress (4 parallel specialists)
+4. Investigation results (completed report)
+5. Settings screen (GitHub auth, repo connection, Fast Mode toggle)
+
+**Advanced AI Config:**
+1. Settings → AI Investigation panel (configurable options)
+2. Token usage display (cost visibility)
+3. Investigation pipeline flowchart (issue → 4 specialists → report)
+
+**Customization Guide:**
+1. Directory structure diagram (prompt file locations)
+2. Annotated XML prompt file (variables and structure)
+3. Context injection flow diagram
+4. Code snippets throughout
+
+### Diagram Style
+- Clean, simple flowcharts
+- Consistent color scheme: Blue (user actions), Green (AI agents), Orange (data flow)
+- Minimal text, focus on flow and relationships
+
+## Navigation & Cross-References
+
+### Linking Strategy
+
+**User Guide → Deeper:**
+- "For detailed configuration, see [Advanced AI Configuration]"
+- "Learn how the 4 specialists work in [Advanced AI Configuration]"
+- "Want to customize agent behavior? See [Customization Guide]"
+
+**Advanced AI Config → Both Directions:**
+- "New to GitHub Issues? Start with the [User Guide]"
+- "Want to modify agent prompts? See [Customization Guide]"
+
+**Customization Guide → Reference:**
+- "Assumes familiarity with concepts from [User Guide] and [Advanced AI Config]"
+
+### Navigation Aids
+- Table of Contents at the top of each document
+- "In this section" callouts at the start of major sections
+- "Next steps" boxes at the end of each workflow section
+
+### External References
+- `guides/opus-4.6-features.md` - Opus 4.6 details (don't duplicate)
+- `ARCHITECTURE.md` - System architecture
+- GitHub CLI docs - Authentication setup
+
+## Key Emphasis
+
+**Integration Workflow** is the primary focus across all documents:
+
+> **Import Issues** → **AI Investigation** → **Create Task** → **Implement** → **Merge**
+
+This pipeline demonstrates the core value of Auto Claude - connecting GitHub issues to autonomous development.
+
+## File Organization
+
+### Naming Convention
+- Lowercase with hyphens (matches existing documentation style)
+- Descriptive names indicating audience and content
+- Keep under 80 characters for GitHub rendering
+
+### README.md (Index Page)
+
+```markdown
+# GitHub Issues Documentation
+
+Choose the guide that matches your needs:
+
+📖 **[User Guide](github-issues-user-guide.md)** - Get started with GitHub Issues integration
+  For: All users | Focus: Using the features
+
+⚙️ **[Advanced AI Configuration](github-issues-advanced-ai-configuration.md)** - Optimize AI investigations
+  For: Technical users | Focus: Performance, costs, Opus 4.6
+
+🔧 **[Customization Guide](github-issues-customization-guide.md)** - Extend and customize the system
+  For: Developers | Focus: Prompts, context, customization
+```
+
+## Markdown Format Guidelines
+
+- Standard GitHub-flavored markdown
+- H1 for title, H2 for main sections, H3 for subsections
+- Code blocks with language specification (`xml`, `python`, `bash`)
+- Callout boxes using `> **Note:**` format
+- Internal links use relative paths
+- Front matter with title and description metadata
+
+## Implementation Notes
+
+### Content Sources
+- `apps/frontend/src/renderer/components/github-issues/` - UI components
+- `apps/frontend/src/main/ipc-handlers/github/` - IPC handlers
+- `apps/backend/runners/github/` - Backend services
+- `guides/opus-4.6-features.md` - Reference for Opus 4.6 details
+- Existing code comments and docstrings
+
+### Screenshots to Capture
+- Need to run the application in development mode (`npm run dev`)
+- Capture each UI state listed in Visual Elements section
+- Save to `guides/github-issues/images/` with descriptive names
+
+### Diagram Creation
+- Use Mermaid syntax for flowcharts (if supported by docs build)
+- Alternatively, describe for manual creation with diagram tools
+
+## Success Criteria
+
+1. ✅ All three documents created in `guides/github-issues/`
+2. ✅ README.md index page created
+3. ✅ Progressive structure allows users to enter at appropriate level
+4. ✅ Integration workflow is clear and emphasized
+5. ✅ Screenshots included for key UI states
+6. ✅ Cross-references enable navigation between documents
+7. ✅ Writing style matches target audience for each document
+8. ✅ Content is accurate based on actual codebase features
+
+## Next Steps
+
+1. Create implementation plan using writing-plans skill
+2. Set up directory structure
+3. Draft content for each document
+4. Capture screenshots
+5. Create diagrams
+6. Review and refine
+7. Commit to repository

CLA.md

@@ -0,0 +1,76 @@
+# Auto Claude Individual Contributor License Agreement
+
+Thank you for your interest in contributing to Auto Claude. This Contributor License Agreement ("Agreement") documents the rights granted by contributors to the Project.
+
+By signing this Agreement, you accept and agree to the following terms and conditions for your present and future Contributions submitted to the Project.
+
+## 1. Definitions
+
+**"You" (or "Your")** means the individual who submits a Contribution to the Project.
+
+**"Contribution"** means any original work of authorship, including any modifications or additions to an existing work, that is intentionally submitted by You to the Project for inclusion in, or documentation of, the Project. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Project or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Project for the purpose of discussing and improving the Project.
+
+**"Project"** means Auto Claude, a multi-agent autonomous coding framework, currently available at https://github.com/AndyMik90/Auto-Claude.
+
+**"Project Owner"** means Andre Mikalsen and any designated successors or assignees.
+
+## 2. Grant of Copyright License
+
+Subject to the terms and conditions of this Agreement, You hereby grant to the Project Owner and to recipients of software distributed by the Project Owner a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to:
+
+- Reproduce, prepare derivative works of, publicly display, publicly perform, and distribute Your Contributions and such derivative works
+- Sublicense any or all of the foregoing rights to third parties
+
+## 3. Grant of Patent License
+
+Subject to the terms and conditions of this Agreement, You hereby grant to the Project Owner and to recipients of software distributed by the Project Owner a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer Your Contributions, where such license applies only to those patent claims licensable by You that are necessarily infringed by Your Contribution(s) alone or by combination of Your Contribution(s) with the Project to which such Contribution(s) was submitted.
+
+## 4. Future Licensing Flexibility
+
+You understand and agree that the Project Owner may, in the future, license the Project, including Your Contributions, under additional licenses beyond the current GNU Affero General Public License version 3.0 (AGPL-3.0). Such additional licenses may include commercial or enterprise licenses.
+
+This provision ensures the Project has proper licensing flexibility should such licensing options be introduced in the future. The open source version of the Project will continue to be available under AGPL-3.0.
+
+## 5. Representations
+
+You represent that:
+
+(a) You are legally entitled to grant the above licenses. If your employer(s) has rights to intellectual property that you create that includes your Contributions, you represent that you have received permission to make Contributions on behalf of that employer, or that your employer has waived such rights for your Contributions to the Project.
+
+(b) Each of Your Contributions is Your original creation. You represent that Your Contribution submissions include complete details of any third-party license or other restriction (including, but not limited to, related patents and trademarks) of which you are personally aware and which are associated with any part of Your Contributions.
+
+(c) Your Contribution does not violate any third-party rights, including but not limited to intellectual property rights, privacy rights, or contractual obligations.
+
+## 6. Support and Warranty Disclaimer
+
+You are not expected to provide support for Your Contributions, except to the extent You desire to provide support. You may provide support for free, for a fee, or not at all.
+
+UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING, YOU PROVIDE YOUR CONTRIBUTIONS ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY, OR FITNESS FOR A PARTICULAR PURPOSE.
+
+## 7. No Obligation to Use
+
+You understand that the decision to include Your Contribution in any project or source repository is entirely at the discretion of the Project Owner, and this Agreement does not guarantee that Your Contributions will be included in any product.
+
+## 8. Contributor Rights
+
+You retain full copyright ownership of Your Contributions. Nothing in this Agreement shall be interpreted to prohibit you from licensing Your Contributions under different terms to third parties or from using Your Contributions for any other purpose.
+
+## 9. Notification
+
+You agree to notify the Project Owner of any facts or circumstances of which you become aware that would make these representations inaccurate in any respect.
+
+---
+
+## How to Sign
+
+To sign this CLA, comment on your Pull Request with:
+
+```
+I have read the CLA Document and I hereby sign the CLA
+```
+
+Your signature will be recorded automatically.
+
+---
+
+*This CLA is based on the Apache Software Foundation Individual Contributor License Agreement v2.0.*

CLAUDE.md

@@ -1,248 +1,314 @@
 # CLAUDE.md
 
-This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+This file provides guidance to Claude Code when working with this repository.
 
-## Project Overview
+Auto Claude is an autonomous multi-agent coding framework that plans, builds, and validates software for you. It's a monorepo with a Python backend (CLI + agent logic) and an Electron/React frontend (desktop UI).
 
-Auto Claude is a multi-agent autonomous coding framework that builds software through coordinated AI agent sessions. It uses the Claude Code SDK to run agents in isolated workspaces with security controls.
+> **Deep-dive reference:** [ARCHITECTURE.md](shared_docs/ARCHITECTURE.md) | **Frontend contributing:** [apps/frontend/CONTRIBUTING.md](apps/frontend/CONTRIBUTING.md)
 
-## Commands
+## Product Overview
+
+Auto Claude is a desktop application (+ CLI) where users describe a goal and AI agents autonomously handle planning, implementation, and QA validation. All work happens in isolated git worktrees so the main branch stays safe.
+
+**Core workflow:** User creates a task → Spec creation pipeline assesses complexity and writes a specification → Planner agent breaks it into subtasks → Coder agent implements (can spawn parallel subagents) → QA reviewer validates → QA fixer resolves issues → User reviews and merges.
+
+**Main features:**
+
+- **Autonomous Tasks** — Multi-agent pipeline (planner, coder, QA) that builds features end-to-end
+- **Kanban Board** — Visual task management from planning through completion
+- **Agent Terminals** — Up to 12 parallel AI-powered terminals with task context injection
+- **Insights** — AI chat interface for exploring and understanding your codebase
+- **Roadmap** — AI-assisted feature planning with strategic roadmap generation
+- **Ideation** — Discover improvements, performance issues, and security vulnerabilities
+- **GitHub/GitLab Integration** — Import issues, AI-powered investigation, PR/MR review and creation
+- **Changelog** — Generate release notes from completed tasks
+- **Memory System** — Graphiti-based knowledge graph retains insights across sessions
+- **Isolated Workspaces** — Git worktree isolation for every build; AI-powered semantic merge
+- **Flexible Authentication** — Use a Claude Code subscription (OAuth) or API profiles with any Anthropic-compatible endpoint (e.g., Anthropic API, z.ai for GLM models)
+- **Multi-Account Swapping** — Register multiple Claude accounts; when one hits a rate limit, Auto Claude automatically switches to an available account
+- **Cross-Platform** — Native desktop app for Windows, macOS, and Linux with auto-updates
+
+## Critical Rules
+
+**Claude Agent SDK only** — All AI interactions use `claude-agent-sdk`. NEVER use `anthropic.Anthropic()` directly. Always use `create_client()` from `core.client`.
+
+**i18n required** — All frontend user-facing text MUST use `react-i18next` translation keys. Never hardcode strings in JSX/TSX. Add keys to both `en/*.json` and `fr/*.json`.
+
+**Platform abstraction** — Never use `process.platform` directly. Import from `apps/frontend/src/main/platform/` or `apps/backend/core/platform/`. CI tests all three platforms.
+
+**No time estimates** — Never provide duration predictions. Use priority-based ordering instead.
+
+**PR target** — Always target the `develop` branch for PRs to AndyMik90/Auto-Claude, NOT `main`.
+
+## Work Approach
+
+**Investigate before speculating** — Always read the actual code before proposing root causes. Spawn agents to grep and read relevant source files before forming any hypothesis. Never guess at causes without evidence from the codebase.
+
+**Spawn agents for complex tasks** — When tackling complex tasks, spawn sub-agents/agent teams immediately rather than trying to handle everything in a single context window. Never attempt to analyze large codebases or multiple features monolithically.
+
+**Minimal fixes only** — Prefer the simplest approach (e.g., prompt-only changes, single guard clause) before suggesting multi-component solutions. If the user asks for X, implement X — don't bundle additional fixes they didn't request.
+
+## Known Gotchas
+
+**Electron path resolution** — For bug fixes in the Electron app, always check path resolution differences between dev and production builds (`app.isPackaged`, `process.resourcesPath`). Paths that work in dev often break when Electron is bundled for production — verify both contexts.
+
+### Resetting PR Review State
+
+To fully clear all PR review data so reviews run fresh, delete/reset these three things in `.auto-claude/github/`:
+
+1. `rm .auto-claude/github/pr/logs_*.json` — review log files
+2. `rm .auto-claude/github/pr/review_*.json` — review result files
+3. Reset `pr/index.json` to `{"reviews": [], "last_updated": null}`
+4. Reset `bot_detection_state.json` to `{"reviewed_commits": {}}` — this is the gatekeeper; without clearing it, the bot detector skips already-seen commits
+## Project Structure
+
+```
+autonomous-coding/
+├── apps/
+│   ├── backend/                 # Python backend/CLI — ALL agent logic
+│   │   ├── core/                # client.py, auth.py, worktree.py, platform/
+│   │   ├── security/            # Command allowlisting, validators, hooks
+│   │   ├── agents/              # planner, coder, session management
+│   │   ├── qa/                  # reviewer, fixer, loop, criteria
+│   │   ├── spec/                # Spec creation pipeline
+│   │   ├── cli/                 # CLI commands (spec, build, workspace, QA)
+│   │   ├── context/             # Task context building, semantic search
+│   │   ├── runners/             # Standalone runners (spec, roadmap, insights, github)
+│   │   ├── services/            # Background services, recovery orchestration
+│   │   ├── integrations/        # graphiti/, linear, github
+│   │   ├── project/             # Project analysis, security profiles
+│   │   ├── merge/               # Intent-aware semantic merge for parallel agents
+│   │   └── prompts/             # Agent system prompts (.md)
+│   └── frontend/                # Electron desktop UI
+│       └── src/
+│           ├── main/            # Electron main process
+│           │   ├── agent/       # Agent queue, process, state, events
+│           │   ├── claude-profile/ # Multi-profile credentials, token refresh, usage
+│           │   ├── terminal/    # PTY daemon, lifecycle, Claude integration
+│           │   ├── platform/    # Cross-platform abstraction
+│           │   ├── ipc-handlers/# 40+ handler modules by domain
+│           │   ├── services/    # SDK session recovery, profile service
+│           │   └── changelog/   # Changelog generation and formatting
+│           ├── preload/         # Electron preload scripts (electronAPI bridge)
+│           ├── renderer/        # React UI
+│           │   ├── components/  # UI components (onboarding, settings, task, terminal, github, etc.)
+│           │   ├── stores/      # 24+ Zustand state stores
+│           │   ├── contexts/    # React contexts (ViewStateContext)
+│           │   ├── hooks/       # Custom hooks (useIpc, useTerminal, etc.)
+│           │   ├── styles/      # CSS / Tailwind styles
+│           │   └── App.tsx      # Root component
+│           ├── shared/          # Shared types, i18n, constants, utils
+│           │   ├── i18n/locales/# en/*.json, fr/*.json
+│           │   ├── constants/   # themes.ts, etc.
+│           │   ├── types/       # 19+ type definition files
+│           │   └── utils/       # ANSI sanitizer, shell escape, provider detection
+│           └── types/           # TypeScript type definitions
+├── guides/                      # Documentation
+├── tests/                       # Backend test suite
+└── scripts/                     # Build and utility scripts
+```
+
+## Commands Quick Reference
 
 ### Setup
-
-**Requirements:**
-- Python 3.12+ (required for backend)
-- Node.js (for frontend)
-
 ```bash
-# Install all dependencies from root
-npm run install:all
-
-# Or install separately:
-# Backend (from apps/backend/)
+npm run install:all              # Install all dependencies from root
+# Or separately:
 cd apps/backend && uv venv && uv pip install -r requirements.txt
-
-# Frontend (from apps/frontend/)
 cd apps/frontend && npm install
-
-# Set up OAuth token
-claude setup-token
-# Add to apps/backend/.env: CLAUDE_CODE_OAUTH_TOKEN=your-token
-```
-
-### Creating and Running Specs
-```bash
-cd apps/backend
-
-# Create a spec interactively
-python spec_runner.py --interactive
-
-# Create spec from task description
-python spec_runner.py --task "Add user authentication"
-
-# Force complexity level (simple/standard/complex)
-python spec_runner.py --task "Fix button" --complexity simple
-
-# Run autonomous build
-python run.py --spec 001
-
-# List all specs
-python run.py --list
-```
-
-### Workspace Management
-```bash
-cd apps/backend
-
-# Review changes in isolated worktree
-python run.py --spec 001 --review
-
-# Merge completed build into project
-python run.py --spec 001 --merge
-
-# Discard build
-python run.py --spec 001 --discard
-```
-
-### QA Validation
-```bash
-cd apps/backend
-
-# Run QA manually
-python run.py --spec 001 --qa
-
-# Check QA status
-python run.py --spec 001 --qa-status
 ```
 
 ### Testing
-```bash
-# Install test dependencies (required first time)
-cd apps/backend && uv pip install -r ../../tests/requirements-test.txt
 
-# Run all tests (use virtual environment pytest)
-apps/backend/.venv/bin/pytest tests/ -v
-
-# Run single test file
-apps/backend/.venv/bin/pytest tests/test_security.py -v
-
-# Run specific test
-apps/backend/.venv/bin/pytest tests/test_security.py::test_bash_command_validation -v
-
-# Skip slow tests
-apps/backend/.venv/bin/pytest tests/ -m "not slow"
-
-# Or from root
-npm run test:backend
-```
-
-### Spec Validation
-```bash
-python apps/backend/validate_spec.py --spec-dir apps/backend/specs/001-feature --checkpoint all
-```
+| Stack | Command | Tool |
+|-------|---------|------|
+| Backend | `apps/backend/.venv/bin/pytest tests/ -v` | pytest |
+| Frontend unit | `cd apps/frontend && npm test` | Vitest |
+| Frontend E2E | `cd apps/frontend && npm run test:e2e` | Playwright |
+| All backend | `npm run test:backend` (from root) | pytest |
 
 ### Releases
 ```bash
-# 1. Bump version on your branch (creates commit, no tag)
-node scripts/bump-version.js patch   # 2.8.0 -> 2.8.1
-node scripts/bump-version.js minor   # 2.8.0 -> 2.9.0
-node scripts/bump-version.js major   # 2.8.0 -> 3.0.0
-
-# 2. Push and create PR to main
-git push origin your-branch
-gh pr create --base main
-
-# 3. Merge PR → GitHub Actions automatically:
-#    - Creates tag
-#    - Builds all platforms
-#    - Creates release with changelog
-#    - Updates README
+node scripts/bump-version.js patch|minor|major  # Bump version
+git push && gh pr create --base main             # PR to main triggers release
 ```
 
-See [RELEASE.md](RELEASE.md) for detailed release process documentation.
+See [RELEASE.md](RELEASE.md) for full release process.
 
-## Architecture
+## Backend Development
 
-### Core Pipeline
+### Claude Agent SDK Usage
 
-**Spec Creation (spec_runner.py)** - Dynamic 3-8 phase pipeline based on task complexity:
-- SIMPLE (3 phases): Discovery → Quick Spec → Validate
-- STANDARD (6-7 phases): Discovery → Requirements → [Research] → Context → Spec → Plan → Validate
-- COMPLEX (8 phases): Full pipeline with Research and Self-Critique phases
+Client: `apps/backend/core/client.py` — `create_client()` returns a configured `ClaudeSDKClient` with security hooks, tool permissions, and MCP server integration.
 
-**Implementation (run.py → agent.py)** - Multi-session build:
-1. Planner Agent creates subtask-based implementation plan
-2. Coder Agent implements subtasks (can spawn subagents for parallel work)
-3. QA Reviewer validates acceptance criteria
-4. QA Fixer resolves issues in a loop
+Model and thinking level are user-configurable (via the Electron UI settings or CLI override). Use `phase_config.py` helpers to resolve the correct values
 
-### Key Components (apps/backend/)
-
-- **client.py** - Claude SDK client with security hooks and tool permissions
-- **security.py** + **project_analyzer.py** - Dynamic command allowlisting based on detected project stack
-- **worktree.py** - Git worktree isolation for safe feature development
-- **memory.py** - File-based session memory (primary, always-available storage)
-- **graphiti_memory.py** - Graph-based cross-session memory with semantic search
-- **graphiti_providers.py** - Multi-provider factory for Graphiti (OpenAI, Anthropic, Azure, Ollama, Google AI)
-- **graphiti_config.py** - Configuration and validation for Graphiti integration
-- **linear_updater.py** - Optional Linear integration for progress tracking
-
-### Agent Prompts (apps/backend/prompts/)
+### Agent Prompts (`apps/backend/prompts/`)
 
 | Prompt | Purpose |
 |--------|---------|
-| planner.md | Creates implementation plan with subtasks |
-| coder.md | Implements individual subtasks |
-| coder_recovery.md | Recovers from stuck/failed subtasks |
-| qa_reviewer.md | Validates acceptance criteria |
-| qa_fixer.md | Fixes QA-reported issues |
-| spec_gatherer.md | Collects user requirements |
-| spec_researcher.md | Validates external integrations |
-| spec_writer.md | Creates spec.md document |
-| spec_critic.md | Self-critique using ultrathink |
+| planner.md | Implementation plan with subtasks |
+| coder.md / coder_recovery.md | Subtask implementation / recovery |
+| qa_reviewer.md / qa_fixer.md | Acceptance validation / issue fixes |
+| spec_gatherer/researcher/writer/critic.md | Spec creation pipeline |
 | complexity_assessor.md | AI-based complexity assessment |
 
 ### Spec Directory Structure
 
-Each spec in `.auto-claude/specs/XXX-name/` contains:
-- `spec.md` - Feature specification
-- `requirements.json` - Structured user requirements
-- `context.json` - Discovered codebase context
-- `implementation_plan.json` - Subtask-based plan with status tracking
-- `qa_report.md` - QA validation results
-- `QA_FIX_REQUEST.md` - Issues to fix (when rejected)
+Each spec in `.auto-claude/specs/XXX-name/` contains: `spec.md`, `requirements.json`, `context.json`, `implementation_plan.json`, `qa_report.md`, `QA_FIX_REQUEST.md`
 
-### Branching & Worktree Strategy
+### Memory System (Graphiti)
 
-Auto Claude uses git worktrees for isolated builds. All branches stay LOCAL until user explicitly pushes:
+Graph-based semantic memory in `integrations/graphiti/`. Configured through the Electron app's onboarding/settings UI (CLI users can alternatively set `GRAPHITI_ENABLED=true` in `.env`). See [ARCHITECTURE.md](shared_docs/ARCHITECTURE.md#memory-system) for details.
 
-```
-main (user's branch)
-└── auto-claude/{spec-name}  ← spec branch (isolated worktree)
+### Opus 4.6 Features
+
+Auto Claude leverages Opus 4.6's advanced capabilities for GitHub issue investigations:
+
+- **Fast Mode:** 2.5x faster investigations (toggle in Settings > GitHub > AI Investigation)
+- **128K Output Tokens:** Root cause specialist gets max tokens for deep analysis
+- **Per-Specialist Limits:** Different token limits per investigation specialist
+- **Adaptive Thinking:** High-effort mode for thorough investigations
+
+See [guides/opus-4.6-features.md](guides/opus-4.6-features.md) for detailed documentation on Opus 4.6 features, pricing, and usage.
+
+## Frontend Development
+
+### Tech Stack
+
+React 19, TypeScript (strict), Electron 39, Zustand 5, Tailwind CSS v4, Radix UI, xterm.js 6, Vite 7, Vitest 4, Biome 2, Motion (Framer Motion)
+
+### Path Aliases (tsconfig.json)
+
+| Alias | Maps to |
+|-------|---------|
+| `@/*` | `src/renderer/*` |
+| `@shared/*` | `src/shared/*` |
+| `@preload/*` | `src/preload/*` |
+| `@features/*` | `src/renderer/features/*` |
+| `@components/*` | `src/renderer/shared/components/*` |
+| `@hooks/*` | `src/renderer/shared/hooks/*` |
+| `@lib/*` | `src/renderer/shared/lib/*` |
+
+### State Management (Zustand)
+
+All state lives in `src/renderer/stores/`. Key stores:
+
+- `project-store.ts` — Active project, project list
+- `task-store.ts` — Tasks/specs management
+- `terminal-store.ts` — Terminal sessions and state
+- `settings-store.ts` — User preferences
+- `github/issues-store.ts`, `github/pr-review-store.ts` — GitHub integration
+- `insights-store.ts`, `roadmap-store.ts`, `kanban-settings-store.ts`
+
+Main process also has stores: `src/main/project-store.ts`, `src/main/terminal-session-store.ts`
+
+### Styling
+
+- **Tailwind CSS v4** with `@tailwindcss/postcss` plugin
+- **7 color themes** (Default, Dusk, Lime, Ocean, Retro, Neo + more) defined in `src/shared/constants/themes.ts`
+- Each theme has light/dark mode variants via CSS custom properties
+- Utility: `clsx` + `tailwind-merge` via `cn()` helper
+- Component variants: `class-variance-authority` (CVA)
+
+### IPC Communication
+
+Main ↔ Renderer communication via Electron IPC:
+- **Handlers:** `src/main/ipc-handlers/` — organized by domain (github, gitlab, ideation, context, etc.)
+- **Preload:** `src/preload/` — exposes safe APIs to renderer
+- Pattern: renderer calls via `window.electronAPI.*`, main handles in IPC handler modules
+
+### Agent Management (`src/main/agent/`)
+
+The frontend manages agent lifecycle end-to-end:
+- **`agent-queue.ts`** — Queue routing, prioritization, spec number locking
+- **`agent-process.ts`** — Spawns and manages agent subprocess communication
+- **`agent-state.ts`** — Tracks running agent state and status
+- **`agent-events.ts`** — Agent lifecycle events and state transitions
+
+### Claude Profile System (`src/main/claude-profile/`)
+
+Multi-profile credential management for switching between Claude accounts:
+- **`credential-utils.ts`** — OS credential storage (Keychain/Windows Credential Manager)
+- **`token-refresh.ts`** — OAuth token lifecycle and automatic refresh
+- **`usage-monitor.ts`** — API usage tracking and rate limiting per profile
+- **`profile-scorer.ts`** — Scores profiles by usage and availability
+
+### Terminal System (`src/main/terminal/`)
+
+Full PTY-based terminal integration:
+- **`pty-daemon.ts`** / **`pty-manager.ts`** — Background PTY process management
+- **`terminal-lifecycle.ts`** — Session creation, cleanup, event handling
+- **`claude-integration-handler.ts`** — Claude SDK integration within terminals
+- Renderer: xterm.js 6 with WebGL, fit, web-links, serialize addons. Store: `terminal-store.ts`
+
+## Code Quality
+
+### Frontend
+- **Linting:** Biome (`npm run lint` / `npm run lint:fix`)
+- **Type checking:** `npm run typecheck` (strict mode)
+- **Pre-commit:** Husky + lint-staged runs Biome on staged `.ts/.tsx/.js/.jsx/.json`
+- **Testing:** Vitest + React Testing Library + jsdom
+
+### Backend
+- **Linting:** Ruff
+- **Testing:** pytest (`apps/backend/.venv/bin/pytest tests/ -v`)
+
+## i18n Guidelines
+
+All frontend UI text uses `react-i18next`. Translation files: `apps/frontend/src/shared/i18n/locales/{en,fr}/*.json`
+
+**Namespaces:** `common`, `navigation`, `settings`, `dialogs`, `tasks`, `errors`, `onboarding`, `welcome`
+
+```tsx
+import { useTranslation } from 'react-i18next';
+const { t } = useTranslation(['navigation', 'common']);
+
+<span>{t('navigation:items.githubPRs')}</span>     // CORRECT
+<span>GitHub PRs</span>                             // WRONG
+
+// With interpolation:
+<span>{t('errors:task.parseError', { error })}</span>
 ```
 
-**Key principles:**
-- ONE branch per spec (`auto-claude/{spec-name}`)
-- Parallel work uses subagents (agent decides when to spawn)
-- NO automatic pushes to GitHub - user controls when to push
-- User reviews in spec worktree (`.worktrees/{spec-name}/`)
-- Final merge: spec branch → main (after user approval)
+When adding new UI text: add keys to ALL language files, use `namespace:section.key` format.
 
-**Workflow:**
-1. Build runs in isolated worktree on spec branch
-2. Agent implements subtasks (can spawn subagents for parallel work)
-3. User tests feature in `.worktrees/{spec-name}/`
-4. User runs `--merge` to add to their project
-5. User pushes to remote when ready
+## Cross-Platform
 
-### Security Model
+Supports Windows, macOS, Linux. CI tests all three.
 
-Three-layer defense:
-1. **OS Sandbox** - Bash command isolation
-2. **Filesystem Permissions** - Operations restricted to project directory
-3. **Command Allowlist** - Dynamic allowlist from project analysis (security.py + project_analyzer.py)
+**Platform modules:** `apps/frontend/src/main/platform/` and `apps/backend/core/platform/`
 
-Security profile cached in `.auto-claude-security.json`.
+| Function | Purpose |
+|----------|---------|
+| `isWindows()` / `isMacOS()` / `isLinux()` | OS detection |
+| `getPathDelimiter()` | `;` (Win) or `:` (Unix) |
+| `findExecutable(name)` | Cross-platform executable lookup |
+| `requiresShell(command)` | `.cmd/.bat` shell detection (Win) |
 
-### Memory System
+Never hardcode paths. Use `findExecutable()` and `joinPaths()`. See [ARCHITECTURE.md](shared_docs/ARCHITECTURE.md#cross-platform-development) for extended guide.
 
-Dual-layer memory architecture:
+## E2E Testing (Electron MCP)
 
-**File-Based Memory (Primary)** - `memory.py`
-- Zero dependencies, always available
-- Human-readable files in `specs/XXX/memory/`
-- Session insights, patterns, gotchas, codebase map
+QA agents can interact with the running Electron app via Chrome DevTools Protocol:
 
-**Graphiti Memory** - `graphiti_memory.py`
-- Graph database with semantic search (LadybugDB - embedded, no Docker)
-- Cross-session context retrieval
-- Multi-provider support:
-  - LLM: OpenAI, Anthropic, Azure OpenAI, Ollama, Google AI (Gemini)
-  - Embedders: OpenAI, Voyage AI, Azure OpenAI, Ollama, Google AI
-- Configure with provider credentials in `.env.example`
+1. Start app: `npm run dev:debug` (debug mode for AI self-validation via Electron MCP)
+2. Set `ELECTRON_MCP_ENABLED=true` in `apps/backend/.env`
+3. Run QA: `python run.py --spec 001 --qa`
 
-## Project Structure
+Tools: `take_screenshot`, `click_by_text`, `fill_input`, `get_page_structure`, `send_keyboard_shortcut`, `eval`. See [ARCHITECTURE.md](shared_docs/ARCHITECTURE.md#end-to-end-testing) for full capabilities.
 
-```
-auto-claude/
-├── apps/
-│   ├── backend/           # Python backend/CLI (the framework code)
-│   └── frontend/          # Electron desktop UI
-├── guides/                # Documentation
-├── tests/                 # Test suite
-└── scripts/               # Build and utility scripts
-```
+## Running the Application
 
-**As a standalone CLI tool**:
 ```bash
-cd apps/backend
-python run.py --spec 001
-```
+# CLI only
+cd apps/backend && python run.py --spec 001
 
-**With the Electron frontend**:
-```bash
-npm start        # Build and run desktop app
-npm run dev      # Run in development mode
-```
+# Desktop app
+npm start          # Production build + run
+npm run dev        # Development mode with HMR
+npm run dev:debug  # Debug mode with verbose output
+npm run dev:mcp    # Electron MCP server for AI debugging
 
-- `.auto-claude/specs/` - Per-project data (specs, plans, QA reports) - gitignored
+# Project data: .auto-claude/specs/ (gitignored)
+```

CONTRIBUTING.md

@@ -2,19 +2,41 @@
 
 Thank you for your interest in contributing to Auto Claude! This document provides guidelines and instructions for contributing to the project.
 
+## How to Contribute
+
+| What you want to do | Where to start |
+|----------------------|----------------|
+| Bug fixes & small improvements | Open a PR directly |
+| New features / architecture changes | Start a [GitHub Discussion](https://github.com/AndyMik90/Auto-Claude/discussions) or ask in [Discord](https://discord.com/channels/1448614759996854284/1451298184612548779) first |
+| Questions & setup help | [Discord #setup-help](https://discord.com/channels/1448614759996854284/1451298184612548779) |
+
+## AI-Assisted Contributions
+
+PRs built with AI tools (Claude, Codex, Copilot, etc.) are welcome here -- given what this project does, it would be odd if they weren't.
+
+That said, we've seen AI-generated PRs that introduce regressions because the contributor didn't verify what the code actually does. To keep quality high, we ask that AI-assisted PRs include the following:
+
+- **Flag it** -- mention AI assistance in the PR description (the PR template has a section for this)
+- **State your testing level** -- untested, lightly tested, or fully tested
+- **Share context if you can** -- prompts or session logs help reviewers understand intent
+- **Confirm you understand the code** -- you should be able to describe what the PR does and how the underlying code works
+
+AI-assisted PRs go through the same review process as any other contribution. Transparency just helps reviewers know where to look more carefully.
+
 ## Table of Contents
 
+- [How to Contribute](#how-to-contribute)
+- [AI-Assisted Contributions](#ai-assisted-contributions)
+- [Contributor License Agreement (CLA)](#contributor-license-agreement-cla)
 - [Prerequisites](#prerequisites)
 - [Quick Start](#quick-start)
 - [Development Setup](#development-setup)
-  - [Python Backend](#python-backend)
-  - [Electron Frontend](#electron-frontend)
-- [Running from Source](#running-from-source)
 - [Pre-commit Hooks](#pre-commit-hooks)
 - [Code Style](#code-style)
 - [Testing](#testing)
 - [Continuous Integration](#continuous-integration)
 - [Git Workflow](#git-workflow)
+  - [Working with Forks](#working-with-forks)
   - [Branch Overview](#branch-overview)
   - [Main Branches](#main-branches)
   - [Supporting Branches](#supporting-branches)
@@ -23,10 +45,30 @@ Thank you for your interest in contributing to Auto Claude! This document provid
   - [Pull Request Targets](#pull-request-targets)
   - [Release Process](#release-process-maintainers)
   - [Commit Messages](#commit-messages)
+  - [PR Hygiene](#pr-hygiene)
 - [Pull Request Process](#pull-request-process)
 - [Issue Reporting](#issue-reporting)
 - [Architecture Overview](#architecture-overview)
 
+## Contributor License Agreement (CLA)
+
+All contributors must sign our Contributor License Agreement (CLA) before contributions can be accepted.
+
+### Why We Require a CLA
+
+Auto Claude is currently licensed under AGPL-3.0. The CLA ensures the project has proper licensing flexibility should we introduce additional licensing options (such as commercial/enterprise licenses) in the future.
+
+You retain full copyright ownership of your contributions.
+
+### How to Sign
+
+1. Open a Pull Request
+2. The CLA bot will automatically comment with instructions
+3. Comment on the PR with: `I have read the CLA Document and I hereby sign the CLA`
+4. Done - you only need to sign once, and it applies to all future contributions
+
+Read the full CLA here: [CLA.md](CLA.md)
+
 ## Prerequisites
 
 Before contributing, ensure you have the following installed:
@@ -35,6 +77,7 @@ Before contributing, ensure you have the following installed:
 - **Node.js 24+** - For the Electron frontend
 - **npm 10+** - Package manager for the frontend (comes with Node.js)
 - **uv** (recommended) or **pip** - Python package manager
+- **CMake** - Required for building native dependencies (e.g., LadybugDB)
 - **Git** - Version control
 
 ### Installing Python 3.12
@@ -54,6 +97,56 @@ brew install python@3.12
 sudo apt install python3.12 python3.12-venv
 ```
 
+**Linux (Fedora):**
+```bash
+sudo dnf install python3.12
+```
+
+### Installing Node.js 24+
+
+**Windows:**
+```bash
+winget install OpenJS.NodeJS.LTS
+```
+
+**macOS:**
+```bash
+brew install node@24
+```
+
+**Linux (Ubuntu/Debian):**
+```bash
+curl -fsSL https://deb.nodesource.com/setup_24.x | sudo -E bash -
+sudo apt install -y nodejs
+```
+
+**Linux (Fedora):**
+```bash
+sudo dnf install nodejs npm
+```
+
+### Installing CMake
+
+**Windows:**
+```bash
+winget install Kitware.CMake
+```
+
+**macOS:**
+```bash
+brew install cmake
+```
+
+**Linux (Ubuntu/Debian):**
+```bash
+sudo apt install cmake
+```
+
+**Linux (Fedora):**
+```bash
+sudo dnf install cmake
+```
+
 ## Quick Start
 
 The fastest way to get started:
@@ -78,92 +171,40 @@ npm start
 The project consists of two main components:
 
 1. **Python Backend** (`apps/backend/`) - The core autonomous coding framework
-2. **Electron Frontend** (`apps/frontend/`) - Optional desktop UI
+2. **Electron Frontend** (`apps/frontend/`) - Desktop UI
 
-### Python Backend
-
-The recommended way is to use `npm run install:backend`, but you can also set up manually:
+From the repository root, two commands handle everything:
 
 ```bash
-# Navigate to the backend directory
-cd apps/backend
+# Install all dependencies (Python backend + Electron frontend)
+npm run install:all
 
-# Create virtual environment
-# Windows:
-py -3.12 -m venv .venv
-.venv\Scripts\activate
-
-# macOS/Linux:
-python3.12 -m venv .venv
-source .venv/bin/activate
-
-# Install dependencies
-pip install -r requirements.txt
-
-# Install test dependencies
-pip install -r ../../tests/requirements-test.txt
-
-# Set up environment
-cp .env.example .env
-# Edit .env and add your CLAUDE_CODE_OAUTH_TOKEN (get it via: claude setup-token)
-```
-
-### Electron Frontend
-
-```bash
-# Navigate to the frontend directory
-cd apps/frontend
-
-# Install dependencies
-npm install
-
-# Start development server
+# Start development mode (hot reload)
 npm run dev
-
-# Build for production
-npm run build
-
-# Package for distribution
-npm run package
 ```
 
-## Running from Source
-
-If you want to run Auto Claude from source (for development or testing unreleased features), follow these steps:
-
-### Step 1: Clone and Set Up
+`npm run install:all` automatically:
+- Detects Python 3.12+ on your system
+- Creates a virtual environment (`apps/backend/.venv`)
+- Installs backend runtime and test dependencies
+- Copies `.env.example` to `.env` (if not already present)
+- Installs frontend npm dependencies
 
+After install, configure your credentials in `apps/backend/.env`:
 ```bash
-git clone https://github.com/AndyMik90/Auto-Claude.git
-cd Auto-Claude/apps/backend
+# Get your Claude Code OAuth token
+claude setup-token
 
-# Using uv (recommended)
-uv venv && uv pip install -r requirements.txt
-
-# Or using standard Python
-python3 -m venv .venv
-source .venv/bin/activate  # On Windows: .venv\Scripts\activate
-pip install -r requirements.txt
-
-# Set up environment
-cd apps/backend
-cp .env.example .env
-# Edit .env and add your CLAUDE_CODE_OAUTH_TOKEN (get it via: claude setup-token)
+# Then edit apps/backend/.env with your token and any other provider keys
 ```
 
-### Step 2: Run the Desktop UI
+### Other Useful Commands
 
 ```bash
-cd ../frontend
-
-# Install dependencies
-npm install
-
-# Development mode (hot reload)
-npm run dev
-
-# Or production build
-npm run build && npm run start
+npm start              # Build and run production
+npm run build          # Build frontend for production
+npm run package        # Package for distribution
+npm run test:backend   # Run Python tests
 ```
 
 <details>
@@ -285,6 +326,64 @@ export default function(props) {
 - End files with a newline
 - Keep line length under 100 characters when practical
 
+### File Encoding (Python)
+
+**Always specify `encoding="utf-8"` for text file operations** to ensure Windows compatibility.
+
+Windows Python defaults to `cp1252` encoding instead of UTF-8, causing errors with:
+- Emoji (🚀, ✅, ❌)
+- International characters (ñ, é, 中文, العربية)
+- Special symbols (™, ©, ®)
+
+**DO:**
+
+```python
+# Reading files
+with open(path, encoding="utf-8") as f:
+    content = f.read()
+
+# Writing files
+with open(path, "w", encoding="utf-8") as f:
+    f.write(content)
+
+# Path methods
+from pathlib import Path
+content = Path(file).read_text(encoding="utf-8")
+Path(file).write_text(content, encoding="utf-8")
+
+# JSON files - reading
+import json
+with open(path, encoding="utf-8") as f:
+    data = json.load(f)
+
+# JSON files - writing
+with open(path, "w", encoding="utf-8") as f:
+    json.dump(data, f, ensure_ascii=False, indent=2)
+```
+
+**DON'T:**
+
+```python
+# Wrong - platform-dependent encoding
+with open(path) as f:
+    content = f.read()
+
+# Wrong - Path methods without encoding
+content = Path(file).read_text()
+
+# Wrong - encoding on json.dump (not open!)
+json.dump(data, f, encoding="utf-8")  # ERROR
+```
+
+**Binary files - NO encoding:**
+
+```python
+with open(path, "rb") as f:  # Correct
+    data = f.read()
+```
+
+Our pre-commit hooks automatically check for missing encoding parameters. See [PR #782](https://github.com/AndyMik90/Auto-Claude/pull/782) for the comprehensive encoding fix and [guides/windows-development.md](guides/windows-development.md) for Windows-specific development guidance.
+
 ## Testing
 
 ### Python Tests
@@ -357,7 +456,6 @@ All pull requests and pushes to `main` trigger automated CI checks via GitHub Ac
 |----------|---------|----------------|
 | **CI** | Push to `main`, PRs | Python tests (3.11 & 3.12), Frontend tests |
 | **Lint** | Push to `main`, PRs | Ruff (Python), ESLint + TypeScript (Frontend) |
-| **Test on Tag** | Version tags (`v*`) | Full test suite before release |
 
 ### PR Requirements
 
@@ -388,6 +486,72 @@ npm run typecheck
 
 We use a **Git Flow** branching strategy to manage releases and parallel development.
 
+### Working with Forks
+
+When contributing to Auto Claude, you'll typically fork the repository first. Proper fork configuration is essential to avoid sync issues.
+
+#### Initial Fork Setup
+
+```bash
+# 1. Fork on GitHub (click the Fork button on the repo page)
+
+# 2. Clone YOUR fork (not the original repo)
+git clone https://github.com/YOUR-USERNAME/Auto-Claude.git
+cd Auto-Claude
+
+# 3. Verify your remotes point to YOUR fork
+git remote -v
+# Should show:
+# origin  https://github.com/YOUR-USERNAME/Auto-Claude.git (fetch)
+# origin  https://github.com/YOUR-USERNAME/Auto-Claude.git (push)
+
+# 4. Add upstream remote to sync with the original repo
+git remote add upstream https://github.com/AndyMik90/Auto-Claude.git
+```
+
+#### Keeping Your Fork Updated
+
+```bash
+# Fetch latest changes from upstream
+git fetch upstream
+
+# Sync your develop branch with upstream
+git checkout develop
+git merge upstream/develop
+git push origin develop
+```
+
+#### Converting a Fork to Standalone
+
+> ⚠️ **Common Issue:** After making a fork standalone (e.g., disconnecting from the original repo on GitHub), your local git configuration may still reference the original forked repository, causing push/pull issues.
+
+If you convert your fork to a standalone repository:
+
+```bash
+# 1. Update origin to point to your standalone repo
+git remote set-url origin https://github.com/YOUR-USERNAME/Your-Standalone-Repo.git
+
+# 2. Remove the upstream remote (no longer applicable)
+git remote remove upstream
+
+# 3. Verify your configuration
+git remote -v
+# Should only show your standalone repo as origin
+
+# 4. Update your default branch tracking if needed
+git branch --set-upstream-to=origin/main main
+git branch --set-upstream-to=origin/develop develop
+```
+
+#### Troubleshooting Fork Issues
+
+| Problem | Cause | Solution |
+|---------|-------|----------|
+| `Permission denied` on push | Origin points to upstream repo | `git remote set-url origin <your-fork-url>` |
+| `Repository not found` | Fork was deleted or made standalone | Update remote URL to current repo location |
+| Can't push to develop | Local branch tracks wrong remote | `git branch --set-upstream-to=origin/develop` |
+| Commits show wrong author | Git config not set | `git config user.email "you@example.com"` |
+
 ### Branch Overview
 
 ```
@@ -596,6 +760,41 @@ git commit -m "WIP"
 - **body**: Detailed explanation if needed (wrap at 72 chars)
 - **footer**: Reference issues, breaking changes
 
+### PR Hygiene
+
+**Rebasing:**
+- **Rebase onto develop** before opening a PR and before merge to maintain linear history
+- Use `git fetch origin && git rebase origin/develop` to sync your branch
+- Use `--force-with-lease` when force-pushing rebased branches (safer than `--force`)
+- Notify reviewers after force-pushing during active review
+- **Exception:** Never rebase after PR is approved and others have reviewed specific commits
+
+**Commit organization:**
+- **Squash fixup commits** (typos, "oops", review feedback) into their parent commits
+- **Keep logically distinct changes** as separate commits that could be reverted independently
+- Each commit should compile and pass tests independently
+- No "WIP", "fix tests", or "lint" commits in final PR - squash these
+
+**Before requesting review:**
+```bash
+# Ensure up-to-date with develop
+git fetch origin && git rebase origin/develop
+
+# Clean up commit history (squash fixups, reword messages)
+git rebase -i origin/develop
+
+# Force push with safety check
+git push --force-with-lease
+
+# Verify everything works
+npm run test:backend
+cd apps/frontend && npm test && npm run lint && npm run typecheck
+```
+
+**PR size:**
+- Keep PRs small (<400 lines changed ideally)
+- Split large features into stacked PRs if possible
+
 ## Pull Request Process
 
 1. **Fork the repository** and create your branch from `develop` (not main!)

README.md

@@ -4,24 +4,51 @@
 
 ![Auto Claude Kanban Board](.github/assets/Auto-Claude-Kanban.png)
 
-[![Version](https://img.shields.io/badge/version-2.7.1-blue?style=flat-square)](https://github.com/AndyMik90/Auto-Claude/releases/latest)
 [![License](https://img.shields.io/badge/license-AGPL--3.0-green?style=flat-square)](./agpl-3.0.txt)
 [![Discord](https://img.shields.io/badge/Discord-Join%20Community-5865F2?style=flat-square&logo=discord&logoColor=white)](https://discord.gg/KCXaPBr4Dj)
+[![YouTube](https://img.shields.io/badge/YouTube-Subscribe-FF0000?style=flat-square&logo=youtube&logoColor=white)](https://www.youtube.com/@AndreMikalsen)
 [![CI](https://img.shields.io/github/actions/workflow/status/AndyMik90/Auto-Claude/ci.yml?branch=main&style=flat-square&label=CI)](https://github.com/AndyMik90/Auto-Claude/actions)
+[![Mentioned in Awesome Claude Code](https://awesome.re/mentioned-badge-flat.svg)](https://github.com/hesreallyhim/awesome-claude-code)
 
 ---
 
 ## Download
 
-Get the latest pre-built release for your platform:
+### Stable Release
 
-| Platform | Download | Notes |
-|----------|----------|-------|
-| **Windows** | [Auto-Claude-2.7.1.exe](https://github.com/AndyMik90/Auto-Claude/releases/latest) | Installer (NSIS) |
-| **macOS (Apple Silicon)** | [Auto-Claude-2.7.1-arm64.dmg](https://github.com/AndyMik90/Auto-Claude/releases/latest) | M1/M2/M3 Macs |
-| **macOS (Intel)** | [Auto-Claude-2.7.1-x64.dmg](https://github.com/AndyMik90/Auto-Claude/releases/latest) | Intel Macs |
-| **Linux** | [Auto-Claude-2.7.1.AppImage](https://github.com/AndyMik90/Auto-Claude/releases/latest) | Universal |
-| **Linux (Debian)** | [Auto-Claude-2.7.1.deb](https://github.com/AndyMik90/Auto-Claude/releases/latest) | Ubuntu/Debian |
+<!-- STABLE_VERSION_BADGE -->
+[![Stable](https://img.shields.io/badge/stable-2.7.5-blue?style=flat-square)](https://github.com/AndyMik90/Auto-Claude/releases/tag/v2.7.5)
+<!-- STABLE_VERSION_BADGE_END -->
+
+<!-- STABLE_DOWNLOADS -->
+| Platform | Download |
+|----------|----------|
+| **Windows** | [Auto-Claude-2.7.5-win32-x64.exe](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.5/Auto-Claude-2.7.5-win32-x64.exe) |
+| **macOS (Apple Silicon)** | [Auto-Claude-2.7.5-darwin-arm64.dmg](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.5/Auto-Claude-2.7.5-darwin-arm64.dmg) |
+| **macOS (Intel)** | [Auto-Claude-2.7.5-darwin-x64.dmg](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.5/Auto-Claude-2.7.5-darwin-x64.dmg) |
+| **Linux** | [Auto-Claude-2.7.5-linux-x86_64.AppImage](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.5/Auto-Claude-2.7.5-linux-x86_64.AppImage) |
+| **Linux (Debian)** | [Auto-Claude-2.7.5-linux-amd64.deb](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.5/Auto-Claude-2.7.5-linux-amd64.deb) |
+| **Linux (Flatpak)** | [Auto-Claude-2.7.5-linux-x86_64.flatpak](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.5/Auto-Claude-2.7.5-linux-x86_64.flatpak) |
+<!-- STABLE_DOWNLOADS_END -->
+
+### Beta Release
+
+> ⚠️ Beta releases may contain bugs and breaking changes. [View all releases](https://github.com/AndyMik90/Auto-Claude/releases)
+
+<!-- BETA_VERSION_BADGE -->
+[![Beta](https://img.shields.io/badge/beta-2.7.6--beta.5-orange?style=flat-square)](https://github.com/AndyMik90/Auto-Claude/releases/tag/v2.7.6-beta.5)
+<!-- BETA_VERSION_BADGE_END -->
+
+<!-- BETA_DOWNLOADS -->
+| Platform | Download |
+|----------|----------|
+| **Windows** | [Auto-Claude-2.7.6-beta.5-win32-x64.exe](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.6-beta.5/Auto-Claude-2.7.6-beta.5-win32-x64.exe) |
+| **macOS (Apple Silicon)** | [Auto-Claude-2.7.6-beta.5-darwin-arm64.dmg](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.6-beta.5/Auto-Claude-2.7.6-beta.5-darwin-arm64.dmg) |
+| **macOS (Intel)** | [Auto-Claude-2.7.6-beta.5-darwin-x64.dmg](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.6-beta.5/Auto-Claude-2.7.6-beta.5-darwin-x64.dmg) |
+| **Linux** | [Auto-Claude-2.7.6-beta.5-linux-x86_64.AppImage](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.6-beta.5/Auto-Claude-2.7.6-beta.5-linux-x86_64.AppImage) |
+| **Linux (Debian)** | [Auto-Claude-2.7.6-beta.5-linux-amd64.deb](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.6-beta.5/Auto-Claude-2.7.6-beta.5-linux-amd64.deb) |
+| **Linux (Flatpak)** | [Auto-Claude-2.7.6-beta.5-linux-x86_64.flatpak](https://github.com/AndyMik90/Auto-Claude/releases/download/v2.7.6-beta.5/Auto-Claude-2.7.6-beta.5-linux-x86_64.flatpak) |
+<!-- BETA_DOWNLOADS_END -->
 
 > All releases include SHA256 checksums and VirusTotal scan results for security verification.
 
@@ -32,7 +59,6 @@ Get the latest pre-built release for your platform:
 - **Claude Pro/Max subscription** - [Get one here](https://claude.ai/upgrade)
 - **Claude Code CLI** - `npm install -g @anthropic-ai/claude-code`
 - **Git repository** - Your project must be initialized as a git repo
-- **Python 3.12+** - Required for the backend and Memory Layer
 
 ---
 
@@ -56,6 +82,8 @@ Get the latest pre-built release for your platform:
 | **Self-Validating QA** | Built-in quality assurance loop catches issues before you review |
 | **AI-Powered Merge** | Automatic conflict resolution when integrating back to main |
 | **Memory Layer** | Agents retain insights across sessions for smarter builds |
+| **GitHub/GitLab Integration** | Import issues, investigate with AI, create merge requests |
+| **Linear Integration** | Sync tasks with Linear for team progress tracking |
 | **Cross-Platform** | Native desktop apps for Windows, macOS, and Linux |
 | **Auto-Updates** | App updates automatically when new versions are released |
 
@@ -119,47 +147,11 @@ See [guides/CLI-USAGE.md](guides/CLI-USAGE.md) for complete CLI documentation.
 
 ---
 
-## Configuration
+## Development
 
-Create `apps/backend/.env` from the example:
+Want to build from source or contribute? See [CONTRIBUTING.md](CONTRIBUTING.md) for complete development setup instructions.
 
-```bash
-cp apps/backend/.env.example apps/backend/.env
-```
-
-| Variable | Required | Description |
-|----------|----------|-------------|
-| `CLAUDE_CODE_OAUTH_TOKEN` | Yes | OAuth token from `claude setup-token` |
-| `GRAPHITI_ENABLED` | No | Enable Memory Layer for cross-session context |
-| `AUTO_BUILD_MODEL` | No | Override the default Claude model |
-
----
-
-## Building from Source
-
-For contributors and development:
-
-```bash
-# Clone the repository
-git clone https://github.com/AndyMik90/Auto-Claude.git
-cd Auto-Claude
-
-# Install all dependencies
-npm run install:all
-
-# Run in development mode
-npm run dev
-
-# Or build and run
-npm start
-```
-
-**System requirements for building:**
-- Node.js 24+
-- Python 3.12+
-- npm 10+
-
-See [CONTRIBUTING.md](CONTRIBUTING.md) for detailed development setup.
+For Linux-specific builds (Flatpak, AppImage), see [guides/linux.md](guides/linux.md).
 
 ---
 
@@ -189,6 +181,7 @@ All releases are:
 | `npm run package:mac` | Package for macOS |
 | `npm run package:win` | Package for Windows |
 | `npm run package:linux` | Package for Linux |
+| `npm run package:flatpak` | Package as Flatpak (see [guides/linux.md](guides/linux.md)) |
 | `npm run lint` | Run linter |
 | `npm test` | Run frontend tests |
 | `npm run test:backend` | Run backend tests |
@@ -220,3 +213,11 @@ We welcome contributions! Please read [CONTRIBUTING.md](CONTRIBUTING.md) for:
 Auto Claude is free to use. If you modify and distribute it, or run it as a service, your code must also be open source under AGPL-3.0.
 
 Commercial licensing available for closed-source use cases.
+
+---
+
+## Star History
+
+[![GitHub Repo stars](https://img.shields.io/github/stars/AndyMik90/Auto-Claude?style=social)](https://github.com/AndyMik90/Auto-Claude/stargazers)
+
+[![Star History Chart](https://api.star-history.com/svg?repos=AndyMik90/Auto-Claude&type=Date)](https://star-history.com/#AndyMik90/Auto-Claude&Date)

RELEASE.md

@@ -69,9 +69,38 @@ This will:
 - Update `apps/frontend/package.json`
 - Update `package.json` (root)
 - Update `apps/backend/__init__.py`
+- Check if `CHANGELOG.md` has an entry for the new version (warns if missing)
 - Create a commit with message `chore: bump version to X.Y.Z`
 
-### Step 2: Push and Create PR
+### Step 2: Update CHANGELOG.md (REQUIRED)
+
+**IMPORTANT: The release will fail if CHANGELOG.md doesn't have an entry for the new version.**
+
+Add release notes to `CHANGELOG.md` at the top of the file:
+
+```markdown
+## 2.8.0 - Your Release Title
+
+### ✨ New Features
+- Feature description
+
+### 🛠️ Improvements
+- Improvement description
+
+### 🐛 Bug Fixes
+- Fix description
+
+---
+```
+
+Then amend the version bump commit:
+
+```bash
+git add CHANGELOG.md
+git commit --amend --no-edit
+```
+
+### Step 3: Push and Create PR
 
 ```bash
 # Push your branch
@@ -81,24 +110,25 @@ git push origin your-branch
 gh pr create --base main --title "Release v2.8.0"
 ```
 
-### Step 3: Merge to Main
+### Step 4: Merge to Main
 
 Once the PR is approved and merged to `main`, GitHub Actions will automatically:
 
 1. **Detect the version bump** (`prepare-release.yml`)
-2. **Create a git tag** (e.g., `v2.8.0`)
-3. **Trigger the release workflow** (`release.yml`)
-4. **Build binaries** for all platforms:
+2. **Validate CHANGELOG.md** has an entry for the new version (FAILS if missing)
+3. **Extract release notes** from CHANGELOG.md
+4. **Create a git tag** (e.g., `v2.8.0`)
+5. **Trigger the release workflow** (`release.yml`)
+6. **Build binaries** for all platforms:
    - macOS Intel (x64) - code signed & notarized
    - macOS Apple Silicon (arm64) - code signed & notarized
    - Windows (NSIS installer) - code signed
    - Linux (AppImage + .deb)
-5. **Generate changelog** from merged PRs (using release-drafter)
-6. **Scan binaries** with VirusTotal
-7. **Create GitHub release** with all artifacts
-8. **Update README** with new version badge and download links
+7. **Scan binaries** with VirusTotal
+8. **Create GitHub release** with release notes from CHANGELOG.md
+9. **Update README** with new version badge and download links
 
-### Step 4: Verify
+### Step 5: Verify
 
 After merging, check:
 - [GitHub Actions](https://github.com/AndyMik90/Auto-Claude/actions) - ensure all workflows pass
@@ -113,29 +143,49 @@ We follow [Semantic Versioning](https://semver.org/):
 - **MINOR** (0.X.0): New features, backwards compatible
 - **PATCH** (0.0.X): Bug fixes, backwards compatible
 
-## Changelog Generation
+## Changelog Management
 
-Changelogs are automatically generated from merged PRs using [Release Drafter](https://github.com/release-drafter/release-drafter).
+Release notes are managed in `CHANGELOG.md` and used for GitHub releases.
 
-### PR Labels for Changelog Categories
+### Changelog Format
 
-| Label | Category |
-|-------|----------|
-| `feature`, `enhancement` | New Features |
-| `bug`, `fix` | Bug Fixes |
-| `improvement`, `refactor` | Improvements |
-| `documentation` | Documentation |
-| (any other) | Other Changes |
+Each version entry in `CHANGELOG.md` should follow this format:
 
-**Tip:** Add appropriate labels to your PRs for better changelog organization.
+```markdown
+## X.Y.Z - Release Title
+
+### ✨ New Features
+- Feature description with context
+
+### 🛠️ Improvements
+- Improvement description
+
+### 🐛 Bug Fixes
+- Fix description
+
+---
+```
+
+### Changelog Validation
+
+The release workflow **validates** that `CHANGELOG.md` has an entry for the version being released:
+
+- If the entry is **missing**, the release is **blocked** with a clear error message
+- If the entry **exists**, its content is used for the GitHub release notes
+
+### Writing Good Release Notes
+
+- **Be specific**: Instead of "Fixed bug", write "Fixed crash when opening large files"
+- **Group by impact**: Features first, then improvements, then fixes
+- **Credit contributors**: Mention contributors for significant changes
+- **Link issues**: Reference GitHub issues where relevant (e.g., "Fixes #123")
 
 ## Workflows
 
 | Workflow | Trigger | Purpose |
 |----------|---------|---------|
-| `prepare-release.yml` | Push to `main` | Detects version bump, creates tag |
-| `release.yml` | Tag `v*` pushed | Builds binaries, creates release |
-| `validate-version.yml` | Tag `v*` pushed | Validates tag matches package.json |
+| `prepare-release.yml` | Push to `main` | Detects version bump, **validates CHANGELOG.md**, creates tag |
+| `release.yml` | Tag `v*` pushed | Builds binaries, extracts changelog, creates release |
 | `update-readme` (in release.yml) | After release | Updates README with new version |
 
 ## Troubleshooting
@@ -153,6 +203,22 @@ Changelogs are automatically generated from merged PRs using [Release Drafter](h
    git diff HEAD~1 --name-only | grep package.json
    ```
 
+### Release blocked: Missing changelog entry
+
+If you see "CHANGELOG VALIDATION FAILED" in the workflow:
+
+1. The `prepare-release.yml` workflow validated that `CHANGELOG.md` doesn't have an entry for the new version
+2. **Fix**: Add an entry to `CHANGELOG.md` with the format `## X.Y.Z - Title`
+3. Commit and push the changelog update
+4. The workflow will automatically retry when the changes are pushed to `main`
+
+```bash
+# Add changelog entry, then:
+git add CHANGELOG.md
+git commit -m "docs: add changelog for vX.Y.Z"
+git push origin main
+```
+
 ### Build failed after tag was created
 
 - The release won't be published if builds fail

apps/backend/.env.example

@@ -7,7 +7,8 @@
 # Auto Claude uses Claude Code OAuth authentication.
 # Direct API keys (ANTHROPIC_API_KEY) are NOT supported to prevent silent billing.
 #
-# Option 1: Run `claude setup-token` to save token to macOS Keychain (recommended)
+# Option 1: Run `claude setup-token` to save token to system keychain (recommended)
+#           (macOS: Keychain, Windows: Credential Manager, Linux: secret-service)
 # Option 2: Set the token explicitly:
 # CLAUDE_CODE_OAUTH_TOKEN=your-oauth-token-here
 #
@@ -31,8 +32,8 @@
 # API_TIMEOUT_MS=600000
 
 # Model override (OPTIONAL)
-# Default: claude-opus-4-5-20251101
-# AUTO_BUILD_MODEL=claude-opus-4-5-20251101
+# Default: claude-opus-4-6
+# AUTO_BUILD_MODEL=claude-opus-4-6
 
 
 # =============================================================================
@@ -75,6 +76,38 @@
 # Pre-configured Project ID (OPTIONAL - will create project if not set)
 # LINEAR_PROJECT_ID=
 
+# =============================================================================
+# GITLAB INTEGRATION (OPTIONAL)
+# =============================================================================
+# Enable GitLab integration for issue tracking and merge requests.
+# Supports both GitLab.com and self-hosted GitLab instances.
+#
+# Authentication Options (choose one):
+#
+#   Option 1: glab CLI OAuth (Recommended)
+#   Install glab CLI: https://gitlab.com/gitlab-org/cli#installation
+#   Then run: glab auth login
+#   This opens your browser for OAuth authentication. Once complete,
+#   Auto Claude will automatically use your glab credentials (no env vars needed).
+#   For self-hosted: glab auth login --hostname gitlab.example.com
+#
+#   Option 2: Personal Access Token
+#   Set GITLAB_TOKEN below. Token auth is used if set, otherwise falls back to glab CLI.
+
+# GitLab Instance URL (OPTIONAL - defaults to gitlab.com)
+# For self-hosted: GITLAB_INSTANCE_URL=https://gitlab.example.com
+# GITLAB_INSTANCE_URL=https://gitlab.com
+
+# GitLab Personal Access Token (OPTIONAL - only needed if not using glab CLI)
+# Required scope: api (covers issues, merge requests, releases, project info)
+# Optional scope: write_repository (only if creating new GitLab projects from local repos)
+# Get from: https://gitlab.com/-/user_settings/personal_access_tokens
+# GITLAB_TOKEN=glpat-xxxxxxxxxxxxxxxxxxxx
+
+# GitLab Project (OPTIONAL - format: group/project or numeric ID)
+# If not set, will auto-detect from git remote
+# GITLAB_PROJECT=mygroup/myproject
+
 # =============================================================================
 # UI SETTINGS (OPTIONAL)
 # =============================================================================
@@ -153,10 +186,10 @@ GRAPHITI_ENABLED=true
 # Choose which providers to use for LLM and embeddings.
 # Default is "openai" for both.
 
-# LLM provider: openai | anthropic | azure_openai | ollama | google
+# LLM provider: openai | anthropic | azure_openai | ollama | google | openrouter
 # GRAPHITI_LLM_PROVIDER=openai
 
-# Embedder provider: openai | voyage | azure_openai | ollama | google
+# Embedder provider: openai | voyage | azure_openai | ollama | google | openrouter
 # GRAPHITI_EMBEDDER_PROVIDER=openai
 
 # =============================================================================
@@ -221,6 +254,28 @@ GRAPHITI_ENABLED=true
 # Google Embedding Model (default: text-embedding-004)
 # GOOGLE_EMBEDDING_MODEL=text-embedding-004
 
+# =============================================================================
+# GRAPHITI: OpenRouter Provider (Multi-provider aggregator)
+# =============================================================================
+# Use OpenRouter to access multiple LLM providers through a single API.
+# OpenRouter provides access to Anthropic, OpenAI, Google, and many other models.
+# Get API key from: https://openrouter.ai/keys
+#
+# Required: OPENROUTER_API_KEY
+
+# OpenRouter API Key
+# OPENROUTER_API_KEY=sk-or-xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+# OpenRouter Base URL (default: https://openrouter.ai/api/v1)
+# OPENROUTER_BASE_URL=https://openrouter.ai/api/v1
+
+# OpenRouter LLM Model (default: anthropic/claude-sonnet-4)
+# Popular choices: anthropic/claude-sonnet-4, openai/gpt-4o, google/gemini-2.0-flash
+# OPENROUTER_LLM_MODEL=anthropic/claude-sonnet-4
+
+# OpenRouter Embedding Model (default: openai/text-embedding-3-small)
+# OPENROUTER_EMBEDDING_MODEL=openai/text-embedding-3-small
+
 # =============================================================================
 # GRAPHITI: Azure OpenAI Provider
 # =============================================================================
@@ -307,3 +362,11 @@ GRAPHITI_ENABLED=true
 # GRAPHITI_LLM_PROVIDER=google
 # GRAPHITI_EMBEDDER_PROVIDER=google
 # GOOGLE_API_KEY=AIzaSyxxxxxxxx
+#
+# --- Example 6: OpenRouter (multi-provider aggregator) ---
+# GRAPHITI_ENABLED=true
+# GRAPHITI_LLM_PROVIDER=openrouter
+# GRAPHITI_EMBEDDER_PROVIDER=openrouter
+# OPENROUTER_API_KEY=sk-or-xxxxxxxx
+# OPENROUTER_LLM_MODEL=anthropic/claude-sonnet-4
+# OPENROUTER_EMBEDDING_MODEL=openai/text-embedding-3-small

apps/backend/.gitignore

@@ -62,5 +62,16 @@ Thumbs.db
 # Tests (development only)
 tests/
 
+# Exceptions: Allow specific test directories
+!integrations/graphiti/tests/
+!tests/integration/
+
 # Auto Claude data directory
 .auto-claude/
+coverage.json
+
+# Auto Claude generated files
+.auto-claude-security.json
+.auto-claude-status
+.security-key
+logs/security/

apps/backend/README.md

@@ -17,12 +17,14 @@ python -m pip install -r requirements.txt
 cp .env.example .env
 ```
 
-Set your Claude API token in `.env`:
-```
-CLAUDE_CODE_OAUTH_TOKEN=your-token-here
+Authenticate with Claude Code (token auto-saved to Keychain):
+```bash
+claude
+# Type: /login
+# Press Enter to open browser
 ```
 
-Get your token by running: `claude setup-token`
+Token is auto-detected from macOS Keychain / Windows Credential Manager.
 
 ### 3. Run
 

apps/backend/__init__.py

@@ -19,5 +19,5 @@ Quick Start:
 See README.md for full documentation.
 """
 
-__version__ = "2.7.2"
+__version__ = "2.7.6-beta.5"
 __author__ = "Auto Claude Team"

apps/backend/agents/README.md

@@ -26,7 +26,7 @@ auto-claude/agents/
 ### `utils.py` (3.6 KB)
 - Git operations: `get_latest_commit()`, `get_commit_count()`
 - Plan management: `load_implementation_plan()`, `find_subtask_in_plan()`, `find_phase_for_subtask()`
-- Workspace sync: `sync_plan_to_source()`
+- Workspace sync: `sync_spec_to_source()`
 
 ### `memory.py` (13 KB)
 - Dual-layer memory system (Graphiti primary, file-based fallback)
@@ -73,7 +73,7 @@ from agents import (
     # Utilities
     get_latest_commit,
     load_implementation_plan,
-    sync_plan_to_source,
+    sync_spec_to_source,
 )
 ```
 

apps/backend/agents/__init__.py

@@ -14,6 +14,10 @@ This module provides:
 Uses lazy imports to avoid circular dependencies.
 """
 
+# Explicit import required by CodeQL static analysis
+# (CodeQL doesn't recognize __getattr__ dynamic exports)
+from .utils import sync_spec_to_source
+
 __all__ = [
     # Main API
     "run_autonomous_agent",
@@ -32,7 +36,7 @@ __all__ = [
     "load_implementation_plan",
     "find_subtask_in_plan",
     "find_phase_for_subtask",
-    "sync_plan_to_source",
+    "sync_spec_to_source",
     # Constants
     "AUTO_CONTINUE_DELAY_SECONDS",
     "HUMAN_INTERVENTION_FILE",
@@ -77,7 +81,7 @@ def __getattr__(name):
         "get_commit_count",
         "get_latest_commit",
         "load_implementation_plan",
-        "sync_plan_to_source",
+        "sync_spec_to_source",
     ):
         from .utils import (
             find_phase_for_subtask,
@@ -85,7 +89,7 @@ def __getattr__(name):
             get_commit_count,
             get_latest_commit,
             load_implementation_plan,
-            sync_plan_to_source,
+            sync_spec_to_source,
         )
 
         return locals()[name]

apps/backend/agents/auto_claude_tools.py

@@ -1,62 +0,0 @@
-"""
-Custom MCP Tools for Auto-Claude Agents
-========================================
-
-DEPRECATED: This module is now a compatibility shim.
-Please import from the tools_pkg package instead:
-
-    from agents.tools_pkg import create_auto_claude_mcp_server, get_allowed_tools
-
-This file remains for backward compatibility with existing imports.
-All functionality has been moved to the tools_pkg package for better
-organization and maintainability.
-"""
-
-# Import everything from the package to maintain backward compatibility
-# Use try/except to handle both relative and absolute imports
-try:
-    from .tools_pkg import (
-        ELECTRON_TOOLS,
-        TOOL_GET_BUILD_PROGRESS,
-        TOOL_GET_SESSION_CONTEXT,
-        TOOL_RECORD_DISCOVERY,
-        TOOL_RECORD_GOTCHA,
-        TOOL_UPDATE_QA_STATUS,
-        TOOL_UPDATE_SUBTASK_STATUS,
-        create_auto_claude_mcp_server,
-        get_allowed_tools,
-        is_electron_mcp_enabled,
-        is_tools_available,
-    )
-except ImportError:
-    # Fallback for direct execution - import from tools_pkg directly
-    from tools_pkg import (
-        ELECTRON_TOOLS,
-        TOOL_GET_BUILD_PROGRESS,
-        TOOL_GET_SESSION_CONTEXT,
-        TOOL_RECORD_DISCOVERY,
-        TOOL_RECORD_GOTCHA,
-        TOOL_UPDATE_QA_STATUS,
-        TOOL_UPDATE_SUBTASK_STATUS,
-        create_auto_claude_mcp_server,
-        get_allowed_tools,
-        is_electron_mcp_enabled,
-        is_tools_available,
-    )
-
-__all__ = [
-    # Main API
-    "create_auto_claude_mcp_server",
-    "get_allowed_tools",
-    "is_tools_available",
-    # Tool name constants
-    "TOOL_UPDATE_SUBTASK_STATUS",
-    "TOOL_GET_BUILD_PROGRESS",
-    "TOOL_RECORD_DISCOVERY",
-    "TOOL_RECORD_GOTCHA",
-    "TOOL_GET_SESSION_CONTEXT",
-    "TOOL_UPDATE_QA_STATUS",
-    # Electron MCP
-    "ELECTRON_TOOLS",
-    "is_electron_mcp_enabled",
-]

apps/backend/agents/base.py

@@ -6,6 +6,7 @@ Shared imports, types, and constants used across agent modules.
 """
 
 import logging
+import re
 
 # Configure logging
 logger = logging.getLogger(__name__)
@@ -13,3 +14,86 @@ logger = logging.getLogger(__name__)
 # Configuration constants
 AUTO_CONTINUE_DELAY_SECONDS = 3
 HUMAN_INTERVENTION_FILE = "PAUSE"
+
+# Retry configuration for subtask execution
+MAX_SUBTASK_RETRIES = 5  # Maximum attempts before marking subtask as stuck
+
+# Retry configuration for 400 tool concurrency errors
+MAX_CONCURRENCY_RETRIES = 5  # Maximum number of retries for tool concurrency errors
+INITIAL_RETRY_DELAY_SECONDS = (
+    2  # Initial retry delay (doubles each retry: 2s, 4s, 8s, 16s, 32s)
+)
+MAX_RETRY_DELAY_SECONDS = 32  # Cap retry delay at 32 seconds
+
+# Pause file constants for intelligent error recovery
+# These files signal pause/resume between frontend and backend
+RATE_LIMIT_PAUSE_FILE = "RATE_LIMIT_PAUSE"  # Created when rate limited
+AUTH_FAILURE_PAUSE_FILE = "AUTH_PAUSE"  # Created when auth fails
+RESUME_FILE = "RESUME"  # Created by frontend to signal resume
+
+# Maximum time to wait for rate limit reset (2 hours)
+# If reset time is beyond this, task should fail rather than wait indefinitely
+MAX_RATE_LIMIT_WAIT_SECONDS = 7200
+
+# Wait intervals for pause/resume checking
+RATE_LIMIT_CHECK_INTERVAL_SECONDS = (
+    30  # Check for RESUME file every 30 seconds during rate limit wait
+)
+AUTH_RESUME_CHECK_INTERVAL_SECONDS = 10  # Check for re-authentication every 10 seconds
+AUTH_RESUME_MAX_WAIT_SECONDS = 86400  # Maximum wait for re-authentication (24 hours)
+
+
+def sanitize_error_message(error_message: str, max_length: int = 500) -> str:
+    """
+    Sanitize error messages to remove potentially sensitive information.
+
+    Redacts:
+    - API keys (sk-..., key-...)
+    - Bearer tokens
+    - Token/secret values
+
+    Args:
+        error_message: The raw error message to sanitize
+        max_length: Maximum length to truncate to (default 500)
+
+    Returns:
+        Sanitized and truncated error message
+    """
+    if not error_message:
+        return ""
+
+    # Redact patterns that look like API keys or tokens
+    # Pattern: sk-... (OpenAI/Anthropic keys like sk-ant-api03-...)
+    sanitized = re.sub(
+        r"\bsk-[a-zA-Z0-9._\-]{20,}\b", "[REDACTED_API_KEY]", error_message
+    )
+
+    # Pattern: key-... (generic API keys)
+    sanitized = re.sub(r"\bkey-[a-zA-Z0-9._\-]{20,}\b", "[REDACTED_API_KEY]", sanitized)
+
+    # Pattern: Bearer ... (bearer tokens)
+    sanitized = re.sub(
+        r"\bBearer\s+[a-zA-Z0-9._\-]{20,}\b", "Bearer [REDACTED_TOKEN]", sanitized
+    )
+
+    # Pattern: token= or token: followed by long strings
+    sanitized = re.sub(
+        r"(token[=:]\s*)[a-zA-Z0-9._\-]{20,}\b",
+        r"\1[REDACTED_TOKEN]",
+        sanitized,
+        flags=re.IGNORECASE,
+    )
+
+    # Pattern: secret= or secret: followed by strings
+    sanitized = re.sub(
+        r"(secret[=:]\s*)[a-zA-Z0-9._\-]{20,}\b",
+        r"\1[REDACTED_SECRET]",
+        sanitized,
+        flags=re.IGNORECASE,
+    )
+
+    # Truncate to max length
+    if len(sanitized) > max_length:
+        sanitized = sanitized[:max_length] + "..."
+
+    return sanitized

apps/backend/agents/investigation_context.py

@@ -0,0 +1,97 @@
+"""
+Investigation context loading for agents.
+
+Provides utilities to load investigation data from spec directories
+for GitHub-sourced tasks.
+"""
+
+import json
+from pathlib import Path
+from typing import Any
+
+
+def load_investigation_context(spec_dir: Path) -> dict[str, Any] | None:
+    """
+    Load investigation context if this spec was created from a GitHub issue.
+
+    Args:
+        spec_dir: Path to the spec directory
+
+    Returns:
+        Structured investigation context with root_cause, fix_approaches,
+        reproducer, gotchas, and patterns_to_follow, or None if no
+        investigation data exists.
+    """
+    investigation_report_path = spec_dir / "investigation_report.json"
+
+    if not investigation_report_path.exists():
+        return None
+
+    try:
+        with open(investigation_report_path) as f:
+            report = json.load(f)
+
+        root_cause = report.get("root_cause", {})
+        fix_advice = report.get("fix_advice", {})
+        reproduction = report.get("reproduction", {})
+
+        # Structure the context for agents
+        return {
+            "root_cause": {
+                "summary": root_cause.get("identified_root_cause"),
+                "evidence": root_cause.get("evidence", ""),
+                "code_paths": root_cause.get("code_paths", []),
+            },
+            "fix_approaches": fix_advice.get("approaches", []),
+            "reproducer": reproduction if reproduction else None,
+            "gotchas": fix_advice.get("gotchas", []),
+            "patterns_to_follow": fix_advice.get("patterns_to_follow", []),
+            "impact": report.get("impact", {}),
+        }
+    except (json.JSONDecodeError, OSError):
+        return None
+
+
+def load_investigation_for_qa(
+    spec_dir: Path, base_branch: str
+) -> dict[str, Any] | None:
+    """
+    Load investigation context for QA validation.
+
+    Similar to load_investigation_context but includes base_branch
+    for QA comparison.
+
+    Args:
+        spec_dir: Path to the spec directory
+        base_branch: Base branch to compare against (e.g., 'main', 'develop')
+
+    Returns:
+        Structured investigation context with root_cause, reproducer,
+        impact, expected_outcome, and base_branch, or None if no
+        investigation data exists.
+    """
+    investigation_report_path = spec_dir / "investigation_report.json"
+
+    if not investigation_report_path.exists():
+        return None
+
+    try:
+        with open(investigation_report_path) as f:
+            report = json.load(f)
+
+        root_cause = report.get("root_cause", {})
+        reproduction = report.get("reproduction", {})
+
+        return {
+            "root_cause": {
+                "summary": root_cause.get("identified_root_cause"),
+                "evidence": root_cause.get("evidence", ""),
+                "code_paths": root_cause.get("code_paths", []),
+            },
+            "reproducer": reproduction if reproduction else None,
+            "impact": report.get("impact", {}),
+            "expected_outcome": report.get("ai_summary"),
+            "base_branch": base_branch,
+        }
+    except (json.JSONDecodeError, OSError):
+        return None

apps/backend/agents/memory_manager.py

@@ -10,6 +10,7 @@ Handles session memory storage using dual-layer approach:
 import logging
 from pathlib import Path
 
+from core.sentry import capture_exception
 from debug import (
     debug,
     debug_detailed,
@@ -24,6 +25,7 @@ from graphiti_config import get_graphiti_status, is_graphiti_enabled
 # Import from parent memory package
 # Now safe since this module is named memory_manager (not memory)
 from memory import save_session_insights as save_file_based_memory
+from memory.graphiti_helpers import get_graphiti_memory
 
 logger = logging.getLogger(__name__)
 
@@ -113,15 +115,15 @@ async def get_graphiti_context(
             debug("memory", "Graphiti not enabled, skipping context retrieval")
         return None
 
+    memory = None
     try:
-        from graphiti_memory import GraphitiMemory
-
-        # Create memory manager
-        memory = GraphitiMemory(spec_dir, project_dir)
-
-        if not memory.is_enabled:
+        # Use centralized helper for GraphitiMemory instantiation (async)
+        memory = await get_graphiti_memory(spec_dir, project_dir)
+        if memory is None:
             if is_debug_enabled():
-                debug_warning("memory", "GraphitiMemory.is_enabled=False")
+                debug_warning(
+                    "memory", "GraphitiMemory not available for context retrieval"
+                )
             return None
 
         # Build search query from subtask description
@@ -130,7 +132,6 @@ async def get_graphiti_context(
         query = f"{subtask_desc} {subtask_id}".strip()
 
         if not query:
-            await memory.close()
             if is_debug_enabled():
                 debug_warning("memory", "Empty query, skipping context retrieval")
             return None
@@ -146,20 +147,26 @@ async def get_graphiti_context(
         # Get relevant context
         context_items = await memory.get_relevant_context(query, num_results=5)
 
+        # Get patterns and gotchas specifically (THE FIX for learning loop!)
+        # This retrieves PATTERN and GOTCHA episode types for cross-session learning
+        patterns, gotchas = await memory.get_patterns_and_gotchas(
+            query, num_results=3, min_score=0.5
+        )
+
         # Also get recent session history
         session_history = await memory.get_session_history(limit=3)
 
-        await memory.close()
-
         if is_debug_enabled():
             debug(
                 "memory",
                 "Graphiti context retrieval complete",
                 context_items_found=len(context_items) if context_items else 0,
+                patterns_found=len(patterns) if patterns else 0,
+                gotchas_found=len(gotchas) if gotchas else 0,
                 session_history_found=len(session_history) if session_history else 0,
             )
 
-        if not context_items and not session_history:
+        if not context_items and not session_history and not patterns and not gotchas:
             if is_debug_enabled():
                 debug("memory", "No relevant context found in Graphiti")
             return None
@@ -175,6 +182,34 @@ async def get_graphiti_context(
                 item_type = item.get("type", "unknown")
                 sections.append(f"- **[{item_type}]** {content}\n")
 
+        # Add patterns section (cross-session learning)
+        if patterns:
+            sections.append("### Learned Patterns\n")
+            sections.append("_Patterns discovered in previous sessions:_\n")
+            for p in patterns:
+                pattern_text = p.get("pattern", "")
+                applies_to = p.get("applies_to", "")
+                if applies_to:
+                    sections.append(
+                        f"- **Pattern**: {pattern_text}\n  _Applies to:_ {applies_to}\n"
+                    )
+                else:
+                    sections.append(f"- **Pattern**: {pattern_text}\n")
+
+        # Add gotchas section (cross-session learning)
+        if gotchas:
+            sections.append("### Known Gotchas\n")
+            sections.append("_Pitfalls to avoid:_\n")
+            for g in gotchas:
+                gotcha_text = g.get("gotcha", "")
+                solution = g.get("solution", "")
+                if solution:
+                    sections.append(
+                        f"- **Gotcha**: {gotcha_text}\n  _Solution:_ {solution}\n"
+                    )
+                else:
+                    sections.append(f"- **Gotcha**: {gotcha_text}\n")
+
         if session_history:
             sections.append("### Recent Session Insights\n")
             for session in session_history[:2]:  # Only show last 2
@@ -193,14 +228,29 @@ async def get_graphiti_context(
 
         return "\n".join(sections)
 
-    except ImportError:
-        logger.debug("Graphiti packages not installed")
-        if is_debug_enabled():
-            debug_warning("memory", "Graphiti packages not installed")
-        return None
     except Exception as e:
         logger.warning(f"Failed to get Graphiti context: {e}")
+        if is_debug_enabled():
+            debug_error("memory", "Graphiti context retrieval failed", error=str(e))
+        # Capture exception to Sentry with full context
+        capture_exception(
+            e,
+            operation="get_graphiti_context",
+            subtask_id=subtask.get("id", "unknown"),
+            subtask_desc=subtask.get("description", "")[:200],
+            spec_dir=str(spec_dir),
+            project_dir=str(project_dir),
+        )
         return None
+    finally:
+        # Always close the memory connection (swallow exceptions to avoid overriding)
+        if memory is not None:
+            try:
+                await memory.close()
+            except Exception as e:
+                logger.debug(
+                    "Failed to close Graphiti memory connection", exc_info=True
+                )
 
 
 async def save_session_memory(
@@ -285,20 +335,19 @@ async def save_session_memory(
         if is_debug_enabled():
             debug("memory", "Attempting PRIMARY storage: Graphiti")
 
+        memory = None
         try:
-            from graphiti_memory import GraphitiMemory
-
-            memory = GraphitiMemory(spec_dir, project_dir)
-
-            if is_debug_enabled():
-                debug_detailed(
-                    "memory",
-                    "GraphitiMemory instance created",
-                    is_enabled=memory.is_enabled,
-                    group_id=getattr(memory, "group_id", "unknown"),
-                )
-
-            if memory.is_enabled:
+            # Use centralized helper for GraphitiMemory instantiation (async)
+            memory = await get_graphiti_memory(spec_dir, project_dir)
+            if memory is None:
+                if is_debug_enabled():
+                    debug_warning("memory", "GraphitiMemory not available")
+                    debug(
+                        "memory",
+                        "get_graphiti_memory() returned None - this usually means Graphiti is disabled or provider config is invalid",
+                    )
+                # Continue to file-based fallback
+            if memory is not None and memory.is_enabled:
                 if is_debug_enabled():
                     debug("memory", "Saving to Graphiti...")
 
@@ -315,8 +364,6 @@ async def save_session_memory(
                     # Fallback to basic session insights
                     result = await memory.save_session_insights(session_num, insights)
 
-                await memory.close()
-
                 if result:
                     logger.info(
                         f"Session {session_num} insights saved to Graphiti (primary)"
@@ -337,23 +384,43 @@ async def save_session_memory(
                         debug_warning(
                             "memory", "Graphiti save returned False, using FALLBACK"
                         )
-            else:
-                logger.warning(
-                    "Graphiti memory not enabled, falling back to file-based"
-                )
+            elif memory is None:
                 if is_debug_enabled():
                     debug_warning(
-                        "memory", "GraphitiMemory.is_enabled=False, using FALLBACK"
+                        "memory", "GraphitiMemory not available, using FALLBACK"
                     )
+            else:
+                # memory is not None but memory.is_enabled is False
+                logger.warning(
+                    "GraphitiMemory.is_enabled=False, falling back to file-based"
+                )
+                if is_debug_enabled():
+                    debug_warning("memory", "GraphitiMemory disabled, using FALLBACK")
 
-        except ImportError as e:
-            logger.debug("Graphiti packages not installed, falling back to file-based")
-            if is_debug_enabled():
-                debug_warning("memory", "Graphiti packages not installed", error=str(e))
         except Exception as e:
             logger.warning(f"Graphiti save failed: {e}, falling back to file-based")
             if is_debug_enabled():
                 debug_error("memory", "Graphiti save failed", error=str(e))
+            # Capture exception to Sentry with full context
+            capture_exception(
+                e,
+                operation="save_session_memory_graphiti",
+                subtask_id=subtask_id,
+                session_num=session_num,
+                success=success,
+                subtasks_completed=subtasks_completed,
+                spec_dir=str(spec_dir),
+                project_dir=str(project_dir),
+            )
+        finally:
+            # Always close the memory connection (swallow exceptions to avoid overriding)
+            if memory is not None:
+                try:
+                    await memory.close()
+                except Exception as e:
+                    logger.debug(
+                        "Failed to close Graphiti memory connection", exc_info=e
+                    )
     else:
         if is_debug_enabled():
             debug("memory", "Graphiti not enabled, skipping to FALLBACK")
@@ -390,6 +457,17 @@ async def save_session_memory(
         logger.error(f"File-based memory save also failed: {e}")
         if is_debug_enabled():
             debug_error("memory", "File-based memory save FAILED", error=str(e))
+        # Capture exception to Sentry with full context
+        capture_exception(
+            e,
+            operation="save_session_memory_file",
+            subtask_id=subtask_id,
+            session_num=session_num,
+            success=success,
+            subtasks_completed=subtasks_completed,
+            spec_dir=str(spec_dir),
+            project_dir=str(project_dir),
+        )
         return False, "none"
 
 

apps/backend/agents/planner.py

@@ -1,179 +1,198 @@
-"""
-Planner Agent Module
-====================
-
-Handles follow-up planner sessions for adding new subtasks to completed specs.
-"""
-
-import logging
-from pathlib import Path
-
-from core.client import create_client
-from phase_config import get_phase_thinking_budget
-from task_logger import (
-    LogPhase,
-    get_task_logger,
-)
-from ui import (
-    BuildState,
-    Icons,
-    StatusManager,
-    bold,
-    box,
-    highlight,
-    icon,
-    muted,
-    print_status,
-)
-
-from .session import run_agent_session
-
-logger = logging.getLogger(__name__)
-
-
-async def run_followup_planner(
-    project_dir: Path,
-    spec_dir: Path,
-    model: str,
-    verbose: bool = False,
-) -> bool:
-    """
-    Run the follow-up planner to add new subtasks to a completed spec.
-
-    This is a simplified version of run_autonomous_agent that:
-    1. Creates a client
-    2. Loads the followup planner prompt
-    3. Runs a single planning session
-    4. Returns after the plan is updated (doesn't enter coding loop)
-
-    The planner agent will:
-    - Read FOLLOWUP_REQUEST.md for the new task
-    - Read the existing implementation_plan.json
-    - Add new phase(s) with pending subtasks
-    - Update the plan status back to in_progress
-
-    Args:
-        project_dir: Root directory for the project
-        spec_dir: Directory containing the completed spec
-        model: Claude model to use
-        verbose: Whether to show detailed output
-
-    Returns:
-        bool: True if planning completed successfully
-    """
-    from implementation_plan import ImplementationPlan
-    from prompts import get_followup_planner_prompt
-
-    # Initialize status manager for ccstatusline
-    status_manager = StatusManager(project_dir)
-    status_manager.set_active(spec_dir.name, BuildState.PLANNING)
-
-    # Initialize task logger for persistent logging
-    task_logger = get_task_logger(spec_dir)
-
-    # Show header
-    content = [
-        bold(f"{icon(Icons.GEAR)} FOLLOW-UP PLANNER SESSION"),
-        "",
-        f"Spec: {highlight(spec_dir.name)}",
-        muted("Adding follow-up work to completed spec."),
-        "",
-        muted("The agent will read your FOLLOWUP_REQUEST.md and add new subtasks."),
-    ]
-    print()
-    print(box(content, width=70, style="heavy"))
-    print()
-
-    # Start planning phase in task logger
-    if task_logger:
-        task_logger.start_phase(LogPhase.PLANNING, "Starting follow-up planning...")
-        task_logger.set_session(1)
-
-    # Create client (fresh context) with planning phase thinking budget
-    planning_thinking_budget = get_phase_thinking_budget(spec_dir, "planning")
-    client = create_client(
-        project_dir,
-        spec_dir,
-        model,
-        max_thinking_tokens=planning_thinking_budget,
-    )
-
-    # Generate follow-up planner prompt
-    prompt = get_followup_planner_prompt(spec_dir)
-
-    print_status("Running follow-up planner...", "progress")
-    print()
-
-    try:
-        # Run single planning session
-        async with client:
-            status, response = await run_agent_session(
-                client, prompt, spec_dir, verbose, phase=LogPhase.PLANNING
-            )
-
-        # End planning phase in task logger
-        if task_logger:
-            task_logger.end_phase(
-                LogPhase.PLANNING,
-                success=(status != "error"),
-                message="Follow-up planning session completed",
-            )
-
-        if status == "error":
-            print()
-            print_status("Follow-up planning failed", "error")
-            status_manager.update(state=BuildState.ERROR)
-            return False
-
-        # Verify the plan was updated (should have pending subtasks now)
-        plan_file = spec_dir / "implementation_plan.json"
-        if plan_file.exists():
-            plan = ImplementationPlan.load(plan_file)
-
-            # Check if there are any pending subtasks
-            all_subtasks = [c for p in plan.phases for c in p.subtasks]
-            pending_subtasks = [c for c in all_subtasks if c.status.value == "pending"]
-
-            if pending_subtasks:
-                # Reset the plan status to in_progress (in case planner didn't)
-                plan.reset_for_followup()
-                plan.save(plan_file)
-
-                print()
-                content = [
-                    bold(f"{icon(Icons.SUCCESS)} FOLLOW-UP PLANNING COMPLETE"),
-                    "",
-                    f"New pending subtasks: {highlight(str(len(pending_subtasks)))}",
-                    f"Total subtasks: {len(all_subtasks)}",
-                    "",
-                    muted("Next steps:"),
-                    f"  Run: {highlight(f'python auto-claude/run.py --spec {spec_dir.name}')}",
-                ]
-                print(box(content, width=70, style="heavy"))
-                print()
-                status_manager.update(state=BuildState.PAUSED)
-                return True
-            else:
-                print()
-                print_status(
-                    "Warning: No pending subtasks found after planning", "warning"
-                )
-                print(muted("The planner may not have added new subtasks."))
-                print(muted("Check implementation_plan.json manually."))
-                status_manager.update(state=BuildState.PAUSED)
-                return False
-        else:
-            print()
-            print_status(
-                "Error: implementation_plan.json not found after planning", "error"
-            )
-            status_manager.update(state=BuildState.ERROR)
-            return False
-
-    except Exception as e:
-        print()
-        print_status(f"Follow-up planning error: {e}", "error")
-        if task_logger:
-            task_logger.log_error(f"Follow-up planning error: {e}", LogPhase.PLANNING)
-        status_manager.update(state=BuildState.ERROR)
-        return False
+"""
+Planner Agent Module
+====================
+
+Handles follow-up planner sessions for adding new subtasks to completed specs.
+"""
+
+import logging
+from pathlib import Path
+
+from core.client import create_client
+from phase_config import (
+    get_fast_mode,
+    get_phase_client_thinking_kwargs,
+    get_phase_model,
+    get_phase_model_betas,
+)
+from phase_event import ExecutionPhase, emit_phase
+from task_logger import (
+    LogPhase,
+    get_task_logger,
+)
+from ui import (
+    BuildState,
+    Icons,
+    StatusManager,
+    bold,
+    box,
+    highlight,
+    icon,
+    muted,
+    print_status,
+)
+
+from .session import run_agent_session
+
+logger = logging.getLogger(__name__)
+
+
+async def run_followup_planner(
+    project_dir: Path,
+    spec_dir: Path,
+    model: str,
+    verbose: bool = False,
+) -> bool:
+    """
+    Run the follow-up planner to add new subtasks to a completed spec.
+
+    This is a simplified version of run_autonomous_agent that:
+    1. Creates a client
+    2. Loads the followup planner prompt
+    3. Runs a single planning session
+    4. Returns after the plan is updated (doesn't enter coding loop)
+
+    The planner agent will:
+    - Read FOLLOWUP_REQUEST.md for the new task
+    - Read the existing implementation_plan.json
+    - Add new phase(s) with pending subtasks
+    - Update the plan status back to in_progress
+
+    Args:
+        project_dir: Root directory for the project
+        spec_dir: Directory containing the completed spec
+        model: Claude model to use
+        verbose: Whether to show detailed output
+
+    Returns:
+        bool: True if planning completed successfully
+    """
+    from implementation_plan import ImplementationPlan
+    from prompts import get_followup_planner_prompt
+
+    # Initialize status manager for ccstatusline
+    status_manager = StatusManager(project_dir)
+    status_manager.set_active(spec_dir.name, BuildState.PLANNING)
+    emit_phase(ExecutionPhase.PLANNING, "Follow-up planning")
+
+    # Initialize task logger for persistent logging
+    task_logger = get_task_logger(spec_dir)
+
+    # Show header
+    content = [
+        bold(f"{icon(Icons.GEAR)} FOLLOW-UP PLANNER SESSION"),
+        "",
+        f"Spec: {highlight(spec_dir.name)}",
+        muted("Adding follow-up work to completed spec."),
+        "",
+        muted("The agent will read your FOLLOWUP_REQUEST.md and add new subtasks."),
+    ]
+    print()
+    print(box(content, width=70, style="heavy"))
+    print()
+
+    # Start planning phase in task logger
+    if task_logger:
+        task_logger.start_phase(LogPhase.PLANNING, "Starting follow-up planning...")
+        task_logger.set_session(1)
+
+    # Create client with phase-specific model and thinking budget
+    # Respects task_metadata.json configuration when no CLI override
+    planning_model = get_phase_model(spec_dir, "planning", model)
+    planning_betas = get_phase_model_betas(spec_dir, "planning", model)
+    thinking_kwargs = get_phase_client_thinking_kwargs(
+        spec_dir, "planning", planning_model
+    )
+    fast_mode = get_fast_mode(spec_dir)
+    logger.info(
+        f"[Planner] [Fast Mode] {'ENABLED' if fast_mode else 'disabled'} for follow-up planning"
+    )
+    client = create_client(
+        project_dir,
+        spec_dir,
+        planning_model,
+        agent_type="planner",
+        betas=planning_betas,
+        fast_mode=fast_mode,
+        **thinking_kwargs,
+    )
+
+    # Generate follow-up planner prompt
+    prompt = get_followup_planner_prompt(spec_dir)
+
+    print_status("Running follow-up planner...", "progress")
+    print()
+
+    try:
+        # Run single planning session
+        async with client:
+            status, response, error_info = await run_agent_session(
+                client, prompt, spec_dir, verbose, phase=LogPhase.PLANNING
+            )
+
+        # End planning phase in task logger
+        if task_logger:
+            task_logger.end_phase(
+                LogPhase.PLANNING,
+                success=(status != "error"),
+                message="Follow-up planning session completed",
+            )
+
+        if status == "error":
+            print()
+            print_status("Follow-up planning failed", "error")
+            status_manager.update(state=BuildState.ERROR)
+            return False
+
+        # Verify the plan was updated (should have pending subtasks now)
+        plan_file = spec_dir / "implementation_plan.json"
+        if plan_file.exists():
+            plan = ImplementationPlan.load(plan_file)
+
+            # Check if there are any pending subtasks
+            all_subtasks = [c for p in plan.phases for c in p.subtasks]
+            pending_subtasks = [c for c in all_subtasks if c.status.value == "pending"]
+
+            if pending_subtasks:
+                # Reset the plan status to in_progress (in case planner didn't)
+                plan.reset_for_followup()
+                await plan.async_save(plan_file)
+
+                print()
+                content = [
+                    bold(f"{icon(Icons.SUCCESS)} FOLLOW-UP PLANNING COMPLETE"),
+                    "",
+                    f"New pending subtasks: {highlight(str(len(pending_subtasks)))}",
+                    f"Total subtasks: {len(all_subtasks)}",
+                    "",
+                    muted("Next steps:"),
+                    f"  Run: {highlight(f'python auto-claude/run.py --spec {spec_dir.name}')}",
+                ]
+                print(box(content, width=70, style="heavy"))
+                print()
+                status_manager.update(state=BuildState.PAUSED)
+                return True
+            else:
+                print()
+                print_status(
+                    "Warning: No pending subtasks found after planning", "warning"
+                )
+                print(muted("The planner may not have added new subtasks."))
+                print(muted("Check implementation_plan.json manually."))
+                status_manager.update(state=BuildState.PAUSED)
+                return False
+        else:
+            print()
+            print_status(
+                "Error: implementation_plan.json not found after planning", "error"
+            )
+            status_manager.update(state=BuildState.ERROR)
+            return False
+
+    except Exception as e:
+        print()
+        print_status(f"Follow-up planning error: {e}", "error")
+        if task_logger:
+            task_logger.log_error(f"Follow-up planning error: {e}", LogPhase.PLANNING)
+        status_manager.update(state=BuildState.ERROR)
+        return False

apps/backend/agents/pr_template_filler.py

@@ -0,0 +1,347 @@
+"""
+PR Template Filler Agent Module
+================================
+
+Detects GitHub PR templates in a project and uses Claude to intelligently
+fill them based on code changes, spec context, commit history, and branch info.
+"""
+
+import logging
+from pathlib import Path
+
+from core.client import create_client
+from task_logger import LogPhase, get_task_logger
+
+from .session import run_agent_session
+
+logger = logging.getLogger(__name__)
+
+# Maximum diff size (in characters) before truncating to file-level summaries
+MAX_DIFF_CHARS = 30_000
+
+
+def detect_pr_template(project_dir: Path | str) -> str | None:
+    """
+    Detect a GitHub PR template in the project.
+
+    Searches for:
+    1. .github/PULL_REQUEST_TEMPLATE.md (single template)
+    2. .github/PULL_REQUEST_TEMPLATE/ directory (picks the first .md file)
+
+    Args:
+        project_dir: Root directory of the project
+
+    Returns:
+        The template content as a string, or None if no template is found.
+    """
+    project_dir = Path(project_dir)
+    # Check for single template file
+    single_template = project_dir / ".github" / "PULL_REQUEST_TEMPLATE.md"
+    if single_template.is_file():
+        try:
+            content = single_template.read_text(encoding="utf-8")
+            if content.strip():
+                logger.info(f"Found PR template: {single_template}")
+                return content
+        except Exception as e:
+            logger.warning(f"Failed to read PR template {single_template}: {e}")
+
+    # Check for template directory (pick first .md file alphabetically)
+    template_dir = project_dir / ".github" / "PULL_REQUEST_TEMPLATE"
+    if template_dir.is_dir():
+        try:
+            md_files = sorted(template_dir.glob("*.md"))
+            if md_files:
+                content = md_files[0].read_text(encoding="utf-8")
+                if content.strip():
+                    logger.info(f"Found PR template: {md_files[0]}")
+                    return content
+        except Exception as e:
+            logger.warning(f"Failed to read PR template from {template_dir}: {e}")
+
+    logger.info("No GitHub PR template found in project")
+    return None
+
+
+def _truncate_diff(diff_summary: str) -> str:
+    """
+    Truncate a large diff to file-level summaries to stay within token limits.
+
+    If the diff is within MAX_DIFF_CHARS, return it unchanged.
+    Otherwise, extract only file-level change summaries (e.g. file names
+    with insertions/deletions counts) and discard line-level detail.
+
+    Args:
+        diff_summary: The full diff summary text
+
+    Returns:
+        The original or truncated diff summary.
+    """
+    if len(diff_summary) <= MAX_DIFF_CHARS:
+        return diff_summary
+
+    lines = diff_summary.splitlines()
+    summary_lines: list[str] = []
+    summary_lines.append("(Diff truncated to file-level summaries due to size)")
+    summary_lines.append("")
+
+    for line in lines:
+        # Keep file-level summary lines (stat lines, file headers, etc.)
+        stripped = line.strip()
+        if (
+            stripped.startswith("diff --git")
+            or stripped.startswith("---")
+            or stripped.startswith("+++")
+            or "file changed" in stripped.lower()
+            or "files changed" in stripped.lower()
+            or "insertion" in stripped.lower()
+            or "deletion" in stripped.lower()
+            or stripped.startswith("rename")
+            or stripped.startswith("new file")
+            or stripped.startswith("deleted file")
+            or stripped.startswith("Binary files")
+        ):
+            summary_lines.append(line)
+
+    # If we couldn't extract meaningful summaries, take the first chunk
+    if len(summary_lines) <= 2:
+        truncated = diff_summary[:MAX_DIFF_CHARS]
+        return truncated + "\n\n(... diff truncated due to size)"
+
+    return "\n".join(summary_lines)
+
+
+def _strip_markdown_fences(content: str) -> str:
+    """
+    Strip markdown code fences from the response if present.
+
+    The AI sometimes wraps the output in ```markdown ... ``` even when instructed
+    not to. This ensures the PR body renders correctly on GitHub.
+
+    Args:
+        content: The response content to clean
+
+    Returns:
+        The content with markdown fences stripped.
+    """
+    result = content
+
+    # Strip opening fence (```markdown or just ```)
+    if result.startswith("```markdown"):
+        result = result[len("```markdown") :].lstrip("\n")
+    elif result.startswith("```md"):
+        result = result[len("```md") :].lstrip("\n")
+    elif result.startswith("```"):
+        result = result[3:].lstrip("\n")
+
+    # Strip closing fence
+    if result.endswith("```"):
+        result = result[:-3].rstrip("\n")
+
+    return result.strip()
+
+
+def _build_prompt(
+    template_content: str,
+    diff_summary: str,
+    spec_overview: str,
+    commit_log: str,
+    branch_name: str,
+    target_branch: str,
+) -> str:
+    """
+    Build the prompt for the PR template filler agent.
+
+    Combines the system prompt context variables into a single message
+    that includes the template and all change context.
+
+    Args:
+        template_content: The PR template markdown
+        diff_summary: Git diff summary (possibly truncated)
+        spec_overview: Spec.md content or summary
+        commit_log: Git log of commits in the PR
+        branch_name: Source branch name
+        target_branch: Target branch name
+
+    Returns:
+        The assembled prompt string.
+    """
+    return f"""Fill out the following GitHub PR template using the provided context.
+Return ONLY the filled template markdown — no preamble, no explanation, no code fences.
+
+## Checkbox Guidelines
+
+IMPORTANT: Be accurate and honest about what has and hasn't been verified.
+
+**Check these based on context (you can infer from the diff/spec):**
+- Base Branch targeting — check based on target_branch value
+- Type of Change (bug fix, feature, docs, refactor, test) — infer from diff and spec
+- Area (Frontend, Backend, Fullstack) — infer from changed file paths
+- Feature Toggle "N/A" — if the feature appears complete and not behind a flag
+- Breaking Changes "No" — if changes appear backward compatible
+
+**Leave UNCHECKED (these require human verification you cannot perform):**
+- "I've tested my changes locally" — you have not tested anything
+- "All CI checks pass" — CI has not run yet
+- "Windows/macOS/Linux tested" — requires manual testing on each platform
+- "All existing tests pass" — CI has not run yet
+- "New features include test coverage" — unless test files are clearly visible in the diff
+- "Bug fixes include regression tests" — unless test files are clearly visible in the diff
+
+**For platform/code quality checkboxes:**
+- "Used centralized platform/ module" — leave unchecked unless you can verify from the diff
+- "No hardcoded paths" — leave unchecked unless you can verify from the diff
+- "PR is small and focused (< 400 lines)" — check only if diff stats show < 400 lines changed
+
+**For the "I've synced with develop branch" checkbox:**
+- Leave unchecked — you cannot verify the sync status
+
+## PR Template
+
+{template_content}
+
+## Change Context
+
+### Branch Information
+- **Source branch:** {branch_name}
+- **Target branch:** {target_branch}
+
+### Git Diff Summary
+```
+{diff_summary}
+```
+
+### Spec Overview
+{spec_overview}
+
+### Commit History
+```
+{commit_log}
+```
+
+Fill every section of the PR template. Follow the checkbox guidelines above carefully.
+Output ONLY the completed template — no code fences, no preamble."""
+
+
+def _load_spec_overview(spec_dir: Path) -> str:
+    """
+    Load the spec.md content for context. Falls back to a brief note if unavailable.
+
+    Args:
+        spec_dir: Directory containing the spec files
+
+    Returns:
+        The spec content or a fallback message.
+    """
+    spec_file = spec_dir / "spec.md"
+    if spec_file.is_file():
+        try:
+            content = spec_file.read_text(encoding="utf-8")
+            # Truncate very long specs to keep prompt manageable
+            if len(content) > 8000:
+                return content[:8000] + "\n\n(... spec truncated for brevity)"
+            return content
+        except Exception as e:
+            logger.warning(f"Failed to read spec.md: {e}")
+    return "(No spec overview available)"
+
+
+async def run_pr_template_filler(
+    project_dir: Path,
+    spec_dir: Path,
+    model: str,
+    thinking_budget: int | None = None,
+    branch_name: str = "",
+    target_branch: str = "develop",
+    diff_summary: str = "",
+    commit_log: str = "",
+    verbose: bool = False,
+) -> str | None:
+    """
+    Run the PR template filler agent to generate a filled PR body.
+
+    Detects the project's PR template, gathers change context, and invokes
+    Claude to intelligently fill out the template sections.
+
+    Args:
+        project_dir: Root directory of the project
+        spec_dir: Directory containing the spec files
+        model: Claude model to use
+        thinking_budget: Max thinking tokens (None to disable extended thinking)
+        branch_name: Source branch name for the PR
+        target_branch: Target branch name for the PR
+        diff_summary: Git diff summary of changes
+        commit_log: Git log of commits included in the PR
+        verbose: Whether to show detailed output
+
+    Returns:
+        The filled template markdown string, or None if template detection fails
+        or the agent encounters an error.
+    """
+    # Detect PR template
+    template_content = detect_pr_template(project_dir)
+    if template_content is None:
+        logger.info("No PR template detected — skipping template filler")
+        return None
+
+    # Load spec overview
+    spec_overview = _load_spec_overview(spec_dir)
+
+    # Truncate diff if too large
+    truncated_diff = _truncate_diff(diff_summary)
+
+    # Build the prompt
+    prompt = _build_prompt(
+        template_content=template_content,
+        diff_summary=truncated_diff,
+        spec_overview=spec_overview,
+        commit_log=commit_log,
+        branch_name=branch_name,
+        target_branch=target_branch,
+    )
+
+    # Initialize task logger
+    task_logger = get_task_logger(spec_dir)
+    if task_logger:
+        task_logger.start_phase(LogPhase.CODING, "PR template filling")
+
+    # Create client following the pattern from planner.py
+    client = create_client(
+        project_dir,
+        spec_dir,
+        model,
+        agent_type="pr_template_filler",
+        max_thinking_tokens=thinking_budget,
+    )
+
+    try:
+        async with client:
+            status, response, _ = await run_agent_session(
+                client, prompt, spec_dir, verbose, phase=LogPhase.CODING
+            )
+
+        if task_logger:
+            task_logger.end_phase(
+                LogPhase.CODING,
+                success=(status != "error"),
+                message="PR template filling completed",
+            )
+
+        if status == "error":
+            logger.error("PR template filler agent returned an error")
+            return None
+
+        # The agent should return only the filled template markdown
+        if response and response.strip():
+            result = _strip_markdown_fences(response.strip())
+            logger.info("PR template filled successfully")
+            return result
+
+        logger.warning("PR template filler returned empty response")
+        return None
+
+    except Exception as e:
+        logger.error(f"PR template filler error: {e}")
+        if task_logger:
+            task_logger.log_error(f"PR template filler error: {e}", LogPhase.CODING)
+        return None

apps/backend/agents/test_refactoring.py

@@ -1,159 +0,0 @@
-#!/usr/bin/env python3
-"""
-Verification script for agent module refactoring.
-
-This script verifies that:
-1. All modules can be imported
-2. All public API functions are accessible
-3. Backwards compatibility is maintained
-"""
-
-import sys
-from pathlib import Path
-
-# Add parent directory to path
-sys.path.insert(0, str(Path(__file__).parent.parent))
-
-
-def test_imports():
-    """Test that all modules can be imported."""
-    print("Testing module imports...")
-
-    # Test base module
-    from agents import base
-
-    assert hasattr(base, "AUTO_CONTINUE_DELAY_SECONDS")
-    assert hasattr(base, "HUMAN_INTERVENTION_FILE")
-    print("  ✓ agents.base")
-
-    # Test utils module
-    from agents import utils
-
-    assert hasattr(utils, "get_latest_commit")
-    assert hasattr(utils, "load_implementation_plan")
-    print("  ✓ agents.utils")
-
-    # Test memory module
-    from agents import memory
-
-    assert hasattr(memory, "save_session_memory")
-    assert hasattr(memory, "get_graphiti_context")
-    print("  ✓ agents.memory")
-
-    # Test session module
-    from agents import session
-
-    assert hasattr(session, "run_agent_session")
-    assert hasattr(session, "post_session_processing")
-    print("  ✓ agents.session")
-
-    # Test planner module
-    from agents import planner
-
-    assert hasattr(planner, "run_followup_planner")
-    print("  ✓ agents.planner")
-
-    # Test coder module
-    from agents import coder
-
-    assert hasattr(coder, "run_autonomous_agent")
-    print("  ✓ agents.coder")
-
-    print("\n✓ All module imports successful!\n")
-
-
-def test_public_api():
-    """Test that the public API is accessible."""
-    print("Testing public API...")
-
-    # Test main agent module exports
-    import agents
-
-    required_functions = [
-        "run_autonomous_agent",
-        "run_followup_planner",
-        "save_session_memory",
-        "get_graphiti_context",
-        "run_agent_session",
-        "post_session_processing",
-        "get_latest_commit",
-        "load_implementation_plan",
-    ]
-
-    for func_name in required_functions:
-        assert hasattr(agents, func_name), f"Missing function: {func_name}"
-        print(f"  ✓ agents.{func_name}")
-
-    print("\n✓ All public API functions accessible!\n")
-
-
-def test_backwards_compatibility():
-    """Test that the old agent.py facade maintains backwards compatibility."""
-    print("Testing backwards compatibility...")
-
-    # Test that agent.py can be imported
-    import agent
-
-    required_functions = [
-        "run_autonomous_agent",
-        "run_followup_planner",
-        "save_session_memory",
-        "save_session_to_graphiti",
-        "run_agent_session",
-        "post_session_processing",
-    ]
-
-    for func_name in required_functions:
-        assert hasattr(agent, func_name), (
-            f"Missing function in agent module: {func_name}"
-        )
-        print(f"  ✓ agent.{func_name}")
-
-    print("\n✓ Backwards compatibility maintained!\n")
-
-
-def test_module_structure():
-    """Test that the module structure is correct."""
-    print("Testing module structure...")
-
-    from pathlib import Path
-
-    agents_dir = Path(__file__).parent
-
-    required_files = [
-        "__init__.py",
-        "base.py",
-        "utils.py",
-        "memory.py",
-        "session.py",
-        "planner.py",
-        "coder.py",
-    ]
-
-    for filename in required_files:
-        filepath = agents_dir / filename
-        assert filepath.exists(), f"Missing file: {filename}"
-        print(f"  ✓ agents/{filename}")
-
-    print("\n✓ Module structure correct!\n")
-
-
-if __name__ == "__main__":
-    try:
-        test_module_structure()
-        test_imports()
-        test_public_api()
-        test_backwards_compatibility()
-
-        print("=" * 60)
-        print("✓ ALL TESTS PASSED - Refactoring verified!")
-        print("=" * 60)
-
-    except AssertionError as e:
-        print(f"\n✗ TEST FAILED: {e}")
-        sys.exit(1)
-    except ImportError as e:
-        print(f"\n✗ IMPORT ERROR: {e}")
-        print("Note: Some imports may fail due to missing dependencies.")
-        print("This is expected in test environments.")
-        sys.exit(0)  # Don't fail on import errors (expected in test env)

apps/backend/agents/tools_pkg/__init__.py

@@ -30,16 +30,32 @@ Usage:
 """
 
 from .models import (
+    # Agent configuration registry
+    AGENT_CONFIGS,
+    # Base tools
+    BASE_READ_TOOLS,
+    BASE_WRITE_TOOLS,
+    # MCP tool lists
+    CONTEXT7_TOOLS,
     ELECTRON_TOOLS,
+    GRAPHITI_MCP_TOOLS,
+    LINEAR_TOOLS,
+    PUPPETEER_TOOLS,
+    # Auto-Claude tool names
     TOOL_GET_BUILD_PROGRESS,
     TOOL_GET_SESSION_CONTEXT,
     TOOL_RECORD_DISCOVERY,
     TOOL_RECORD_GOTCHA,
     TOOL_UPDATE_QA_STATUS,
     TOOL_UPDATE_SUBTASK_STATUS,
+    WEB_TOOLS,
+    # Config functions
+    get_agent_config,
+    get_default_thinking_level,
+    get_required_mcp_servers,
     is_electron_mcp_enabled,
 )
-from .permissions import get_allowed_tools
+from .permissions import get_all_agent_types, get_allowed_tools
 from .registry import create_auto_claude_mcp_server, is_tools_available
 
 __all__ = [
@@ -47,14 +63,29 @@ __all__ = [
     "create_auto_claude_mcp_server",
     "get_allowed_tools",
     "is_tools_available",
-    # Tool name constants
+    # Agent configuration registry
+    "AGENT_CONFIGS",
+    "get_agent_config",
+    "get_required_mcp_servers",
+    "get_default_thinking_level",
+    "get_all_agent_types",
+    # Base tool lists
+    "BASE_READ_TOOLS",
+    "BASE_WRITE_TOOLS",
+    "WEB_TOOLS",
+    # MCP tool lists
+    "CONTEXT7_TOOLS",
+    "LINEAR_TOOLS",
+    "GRAPHITI_MCP_TOOLS",
+    "ELECTRON_TOOLS",
+    "PUPPETEER_TOOLS",
+    # Auto-Claude tool name constants
     "TOOL_UPDATE_SUBTASK_STATUS",
     "TOOL_GET_BUILD_PROGRESS",
     "TOOL_RECORD_DISCOVERY",
     "TOOL_RECORD_GOTCHA",
     "TOOL_GET_SESSION_CONTEXT",
     "TOOL_UPDATE_QA_STATUS",
-    # Electron MCP
-    "ELECTRON_TOOLS",
+    # Config
     "is_electron_mcp_enabled",
 ]

apps/backend/agents/tools_pkg/models.py

@@ -3,12 +3,32 @@ Tool Models and Constants
 ==========================
 
 Defines tool name constants and configuration for auto-claude MCP tools.
+
+This module is the single source of truth for all tool definitions used by
+the Claude Agent SDK client. Tool lists are organized by category:
+
+- Base tools: Core file operations (Read, Write, Edit, etc.)
+- Web tools: Documentation and research (WebFetch, WebSearch)
+- MCP tools: External integrations (Context7, Linear, Graphiti, etc.)
+- Auto-Claude tools: Custom build management tools
 """
 
 import os
 
 # =============================================================================
-# Tool Name Constants
+# Base Tools (Built-in Claude Code tools)
+# =============================================================================
+
+# Core file operation tools
+BASE_READ_TOOLS = ["Read", "Glob", "Grep"]
+BASE_WRITE_TOOLS = ["Write", "Edit", "Bash"]
+
+# Web tools for documentation lookup and research
+# Always available to all agents for accessing external information
+WEB_TOOLS = ["WebFetch", "WebSearch"]
+
+# =============================================================================
+# Auto-Claude MCP Tools (Custom build management)
 # =============================================================================
 
 # Auto-Claude MCP tool names (prefixed with mcp__auto-claude__)
@@ -19,8 +39,54 @@ TOOL_RECORD_GOTCHA = "mcp__auto-claude__record_gotcha"
 TOOL_GET_SESSION_CONTEXT = "mcp__auto-claude__get_session_context"
 TOOL_UPDATE_QA_STATUS = "mcp__auto-claude__update_qa_status"
 
+# =============================================================================
+# External MCP Tools
+# =============================================================================
+
+# Context7 MCP tools for documentation lookup (always enabled)
+CONTEXT7_TOOLS = [
+    "mcp__context7__resolve-library-id",
+    "mcp__context7__query-docs",
+]
+
+# Linear MCP tools for project management (when LINEAR_API_KEY is set)
+LINEAR_TOOLS = [
+    "mcp__linear-server__list_teams",
+    "mcp__linear-server__get_team",
+    "mcp__linear-server__list_projects",
+    "mcp__linear-server__get_project",
+    "mcp__linear-server__create_project",
+    "mcp__linear-server__update_project",
+    "mcp__linear-server__list_issues",
+    "mcp__linear-server__get_issue",
+    "mcp__linear-server__create_issue",
+    "mcp__linear-server__update_issue",
+    "mcp__linear-server__list_comments",
+    "mcp__linear-server__create_comment",
+    "mcp__linear-server__list_issue_statuses",
+    "mcp__linear-server__list_issue_labels",
+    "mcp__linear-server__list_users",
+    "mcp__linear-server__get_user",
+]
+
+# Graphiti MCP tools for knowledge graph memory (when GRAPHITI_MCP_URL is set)
+# See: https://github.com/getzep/graphiti
+GRAPHITI_MCP_TOOLS = [
+    "mcp__graphiti-memory__search_nodes",  # Search entity summaries
+    "mcp__graphiti-memory__search_facts",  # Search relationships between entities
+    "mcp__graphiti-memory__add_episode",  # Add data to knowledge graph
+    "mcp__graphiti-memory__get_episodes",  # Retrieve recent episodes
+    "mcp__graphiti-memory__get_entity_edge",  # Get specific entity/relationship
+]
+
+# =============================================================================
+# Browser Automation MCP Tools (QA agents only)
+# =============================================================================
+
 # Puppeteer MCP tools for web browser automation
 # Used for web frontend validation (non-Electron web apps)
+# NOTE: Screenshots must be compressed (1280x720, quality 60, JPEG) to stay under
+# Claude SDK's 1MB JSON message buffer limit. See GitHub issue #74.
 PUPPETEER_TOOLS = [
     "mcp__puppeteer__puppeteer_connect_active_tab",
     "mcp__puppeteer__puppeteer_navigate",
@@ -36,6 +102,7 @@ PUPPETEER_TOOLS = [
 # Uses electron-mcp-server to connect to Electron apps via Chrome DevTools Protocol.
 # Electron app must be started with --remote-debugging-port=9222 (or ELECTRON_DEBUG_PORT).
 # These tools are only available to QA agents (qa_reviewer, qa_fixer), not Coder/Planner.
+# NOTE: Screenshots must be compressed to stay under Claude SDK's 1MB JSON message buffer limit.
 ELECTRON_TOOLS = [
     "mcp__electron__get_electron_window_info",  # Get info about running Electron windows
     "mcp__electron__take_screenshot",  # Capture screenshot of Electron window
@@ -43,10 +110,6 @@ ELECTRON_TOOLS = [
     "mcp__electron__read_electron_logs",  # Read console logs from Electron app
 ]
 
-# Base tools available to all agents
-BASE_READ_TOOLS = ["Read", "Glob", "Grep"]
-BASE_WRITE_TOOLS = ["Write", "Edit", "Bash"]
-
 # =============================================================================
 # Configuration
 # =============================================================================
@@ -61,3 +124,422 @@ def is_electron_mcp_enabled() -> bool:
     via Chrome DevTools Protocol on the configured debug port.
     """
     return os.environ.get("ELECTRON_MCP_ENABLED", "").lower() == "true"
+
+
+# =============================================================================
+# Agent Configuration Registry
+# =============================================================================
+# Single source of truth for phase → tools → MCP servers mapping.
+# This enables phase-aware tool control and context window optimization.
+
+AGENT_CONFIGS = {
+    # ═══════════════════════════════════════════════════════════════════════
+    # SPEC CREATION PHASES (Minimal tools, fast startup)
+    # ═══════════════════════════════════════════════════════════════════════
+    "spec_gatherer": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": [],  # No MCP needed - just reads project
+        "auto_claude_tools": [],
+        "thinking_default": "medium",
+    },
+    "spec_researcher": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7"],  # Needs docs lookup
+        "auto_claude_tools": [],
+        "thinking_default": "medium",
+    },
+    "spec_writer": {
+        "tools": BASE_READ_TOOLS + BASE_WRITE_TOOLS,
+        "mcp_servers": [],  # Just writes spec.md
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+    "spec_critic": {
+        "tools": BASE_READ_TOOLS,
+        "mcp_servers": [],  # Self-critique, no external tools
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+    "spec_discovery": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "medium",
+    },
+    "spec_context": {
+        "tools": BASE_READ_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "medium",
+    },
+    "spec_validation": {
+        "tools": BASE_READ_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+    "spec_compaction": {
+        "tools": BASE_READ_TOOLS + BASE_WRITE_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "medium",
+    },
+    # ═══════════════════════════════════════════════════════════════════════
+    # BUILD PHASES (Full tools + Graphiti memory)
+    # Note: "linear" is conditional on project setting "update_linear_with_tasks"
+    # ═══════════════════════════════════════════════════════════════════════
+    "planner": {
+        "tools": BASE_READ_TOOLS + BASE_WRITE_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7", "graphiti", "auto-claude"],
+        "mcp_servers_optional": ["linear"],  # Only if project setting enabled
+        "auto_claude_tools": [
+            TOOL_GET_BUILD_PROGRESS,
+            TOOL_GET_SESSION_CONTEXT,
+            TOOL_RECORD_DISCOVERY,
+        ],
+        "thinking_default": "high",
+    },
+    "coder": {
+        "tools": BASE_READ_TOOLS + BASE_WRITE_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7", "graphiti", "auto-claude"],
+        "mcp_servers_optional": ["linear"],
+        "auto_claude_tools": [
+            TOOL_UPDATE_SUBTASK_STATUS,
+            TOOL_GET_BUILD_PROGRESS,
+            TOOL_RECORD_DISCOVERY,
+            TOOL_RECORD_GOTCHA,
+            TOOL_GET_SESSION_CONTEXT,
+        ],
+        "thinking_default": "low",  # Coding uses minimal thinking (effort: low for Opus, 1024 tokens for Sonnet/Haiku)
+    },
+    # ═══════════════════════════════════════════════════════════════════════
+    # QA PHASES (Read + test + browser + Graphiti memory)
+    # ═══════════════════════════════════════════════════════════════════════
+    "qa_reviewer": {
+        # Read + Write/Edit (for QA reports and plan updates) + Bash (for tests)
+        # Note: Reviewer writes to spec directory only (qa_report.md, implementation_plan.json)
+        "tools": BASE_READ_TOOLS + BASE_WRITE_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7", "graphiti", "auto-claude", "browser"],
+        "mcp_servers_optional": ["linear"],  # For updating issue status
+        "auto_claude_tools": [
+            TOOL_GET_BUILD_PROGRESS,
+            TOOL_UPDATE_QA_STATUS,
+            TOOL_GET_SESSION_CONTEXT,
+        ],
+        "thinking_default": "high",
+    },
+    "qa_fixer": {
+        "tools": BASE_READ_TOOLS + BASE_WRITE_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7", "graphiti", "auto-claude", "browser"],
+        "mcp_servers_optional": ["linear"],
+        "auto_claude_tools": [
+            TOOL_UPDATE_SUBTASK_STATUS,
+            TOOL_GET_BUILD_PROGRESS,
+            TOOL_UPDATE_QA_STATUS,
+            TOOL_RECORD_GOTCHA,
+        ],
+        "thinking_default": "medium",
+    },
+    # ═══════════════════════════════════════════════════════════════════════
+    # UTILITY PHASES (Minimal, no MCP)
+    # ═══════════════════════════════════════════════════════════════════════
+    "insights": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        # Note: Default to "low" for minimal thinking overhead
+        # Haiku doesn't support thinking; create_simple_client() handles this
+        "thinking_default": "low",
+    },
+    "merge_resolver": {
+        "tools": [],  # Text-only analysis
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "low",
+    },
+    "commit_message": {
+        "tools": [],
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "low",
+    },
+    "pr_template_filler": {
+        "tools": BASE_READ_TOOLS,  # Read-only — reads diff, template, spec
+        "mcp_servers": [],  # No MCP needed, context passed via prompt
+        "auto_claude_tools": [],
+        "thinking_default": "low",  # Fast utility task for structured fill-in
+    },
+    "pr_reviewer": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,  # Read-only
+        "mcp_servers": ["context7"],
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+    "pr_orchestrator_parallel": {
+        # Read-only for parallel PR orchestrator
+        # NOTE: Do NOT add "Task" here - the SDK auto-allows Task when agents are defined
+        # via the --agents flag. Explicitly adding it interferes with agent registration.
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7"],
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+    "pr_followup_parallel": {
+        # Read-only for parallel followup reviewer
+        # NOTE: Do NOT add "Task" here - same reason as pr_orchestrator_parallel
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7"],
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+    "pr_followup_extraction": {
+        # Lightweight extraction call for recovering data when structured output fails
+        # Pure structured output extraction, no tools needed
+        "tools": [],
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "low",
+    },
+    "pr_finding_validator": {
+        # Standalone validator for re-checking findings against actual code
+        # Called separately from orchestrator to validate findings with fresh context
+        "tools": BASE_READ_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "medium",
+    },
+    "investigation_specialist": {
+        # Read-only specialist for issue investigation (root cause, impact, fix, reproduction)
+        "tools": BASE_READ_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "medium",
+    },
+    # ═══════════════════════════════════════════════════════════════════════
+    # ANALYSIS PHASES
+    # ═══════════════════════════════════════════════════════════════════════
+    "analysis": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7"],
+        "auto_claude_tools": [],
+        "thinking_default": "medium",
+    },
+    "batch_analysis": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "low",
+    },
+    "batch_validation": {
+        "tools": BASE_READ_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "low",
+    },
+    # ═══════════════════════════════════════════════════════════════════════
+    # ROADMAP & IDEATION
+    # ═══════════════════════════════════════════════════════════════════════
+    "roadmap_discovery": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7"],
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+    "competitor_analysis": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": ["context7"],  # WebSearch for competitor research
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+    "ideation": {
+        "tools": BASE_READ_TOOLS + WEB_TOOLS,
+        "mcp_servers": [],
+        "auto_claude_tools": [],
+        "thinking_default": "high",
+    },
+}
+
+
+# =============================================================================
+# Agent Config Helper Functions
+# =============================================================================
+
+
+def get_agent_config(agent_type: str) -> dict:
+    """
+    Get full configuration for an agent type.
+
+    Args:
+        agent_type: The agent type identifier (e.g., 'coder', 'planner', 'qa_reviewer')
+
+    Returns:
+        Configuration dict containing tools, mcp_servers, auto_claude_tools, thinking_default
+
+    Raises:
+        ValueError: If agent_type is not found in AGENT_CONFIGS (strict mode)
+    """
+    if agent_type not in AGENT_CONFIGS:
+        raise ValueError(
+            f"Unknown agent type: '{agent_type}'. "
+            f"Valid types: {sorted(AGENT_CONFIGS.keys())}"
+        )
+    return AGENT_CONFIGS[agent_type]
+
+
+def _map_mcp_server_name(
+    name: str, custom_server_ids: list[str] | None = None
+) -> str | None:
+    """
+    Map user-friendly MCP server names to internal identifiers.
+    Also accepts custom server IDs directly.
+
+    Args:
+        name: User-provided MCP server name
+        custom_server_ids: List of custom server IDs to accept as-is
+
+    Returns:
+        Internal server identifier or None if not recognized
+    """
+    if not name:
+        return None
+    mappings = {
+        "context7": "context7",
+        "graphiti-memory": "graphiti",
+        "graphiti": "graphiti",
+        "linear": "linear",
+        "electron": "electron",
+        "puppeteer": "puppeteer",
+        "auto-claude": "auto-claude",
+    }
+    # Check if it's a known mapping
+    mapped = mappings.get(name.lower().strip())
+    if mapped:
+        return mapped
+    # Check if it's a custom server ID (accept as-is)
+    if custom_server_ids and name in custom_server_ids:
+        return name
+    return None
+
+
+def get_required_mcp_servers(
+    agent_type: str,
+    project_capabilities: dict | None = None,
+    linear_enabled: bool = False,
+    mcp_config: dict | None = None,
+) -> list[str]:
+    """
+    Get MCP servers required for this agent type.
+
+    Handles dynamic server selection:
+    - "browser" → electron (if is_electron) or puppeteer (if is_web_frontend)
+    - "linear" → only if in mcp_servers_optional AND linear_enabled is True
+    - "graphiti" → only if GRAPHITI_MCP_URL is set
+    - Respects per-project MCP config overrides from .auto-claude/.env
+    - Applies per-agent ADD/REMOVE overrides from AGENT_MCP_<agent>_ADD/REMOVE
+
+    Args:
+        agent_type: The agent type identifier
+        project_capabilities: Dict from detect_project_capabilities() or None
+        linear_enabled: Whether Linear integration is enabled for this project
+        mcp_config: Per-project MCP server toggles from .auto-claude/.env
+                   Keys: CONTEXT7_ENABLED, LINEAR_MCP_ENABLED, ELECTRON_MCP_ENABLED,
+                         PUPPETEER_MCP_ENABLED, AGENT_MCP_<agent>_ADD/REMOVE
+
+    Returns:
+        List of MCP server names to start
+    """
+    config = get_agent_config(agent_type)
+    servers = list(config.get("mcp_servers", []))
+
+    # Load per-project config (or use defaults)
+    if mcp_config is None:
+        mcp_config = {}
+
+    # Filter context7 if explicitly disabled by project config
+    if "context7" in servers:
+        context7_enabled = mcp_config.get("CONTEXT7_ENABLED", "true")
+        if str(context7_enabled).lower() == "false":
+            servers = [s for s in servers if s != "context7"]
+
+    # Handle optional servers (e.g., Linear if project setting enabled)
+    optional = config.get("mcp_servers_optional", [])
+    if "linear" in optional and linear_enabled:
+        # Also check per-project LINEAR_MCP_ENABLED override
+        linear_mcp_enabled = mcp_config.get("LINEAR_MCP_ENABLED", "true")
+        if str(linear_mcp_enabled).lower() != "false":
+            servers.append("linear")
+
+    # Handle dynamic "browser" → electron/puppeteer based on project type and config
+    if "browser" in servers:
+        servers = [s for s in servers if s != "browser"]
+        if project_capabilities:
+            is_electron = project_capabilities.get("is_electron", False)
+            is_web_frontend = project_capabilities.get("is_web_frontend", False)
+
+            # Check per-project overrides (default false for both)
+            electron_enabled = mcp_config.get("ELECTRON_MCP_ENABLED", "false")
+            puppeteer_enabled = mcp_config.get("PUPPETEER_MCP_ENABLED", "false")
+
+            # Electron: enabled by project config OR global env var
+            if is_electron and (
+                str(electron_enabled).lower() == "true" or is_electron_mcp_enabled()
+            ):
+                servers.append("electron")
+            # Puppeteer: enabled by project config (no global env var)
+            elif is_web_frontend and not is_electron:
+                if str(puppeteer_enabled).lower() == "true":
+                    servers.append("puppeteer")
+
+    # Filter graphiti if not enabled
+    if "graphiti" in servers:
+        if not os.environ.get("GRAPHITI_MCP_URL"):
+            servers = [s for s in servers if s != "graphiti"]
+
+    # ========== Apply per-agent MCP overrides ==========
+    # Format: AGENT_MCP_<agent_type>_ADD=server1,server2
+    #         AGENT_MCP_<agent_type>_REMOVE=server1,server2
+    add_key = f"AGENT_MCP_{agent_type}_ADD"
+    remove_key = f"AGENT_MCP_{agent_type}_REMOVE"
+
+    # Extract custom server IDs for mapping (allows custom servers to be recognized)
+    custom_servers = mcp_config.get("CUSTOM_MCP_SERVERS", [])
+    custom_server_ids = [s.get("id") for s in custom_servers if s.get("id")]
+
+    # Process additions
+    if add_key in mcp_config:
+        additions = [
+            s.strip() for s in str(mcp_config[add_key]).split(",") if s.strip()
+        ]
+        for server in additions:
+            mapped = _map_mcp_server_name(server, custom_server_ids)
+            if mapped and mapped not in servers:
+                servers.append(mapped)
+
+    # Process removals (but never remove auto-claude)
+    if remove_key in mcp_config:
+        removals = [
+            s.strip() for s in str(mcp_config[remove_key]).split(",") if s.strip()
+        ]
+        for server in removals:
+            mapped = _map_mcp_server_name(server, custom_server_ids)
+            if mapped and mapped != "auto-claude":  # auto-claude cannot be removed
+                servers = [s for s in servers if s != mapped]
+
+    return servers
+
+
+def get_default_thinking_level(agent_type: str) -> str:
+    """
+    Get default thinking level string for agent type.
+
+    This returns the thinking level name (e.g., 'medium', 'high'), not the token budget.
+    To convert to tokens, use phase_config.get_thinking_budget(level).
+
+    Args:
+        agent_type: The agent type identifier
+
+    Returns:
+        Thinking level string (low, medium, high)
+    """
+    config = get_agent_config(agent_type)
+    return config.get("thinking_default", "medium")

apps/backend/agents/tools_pkg/permissions.py

@@ -8,26 +8,30 @@ pollution and accidental misuse.
 Supports dynamic tool filtering based on project capabilities to optimize
 context window usage. For example, Electron tools are only included for
 Electron projects, not for Next.js or CLI projects.
+
+This module now uses AGENT_CONFIGS from models.py as the single source of truth
+for tool permissions. The get_allowed_tools() function remains the primary API
+for backwards compatibility.
 """
 
 from .models import (
-    BASE_READ_TOOLS,
-    BASE_WRITE_TOOLS,
+    AGENT_CONFIGS,
+    CONTEXT7_TOOLS,
     ELECTRON_TOOLS,
+    GRAPHITI_MCP_TOOLS,
+    LINEAR_TOOLS,
     PUPPETEER_TOOLS,
-    TOOL_GET_BUILD_PROGRESS,
-    TOOL_GET_SESSION_CONTEXT,
-    TOOL_RECORD_DISCOVERY,
-    TOOL_RECORD_GOTCHA,
-    TOOL_UPDATE_QA_STATUS,
-    TOOL_UPDATE_SUBTASK_STATUS,
-    is_electron_mcp_enabled,
+    get_agent_config,
+    get_required_mcp_servers,
 )
+from .registry import is_tools_available
 
 
 def get_allowed_tools(
     agent_type: str,
     project_capabilities: dict | None = None,
+    linear_enabled: bool = False,
+    mcp_config: dict | None = None,
 ) -> list[str]:
     """
     Get the list of allowed tools for a specific agent type.
@@ -35,107 +39,82 @@ def get_allowed_tools(
     This ensures each agent only sees tools relevant to their role,
     preventing context pollution and accidental misuse.
 
-    When project_capabilities is provided, MCP tools are filtered based on
-    the project type. For example:
-    - Electron projects get Electron MCP tools
-    - Web frontends (non-Electron) get Puppeteer MCP tools
-    - CLI projects get neither
+    Uses AGENT_CONFIGS as the single source of truth for tool permissions.
+    Dynamic MCP tools are added based on project capabilities and required servers.
 
     Args:
-        agent_type: One of 'planner', 'coder', 'qa_reviewer', 'qa_fixer'
+        agent_type: Agent type identifier (e.g., 'coder', 'planner', 'qa_reviewer')
         project_capabilities: Optional dict from detect_project_capabilities()
                             containing flags like is_electron, is_web_frontend, etc.
+        linear_enabled: Whether Linear integration is enabled for this project
+        mcp_config: Per-project MCP server toggles from .auto-claude/.env
 
     Returns:
         List of allowed tool names
+
+    Raises:
+        ValueError: If agent_type is not found in AGENT_CONFIGS
     """
-    # Auto-claude tool mappings by agent type
-    tool_mappings = {
-        "planner": {
-            "base": BASE_READ_TOOLS + BASE_WRITE_TOOLS,
-            "auto_claude": [
-                TOOL_GET_BUILD_PROGRESS,
-                TOOL_GET_SESSION_CONTEXT,
-                TOOL_RECORD_DISCOVERY,
-            ],
-        },
-        "coder": {
-            "base": BASE_READ_TOOLS + BASE_WRITE_TOOLS,
-            "auto_claude": [
-                TOOL_UPDATE_SUBTASK_STATUS,
-                TOOL_GET_BUILD_PROGRESS,
-                TOOL_RECORD_DISCOVERY,
-                TOOL_RECORD_GOTCHA,
-                TOOL_GET_SESSION_CONTEXT,
-            ],
-        },
-        "qa_reviewer": {
-            "base": BASE_READ_TOOLS + ["Bash"],  # Can run tests but not edit
-            "auto_claude": [
-                TOOL_GET_BUILD_PROGRESS,
-                TOOL_UPDATE_QA_STATUS,
-                TOOL_GET_SESSION_CONTEXT,
-            ],
-        },
-        "qa_fixer": {
-            "base": BASE_READ_TOOLS + BASE_WRITE_TOOLS,
-            "auto_claude": [
-                TOOL_UPDATE_SUBTASK_STATUS,
-                TOOL_GET_BUILD_PROGRESS,
-                TOOL_UPDATE_QA_STATUS,
-                TOOL_RECORD_GOTCHA,
-            ],
-        },
-    }
+    # Get agent configuration (raises ValueError if unknown type)
+    config = get_agent_config(agent_type)
 
-    if agent_type not in tool_mappings:
-        # Default to coder tools
-        agent_type = "coder"
+    # Start with base tools from config
+    tools = list(config.get("tools", []))
 
-    mapping = tool_mappings[agent_type]
-    tools = mapping["base"] + mapping["auto_claude"]
+    # Get required MCP servers for this agent
+    required_servers = get_required_mcp_servers(
+        agent_type,
+        project_capabilities,
+        linear_enabled,
+        mcp_config,
+    )
 
-    # Add MCP tools for QA agents only, based on project capabilities
-    if agent_type in ("qa_reviewer", "qa_fixer"):
-        tools.extend(_get_qa_mcp_tools(project_capabilities))
+    # Add auto-claude tools ONLY if the MCP server is available
+    # This prevents allowing tools that won't work because the server isn't running
+    if "auto-claude" in required_servers and is_tools_available():
+        tools.extend(config.get("auto_claude_tools", []))
+
+    # Add MCP tool names based on required servers
+    tools.extend(_get_mcp_tools_for_servers(required_servers))
 
     return tools
 
 
-def _get_qa_mcp_tools(project_capabilities: dict | None) -> list[str]:
+def _get_mcp_tools_for_servers(servers: list[str]) -> list[str]:
     """
-    Get the list of MCP tools for QA agents based on project capabilities.
+    Get the list of MCP tools for a list of required servers.
 
-    This function determines which MCP tools to include based on:
-    1. Project type detection (Electron, web frontend, etc.)
-    2. Environment variables (ELECTRON_MCP_ENABLED)
+    Maps server names to their corresponding tool lists.
 
     Args:
-        project_capabilities: Dict from detect_project_capabilities() or None
+        servers: List of MCP server names (e.g., ['context7', 'linear', 'electron'])
 
     Returns:
-        List of MCP tool names to include
+        List of MCP tool names for all specified servers
     """
     tools = []
 
-    # If no capabilities provided, fall back to legacy behavior
-    # (check env var only)
-    if project_capabilities is None:
-        if is_electron_mcp_enabled():
+    for server in servers:
+        if server == "context7":
+            tools.extend(CONTEXT7_TOOLS)
+        elif server == "linear":
+            tools.extend(LINEAR_TOOLS)
+        elif server == "graphiti":
+            tools.extend(GRAPHITI_MCP_TOOLS)
+        elif server == "electron":
             tools.extend(ELECTRON_TOOLS)
-        return tools
-
-    # Project-capability-based tool selection
-    is_electron = project_capabilities.get("is_electron", False)
-    is_web_frontend = project_capabilities.get("is_web_frontend", False)
-
-    # Electron projects get Electron MCP tools (if enabled)
-    if is_electron and is_electron_mcp_enabled():
-        tools.extend(ELECTRON_TOOLS)
-
-    # Web frontends (non-Electron) get Puppeteer tools
-    # Puppeteer is always available, no env var check needed
-    if is_web_frontend and not is_electron:
-        tools.extend(PUPPETEER_TOOLS)
+        elif server == "puppeteer":
+            tools.extend(PUPPETEER_TOOLS)
+        # auto-claude tools are already added via config["auto_claude_tools"]
 
     return tools
+
+
+def get_all_agent_types() -> list[str]:
+    """
+    Get all registered agent types.
+
+    Returns:
+        Sorted list of all agent type identifiers
+    """
+    return sorted(AGENT_CONFIGS.keys())

apps/backend/agents/tools_pkg/tools/memory.py

@@ -4,9 +4,16 @@ Session Memory Tools
 
 Tools for recording and retrieving session memory, including discoveries,
 gotchas, and patterns.
+
+Dual-storage approach:
+- File-based: Always available, works offline, spec-specific
+- LadybugDB: When Graphiti is enabled, also saves to graph database for
+  cross-session retrieval and Memory UI display
 """
 
+import asyncio
 import json
+import logging
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import Any
@@ -19,6 +26,110 @@ except ImportError:
     SDK_TOOLS_AVAILABLE = False
     tool = None
 
+logger = logging.getLogger(__name__)
+
+
+async def _save_to_graphiti_async(
+    spec_dir: Path,
+    project_dir: Path,
+    save_type: str,
+    data: dict,
+) -> bool:
+    """
+    Save data to Graphiti/LadybugDB (async implementation).
+
+    Args:
+        spec_dir: Spec directory for GraphitiMemory initialization
+        project_dir: Project root directory
+        save_type: Type of save - 'discovery', 'gotcha', or 'pattern'
+        data: Data to save
+
+    Returns:
+        True if save succeeded, False otherwise
+    """
+    try:
+        # Use centralized helper for GraphitiMemory instantiation
+        # The helper handles enablement checks internally
+        from memory.graphiti_helpers import get_graphiti_memory
+
+        memory = await get_graphiti_memory(spec_dir, project_dir)
+        if memory is None:
+            return False
+
+        try:
+            if save_type == "discovery":
+                # Save as codebase discovery
+                # Format: {file_path: description}
+                result = await memory.save_codebase_discoveries(
+                    {data["file_path"]: data["description"]}
+                )
+            elif save_type == "gotcha":
+                # Save as gotcha
+                gotcha_text = data["gotcha"]
+                if data.get("context"):
+                    gotcha_text += f" (Context: {data['context']})"
+                result = await memory.save_gotcha(gotcha_text)
+            elif save_type == "pattern":
+                # Save as pattern
+                result = await memory.save_pattern(data["pattern"])
+            else:
+                result = False
+            return result
+        finally:
+            # Always close the memory connection (swallow exceptions to avoid overriding)
+            try:
+                await memory.close()
+            except Exception as e:
+                logger.debug(
+                    "Failed to close Graphiti memory connection", exc_info=True
+                )
+
+    except Exception as e:
+        logger.warning(f"Failed to save to Graphiti: {e}")
+        return False
+
+
+def _save_to_graphiti_sync(
+    spec_dir: Path,
+    project_dir: Path,
+    save_type: str,
+    data: dict,
+) -> bool:
+    """
+    Save data to Graphiti/LadybugDB (synchronous wrapper for sync contexts only).
+
+    NOTE: This should only be called from synchronous code. For async callers,
+    use _save_to_graphiti_async() directly to ensure proper resource cleanup.
+
+    Args:
+        spec_dir: Spec directory for GraphitiMemory initialization
+        project_dir: Project root directory
+        save_type: Type of save - 'discovery', 'gotcha', or 'pattern'
+        data: Data to save
+
+    Returns:
+        True if save succeeded, False otherwise
+    """
+    try:
+        # Check if we're already in an async context
+        try:
+            asyncio.get_running_loop()
+            # We're in an async context - caller should use _save_to_graphiti_async
+            # Log a warning and return False to avoid the resource leak bug
+            logger.warning(
+                "_save_to_graphiti_sync called from async context. "
+                "Use _save_to_graphiti_async instead for proper cleanup."
+            )
+            return False
+        except RuntimeError:
+            # No running loop - safe to create one
+            return asyncio.run(
+                _save_to_graphiti_async(spec_dir, project_dir, save_type, data)
+            )
+    except Exception as e:
+        logger.warning(f"Failed to save to Graphiti: {e}")
+        return False
+
 
 def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
     """
@@ -45,7 +156,7 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
         {"file_path": str, "description": str, "category": str},
     )
     async def record_discovery(args: dict[str, Any]) -> dict[str, Any]:
-        """Record a discovery to the codebase map."""
+        """Record a discovery to the codebase map (file + Graphiti)."""
         file_path = args["file_path"]
         description = args["description"]
         category = args.get("category", "general")
@@ -54,11 +165,13 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
         memory_dir.mkdir(exist_ok=True)
 
         codebase_map_file = memory_dir / "codebase_map.json"
+        saved_to_graphiti = False
 
         try:
+            # PRIMARY: Save to file-based storage (always works)
             # Load existing map or create new
             if codebase_map_file.exists():
-                with open(codebase_map_file) as f:
+                with open(codebase_map_file, encoding="utf-8") as f:
                     codebase_map = json.load(f)
             else:
                 codebase_map = {
@@ -74,14 +187,26 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
             }
             codebase_map["last_updated"] = datetime.now(timezone.utc).isoformat()
 
-            with open(codebase_map_file, "w") as f:
+            with open(codebase_map_file, "w", encoding="utf-8") as f:
                 json.dump(codebase_map, f, indent=2)
 
+            # SECONDARY: Also save to Graphiti/LadybugDB (for Memory UI)
+            saved_to_graphiti = await _save_to_graphiti_async(
+                spec_dir,
+                project_dir,
+                "discovery",
+                {
+                    "file_path": file_path,
+                    "description": f"[{category}] {description}",
+                },
+            )
+
+            storage_note = " (also saved to memory graph)" if saved_to_graphiti else ""
             return {
                 "content": [
                     {
                         "type": "text",
-                        "text": f"Recorded discovery for '{file_path}': {description}",
+                        "text": f"Recorded discovery for '{file_path}': {description}{storage_note}",
                     }
                 ]
             }
@@ -102,7 +227,7 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
         {"gotcha": str, "context": str},
     )
     async def record_gotcha(args: dict[str, Any]) -> dict[str, Any]:
-        """Record a gotcha to session memory."""
+        """Record a gotcha to session memory (file + Graphiti)."""
         gotcha = args["gotcha"]
         context = args.get("context", "")
 
@@ -110,8 +235,10 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
         memory_dir.mkdir(exist_ok=True)
 
         gotchas_file = memory_dir / "gotchas.md"
+        saved_to_graphiti = False
 
         try:
+            # PRIMARY: Save to file-based storage (always works)
             timestamp = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M")
 
             entry = f"\n## [{timestamp}]\n{gotcha}"
@@ -119,14 +246,27 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
                 entry += f"\n\n_Context: {context}_"
             entry += "\n"
 
-            with open(gotchas_file, "a") as f:
+            with open(gotchas_file, "a", encoding="utf-8") as f:
                 if not gotchas_file.exists() or gotchas_file.stat().st_size == 0:
                     f.write(
                         "# Gotchas & Pitfalls\n\nThings to watch out for in this codebase.\n"
                     )
                 f.write(entry)
 
-            return {"content": [{"type": "text", "text": f"Recorded gotcha: {gotcha}"}]}
+            # SECONDARY: Also save to Graphiti/LadybugDB (for Memory UI)
+            saved_to_graphiti = await _save_to_graphiti_async(
+                spec_dir,
+                project_dir,
+                "gotcha",
+                {"gotcha": gotcha, "context": context},
+            )
+
+            storage_note = " (also saved to memory graph)" if saved_to_graphiti else ""
+            return {
+                "content": [
+                    {"type": "text", "text": f"Recorded gotcha: {gotcha}{storage_note}"}
+                ]
+            }
 
         except Exception as e:
             return {
@@ -163,7 +303,7 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
         codebase_map_file = memory_dir / "codebase_map.json"
         if codebase_map_file.exists():
             try:
-                with open(codebase_map_file) as f:
+                with open(codebase_map_file, encoding="utf-8") as f:
                     codebase_map = json.load(f)
 
                 discoveries = codebase_map.get("discovered_files", {})
@@ -179,7 +319,7 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
         gotchas_file = memory_dir / "gotchas.md"
         if gotchas_file.exists():
             try:
-                content = gotchas_file.read_text()
+                content = gotchas_file.read_text(encoding="utf-8")
                 if content.strip():
                     result_parts.append("\n## Gotchas")
                     # Take last 1000 chars to avoid too much context
@@ -193,7 +333,7 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
         patterns_file = memory_dir / "patterns.md"
         if patterns_file.exists():
             try:
-                content = patterns_file.read_text()
+                content = patterns_file.read_text(encoding="utf-8")
                 if content.strip():
                     result_parts.append("\n## Patterns")
                     result_parts.append(

apps/backend/agents/tools_pkg/tools/progress.py

@@ -57,7 +57,7 @@ def create_progress_tools(spec_dir: Path, project_dir: Path) -> list:
             }
 
         try:
-            with open(plan_file) as f:
+            with open(plan_file, encoding="utf-8") as f:
                 plan = json.load(f)
 
             stats = {

apps/backend/agents/tools_pkg/tools/qa.py

@@ -6,10 +6,14 @@ Tools for managing QA status and sign-off in implementation_plan.json.
 """
 
 import json
+import logging
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import Any
 
+from core.file_utils import write_json_atomic
+from spec.validate_pkg.auto_fix import auto_fix_plan
+
 try:
     from claude_agent_sdk import tool
 
@@ -19,6 +23,49 @@ except ImportError:
     tool = None
 
 
+def _apply_qa_update(
+    plan: dict[str, Any],
+    status: str,
+    issues: list[Any],
+    tests_passed: dict[str, Any],
+) -> int:
+    """
+    Apply QA update to the plan and return the new QA session number.
+
+    Args:
+        plan: The implementation plan dict
+        status: QA status (pending, in_review, approved, rejected, fixes_applied)
+        issues: List of issues found
+        tests_passed: Dict of test results
+
+    Returns:
+        The new QA session number
+    """
+    # Get current QA session number
+    current_qa = plan.get("qa_signoff", {})
+    qa_session = current_qa.get("qa_session", 0)
+    if status in ["in_review", "rejected"]:
+        qa_session += 1
+
+    plan["qa_signoff"] = {
+        "status": status,
+        "qa_session": qa_session,
+        "issues_found": issues,
+        "tests_passed": tests_passed,
+        "timestamp": datetime.now(timezone.utc).isoformat(),
+        "ready_for_qa_revalidation": status == "fixes_applied",
+    }
+
+    # NOTE: Do NOT write plan["status"] or plan["planStatus"] here.
+    # The frontend XState task state machine owns status transitions.
+    # Writing status here races with XState's persistPlanStatusAndReasonSync()
+    # and can clobber the reviewReason field, causing tasks to appear "incomplete".
+
+    plan["last_updated"] = datetime.now(timezone.utc).isoformat()
+
+    return qa_session
+
+
 def create_qa_tools(spec_dir: Path, project_dir: Path) -> list:
     """
     Create QA management tools.
@@ -89,37 +136,13 @@ def create_qa_tools(spec_dir: Path, project_dir: Path) -> list:
             except json.JSONDecodeError:
                 tests_passed = {}
 
-            with open(plan_file) as f:
+            with open(plan_file, encoding="utf-8") as f:
                 plan = json.load(f)
 
-            # Get current QA session number
-            current_qa = plan.get("qa_signoff", {})
-            qa_session = current_qa.get("qa_session", 0)
-            if status in ["in_review", "rejected"]:
-                qa_session += 1
+            qa_session = _apply_qa_update(plan, status, issues, tests_passed)
 
-            plan["qa_signoff"] = {
-                "status": status,
-                "qa_session": qa_session,
-                "issues_found": issues,
-                "tests_passed": tests_passed,
-                "timestamp": datetime.now(timezone.utc).isoformat(),
-                "ready_for_qa_revalidation": status == "fixes_applied",
-            }
-
-            # Update plan status to match QA result
-            # This ensures the UI shows the correct column after QA
-            if status == "approved":
-                plan["status"] = "human_review"
-                plan["planStatus"] = "review"
-            elif status == "rejected":
-                plan["status"] = "human_review"
-                plan["planStatus"] = "review"
-
-            plan["last_updated"] = datetime.now(timezone.utc).isoformat()
-
-            with open(plan_file, "w") as f:
-                json.dump(plan, f, indent=2)
+            # Use atomic write to prevent file corruption
+            write_json_atomic(plan_file, plan, indent=2)
 
             return {
                 "content": [
@@ -130,6 +153,47 @@ def create_qa_tools(spec_dir: Path, project_dir: Path) -> list:
                 ]
             }
 
+        except json.JSONDecodeError as e:
+            # Attempt to auto-fix the plan and retry
+            if auto_fix_plan(spec_dir):
+                # Retry after fix
+                try:
+                    with open(plan_file, encoding="utf-8") as f:
+                        plan = json.load(f)
+
+                    qa_session = _apply_qa_update(plan, status, issues, tests_passed)
+                    write_json_atomic(plan_file, plan, indent=2)
+
+                    return {
+                        "content": [
+                            {
+                                "type": "text",
+                                "text": f"Updated QA status to '{status}' (session {qa_session}) (after auto-fix)",
+                            }
+                        ]
+                    }
+                except Exception as retry_err:
+                    logging.warning(
+                        f"QA update retry failed after auto-fix: {retry_err} (original error: {e})"
+                    )
+                    return {
+                        "content": [
+                            {
+                                "type": "text",
+                                "text": f"Error: QA update failed after auto-fix: {retry_err} (original JSON error: {e})",
+                            }
+                        ]
+                    }
+
+            return {
+                "content": [
+                    {
+                        "type": "text",
+                        "text": f"Error: Invalid JSON in implementation_plan.json: {e}",
+                    }
+                ]
+            }
+
         except Exception as e:
             return {
                 "content": [{"type": "text", "text": f"Error updating QA status: {e}"}]

apps/backend/agents/tools_pkg/tools/subtask.py

@@ -6,10 +6,14 @@ Tools for managing subtask status in implementation_plan.json.
 """
 
 import json
+import logging
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import Any
 
+from core.file_utils import write_json_atomic
+from spec.validate_pkg.auto_fix import auto_fix_plan
+
 try:
     from claude_agent_sdk import tool
 
@@ -19,6 +23,43 @@ except ImportError:
     tool = None
 
 
+def _update_subtask_in_plan(
+    plan: dict[str, Any],
+    subtask_id: str,
+    status: str,
+    notes: str,
+) -> bool:
+    """
+    Update a subtask in the plan.
+
+    Args:
+        plan: The implementation plan dict
+        subtask_id: ID of the subtask to update
+        status: New status (pending, in_progress, completed, failed)
+        notes: Optional notes to add
+
+    Returns:
+        True if subtask was found and updated, False otherwise
+    """
+    subtask_found = False
+    for phase in plan.get("phases", []):
+        for subtask in phase.get("subtasks", []):
+            if subtask.get("id") == subtask_id:
+                subtask["status"] = status
+                if notes:
+                    subtask["notes"] = notes
+                subtask["updated_at"] = datetime.now(timezone.utc).isoformat()
+                subtask_found = True
+                break
+        if subtask_found:
+            break
+
+    if subtask_found:
+        plan["last_updated"] = datetime.now(timezone.utc).isoformat()
+
+    return subtask_found
+
+
 def create_subtask_tools(spec_dir: Path, project_dir: Path) -> list:
     """
     Create subtask management tools.
@@ -72,22 +113,10 @@ def create_subtask_tools(spec_dir: Path, project_dir: Path) -> list:
             }
 
         try:
-            with open(plan_file) as f:
+            with open(plan_file, encoding="utf-8") as f:
                 plan = json.load(f)
 
-            # Find and update the subtask
-            subtask_found = False
-            for phase in plan.get("phases", []):
-                for subtask in phase.get("subtasks", []):
-                    if subtask.get("id") == subtask_id:
-                        subtask["status"] = status
-                        if notes:
-                            subtask["notes"] = notes
-                        subtask["updated_at"] = datetime.now(timezone.utc).isoformat()
-                        subtask_found = True
-                        break
-                if subtask_found:
-                    break
+            subtask_found = _update_subtask_in_plan(plan, subtask_id, status, notes)
 
             if not subtask_found:
                 return {
@@ -99,11 +128,8 @@ def create_subtask_tools(spec_dir: Path, project_dir: Path) -> list:
                     ]
                 }
 
-            # Update plan metadata
-            plan["last_updated"] = datetime.now(timezone.utc).isoformat()
-
-            with open(plan_file, "w") as f:
-                json.dump(plan, f, indent=2)
+            # Use atomic write to prevent file corruption
+            write_json_atomic(plan_file, plan, indent=2)
 
             return {
                 "content": [
@@ -115,6 +141,49 @@ def create_subtask_tools(spec_dir: Path, project_dir: Path) -> list:
             }
 
         except json.JSONDecodeError as e:
+            # Attempt to auto-fix the plan and retry
+            if auto_fix_plan(spec_dir):
+                # Retry after fix
+                try:
+                    with open(plan_file, encoding="utf-8") as f:
+                        plan = json.load(f)
+
+                    subtask_found = _update_subtask_in_plan(
+                        plan, subtask_id, status, notes
+                    )
+
+                    if subtask_found:
+                        write_json_atomic(plan_file, plan, indent=2)
+                        return {
+                            "content": [
+                                {
+                                    "type": "text",
+                                    "text": f"Successfully updated subtask '{subtask_id}' to status '{status}' (after auto-fix)",
+                                }
+                            ]
+                        }
+                    else:
+                        return {
+                            "content": [
+                                {
+                                    "type": "text",
+                                    "text": f"Error: Subtask '{subtask_id}' not found in implementation plan (after auto-fix)",
+                                }
+                            ]
+                        }
+                except Exception as retry_err:
+                    logging.warning(
+                        f"Subtask update retry failed after auto-fix: {retry_err}"
+                    )
+                    return {
+                        "content": [
+                            {
+                                "type": "text",
+                                "text": f"Error: Subtask update failed after auto-fix: {retry_err}",
+                            }
+                        ]
+                    }
+
             return {
                 "content": [
                     {

apps/backend/agents/utils.py

@@ -8,40 +8,38 @@ Helper functions for git operations, plan management, and file syncing.
 import json
 import logging
 import shutil
-import subprocess
 from pathlib import Path
 
+from core.git_executable import run_git
+
 logger = logging.getLogger(__name__)
 
 
 def get_latest_commit(project_dir: Path) -> str | None:
     """Get the hash of the latest git commit."""
-    try:
-        result = subprocess.run(
-            ["git", "rev-parse", "HEAD"],
-            cwd=project_dir,
-            capture_output=True,
-            text=True,
-            check=True,
-        )
+    result = run_git(
+        ["rev-parse", "HEAD"],
+        cwd=project_dir,
+        timeout=10,
+    )
+    if result.returncode == 0:
         return result.stdout.strip()
-    except subprocess.CalledProcessError:
-        return None
+    return None
 
 
 def get_commit_count(project_dir: Path) -> int:
     """Get the total number of commits."""
-    try:
-        result = subprocess.run(
-            ["git", "rev-list", "--count", "HEAD"],
-            cwd=project_dir,
-            capture_output=True,
-            text=True,
-            check=True,
-        )
-        return int(result.stdout.strip())
-    except (subprocess.CalledProcessError, ValueError):
-        return 0
+    result = run_git(
+        ["rev-list", "--count", "HEAD"],
+        cwd=project_dir,
+        timeout=10,
+    )
+    if result.returncode == 0:
+        try:
+            return int(result.stdout.strip())
+        except ValueError:
+            return 0
+    return 0
 
 
 def load_implementation_plan(spec_dir: Path) -> dict | None:
@@ -50,9 +48,9 @@ def load_implementation_plan(spec_dir: Path) -> dict | None:
     if not plan_file.exists():
         return None
     try:
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             return json.load(f)
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return None
 
 
@@ -74,16 +72,32 @@ def find_phase_for_subtask(plan: dict, subtask_id: str) -> dict | None:
     return None
 
 
-def sync_plan_to_source(spec_dir: Path, source_spec_dir: Path | None) -> bool:
+def sync_spec_to_source(spec_dir: Path, source_spec_dir: Path | None) -> bool:
     """
-    Sync implementation_plan.json from worktree back to source spec directory.
+    Sync ALL spec files from worktree back to source spec directory.
 
-    When running in isolated mode (worktrees), the agent updates the implementation
-    plan inside the worktree. This function syncs those changes back to the main
-    project's spec directory so the frontend/UI can see the progress.
+    When running in isolated mode (worktrees), the agent creates and updates
+    many files inside the worktree's spec directory. This function syncs ALL
+    of them back to the main project's spec directory.
+
+    IMPORTANT: Since .auto-claude/ is gitignored, this sync happens to the
+    local filesystem regardless of what branch the user is on. The worktree
+    may be on a different branch (e.g., auto-claude/093-task), but the sync
+    target is always the main project's .auto-claude/specs/ directory.
+
+    Files synced (all files in spec directory):
+    - implementation_plan.json - Task status and subtask completion
+    - build-progress.txt - Session-by-session progress notes
+    - task_logs.json - Execution logs
+    - review_state.json - QA review state
+    - critique_report.json - Spec critique findings
+    - suggested_commit_message.txt - Commit suggestions
+    - REGRESSION_TEST_REPORT.md - Test regression report
+    - spec.md, context.json, etc. - Original spec files (for completeness)
+    - memory/ directory - Codebase map, patterns, gotchas, session insights
 
     Args:
-        spec_dir: Current spec directory (may be inside worktree)
+        spec_dir: Current spec directory (inside worktree)
         source_spec_dir: Original spec directory in main project (outside worktree)
 
     Returns:
@@ -100,17 +114,68 @@ def sync_plan_to_source(spec_dir: Path, source_spec_dir: Path | None) -> bool:
     if spec_dir_resolved == source_spec_dir_resolved:
         return False  # Same directory, no sync needed
 
-    # Sync the implementation plan
-    plan_file = spec_dir / "implementation_plan.json"
-    if not plan_file.exists():
-        return False
+    synced_any = False
 
-    source_plan_file = source_spec_dir / "implementation_plan.json"
+    # Ensure source directory exists
+    source_spec_dir.mkdir(parents=True, exist_ok=True)
 
     try:
-        shutil.copy2(plan_file, source_plan_file)
-        logger.debug(f"Synced implementation plan to source: {source_plan_file}")
-        return True
+        # Sync all files and directories from worktree spec to source spec
+        for item in spec_dir.iterdir():
+            # Skip symlinks to prevent path traversal attacks
+            if item.is_symlink():
+                logger.warning(f"Skipping symlink during sync: {item.name}")
+                continue
+
+            source_item = source_spec_dir / item.name
+
+            if item.is_file():
+                # Copy file (preserves timestamps)
+                shutil.copy2(item, source_item)
+                logger.debug(f"Synced {item.name} to source")
+                synced_any = True
+
+            elif item.is_dir():
+                # Recursively sync directory
+                _sync_directory(item, source_item)
+                synced_any = True
+
     except Exception as e:
-        logger.warning(f"Failed to sync implementation plan to source: {e}")
-        return False
+        logger.warning(f"Failed to sync spec directory to source: {e}")
+
+    return synced_any
+
+
+def _sync_directory(source_dir: Path, target_dir: Path) -> None:
+    """
+    Recursively sync a directory from source to target.
+
+    Args:
+        source_dir: Source directory (in worktree)
+        target_dir: Target directory (in main project)
+    """
+    # Create target directory if needed
+    target_dir.mkdir(parents=True, exist_ok=True)
+
+    for item in source_dir.iterdir():
+        # Skip symlinks to prevent path traversal attacks
+        if item.is_symlink():
+            logger.warning(
+                f"Skipping symlink during sync: {source_dir.name}/{item.name}"
+            )
+            continue
+
+        target_item = target_dir / item.name
+
+        if item.is_file():
+            shutil.copy2(item, target_item)
+            logger.debug(f"Synced {source_dir.name}/{item.name} to source")
+        elif item.is_dir():
+            # Recurse into subdirectories
+            _sync_directory(item, target_item)
+
+
+# Keep the old name as an alias for backward compatibility
+def sync_plan_to_source(spec_dir: Path, source_spec_dir: Path | None) -> bool:
+    """Alias for sync_spec_to_source for backward compatibility."""
+    return sync_spec_to_source(spec_dir, source_spec_dir)

apps/backend/analysis/__init__.py

@@ -23,7 +23,8 @@ from .ci_discovery import CIDiscovery
 from .project_analyzer import ProjectAnalyzer
 from .risk_classifier import RiskClassifier
 from .security_scanner import SecurityScanner
-from .test_discovery import TestDiscovery
+
+# TestDiscovery was removed - tests are now co-located in their respective modules
 
 # insight_extractor is a module with functions, not a class, so don't import it here
 # Import it directly when needed: from analysis import insight_extractor
@@ -37,5 +38,5 @@ __all__ = [
     "RiskClassifier",
     "SecurityScanner",
     "CIDiscovery",
-    "TestDiscovery",
+    # "TestDiscovery",  # Removed - tests now co-located in their modules
 ]

apps/backend/analysis/analyzers/__init__.py

@@ -46,7 +46,7 @@ def analyze_project(project_dir: Path, output_file: Path | None = None) -> dict:
 
     if output_file:
         output_file.parent.mkdir(parents=True, exist_ok=True)
-        with open(output_file, "w") as f:
+        with open(output_file, "w", encoding="utf-8") as f:
             json.dump(results, f, indent=2)
         print(f"Project index saved to: {output_file}")
 
@@ -87,7 +87,7 @@ def analyze_service(
 
     if output_file:
         output_file.parent.mkdir(parents=True, exist_ok=True)
-        with open(output_file, "w") as f:
+        with open(output_file, "w", encoding="utf-8") as f:
             json.dump(results, f, indent=2)
         print(f"Service analysis saved to: {output_file}")
 

apps/backend/analysis/analyzers/base.py

@@ -99,7 +99,7 @@ class BaseAnalyzer:
     def _read_file(self, path: str) -> str:
         """Read a file relative to the analyzer's path."""
         try:
-            return (self.path / path).read_text()
+            return (self.path / path).read_text(encoding="utf-8")
         except (OSError, UnicodeDecodeError):
             return ""
 

apps/backend/analysis/analyzers/context/auth_detector.py

@@ -126,7 +126,7 @@ class AuthDetector(BaseAnalyzer):
 
         for py_file in all_py_files:
             try:
-                content = py_file.read_text()
+                content = py_file.read_text(encoding="utf-8")
                 # Find custom decorators
                 if (
                     "@require" in content

apps/backend/analysis/analyzers/context/jobs_detector.py

@@ -52,7 +52,7 @@ class JobsDetector(BaseAnalyzer):
         tasks = []
         for task_file in celery_files:
             try:
-                content = task_file.read_text()
+                content = task_file.read_text(encoding="utf-8")
                 # Find @celery.task or @shared_task decorators
                 task_pattern = r"@(?:celery\.task|shared_task|app\.task)\s*(?:\([^)]*\))?\s*def\s+(\w+)"
                 task_matches = re.findall(task_pattern, content)

apps/backend/analysis/analyzers/context/monitoring_detector.py

@@ -77,7 +77,7 @@ class MonitoringDetector(BaseAnalyzer):
                 continue
 
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
                 # Look for actual Prometheus imports or usage patterns
                 prometheus_patterns = [
                     "from prometheus_client import",

apps/backend/analysis/analyzers/database_detector.py

@@ -52,7 +52,7 @@ class DatabaseDetector(BaseAnalyzer):
 
         for file_path in py_files:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -119,7 +119,7 @@ class DatabaseDetector(BaseAnalyzer):
 
         for file_path in model_files:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -168,7 +168,7 @@ class DatabaseDetector(BaseAnalyzer):
             return models
 
         try:
-            content = schema_file.read_text()
+            content = schema_file.read_text(encoding="utf-8")
         except (OSError, UnicodeDecodeError):
             return models
 
@@ -216,7 +216,7 @@ class DatabaseDetector(BaseAnalyzer):
 
         for file_path in ts_files:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -265,7 +265,7 @@ class DatabaseDetector(BaseAnalyzer):
 
         for file_path in schema_files:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -295,7 +295,7 @@ class DatabaseDetector(BaseAnalyzer):
 
         for file_path in model_files:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 

apps/backend/analysis/analyzers/framework_analyzer.py

@@ -75,6 +75,15 @@ class FrameworkAnalyzer(BaseAnalyzer):
             content = self._read_file("Cargo.toml")
             self._detect_rust_framework(content)
 
+        # Swift/iOS detection (check BEFORE Ruby - iOS projects often have Gemfile for CocoaPods/Fastlane)
+        elif self._exists("Package.swift") or any(self.path.glob("*.xcodeproj")):
+            self.analysis["language"] = "Swift"
+            if self._exists("Package.swift"):
+                self.analysis["package_manager"] = "Swift Package Manager"
+            else:
+                self.analysis["package_manager"] = "Xcode"
+            self._detect_swift_framework()
+
         # Ruby detection
         elif self._exists("Gemfile"):
             self.analysis["language"] = "Ruby"
@@ -226,10 +235,15 @@ class FrameworkAnalyzer(BaseAnalyzer):
 
         # Scripts
         scripts = pkg.get("scripts", {})
+        pkg_mgr = self.analysis.get("package_manager", "npm")
         if "dev" in scripts:
-            self.analysis["dev_command"] = "npm run dev"
+            self.analysis["dev_command"] = f"{pkg_mgr} run dev"
         elif "start" in scripts:
-            self.analysis["dev_command"] = "npm run start"
+            self.analysis["dev_command"] = f"{pkg_mgr} run start"
+
+        # Capture available scripts for downstream consumers (QA agents, init.sh)
+        if scripts:
+            self.analysis["scripts"] = dict(scripts)
 
     def _detect_go_framework(self, content: str) -> None:
         """Detect Go framework."""
@@ -290,12 +304,115 @@ class FrameworkAnalyzer(BaseAnalyzer):
         if "sidekiq" in content.lower():
             self.analysis["task_queue"] = "Sidekiq"
 
+    def _detect_swift_framework(self) -> None:
+        """Detect Swift/iOS framework and dependencies."""
+        try:
+            # Scan Swift files for imports, excluding hidden/vendor dirs
+            swift_files = []
+            for swift_file in self.path.rglob("*.swift"):
+                # Skip hidden directories, node_modules, .worktrees, etc.
+                if any(
+                    part.startswith(".") or part in ("node_modules", "Pods", "Carthage")
+                    for part in swift_file.parts
+                ):
+                    continue
+                swift_files.append(swift_file)
+                if len(swift_files) >= 50:  # Limit for performance
+                    break
+
+            imports = set()
+            for swift_file in swift_files:
+                try:
+                    content = swift_file.read_text(encoding="utf-8", errors="ignore")
+                    for line in content.split("\n"):
+                        line = line.strip()
+                        if line.startswith("import "):
+                            module = line.replace("import ", "").split()[0]
+                            imports.add(module)
+                except Exception:
+                    continue
+
+            # Detect UI framework
+            if "SwiftUI" in imports:
+                self.analysis["framework"] = "SwiftUI"
+                self.analysis["type"] = "mobile"
+            elif "UIKit" in imports:
+                self.analysis["framework"] = "UIKit"
+                self.analysis["type"] = "mobile"
+            elif "AppKit" in imports:
+                self.analysis["framework"] = "AppKit"
+                self.analysis["type"] = "desktop"
+
+            # Detect iOS/Apple frameworks
+            apple_frameworks = []
+            framework_map = {
+                "Combine": "Combine",
+                "CoreData": "CoreData",
+                "MapKit": "MapKit",
+                "WidgetKit": "WidgetKit",
+                "CoreLocation": "CoreLocation",
+                "StoreKit": "StoreKit",
+                "CloudKit": "CloudKit",
+                "ActivityKit": "ActivityKit",
+                "UserNotifications": "UserNotifications",
+            }
+            for key, name in framework_map.items():
+                if key in imports:
+                    apple_frameworks.append(name)
+
+            if apple_frameworks:
+                self.analysis["apple_frameworks"] = apple_frameworks
+
+            # Detect SPM dependencies from Package.swift or xcodeproj
+            dependencies = self._detect_spm_dependencies()
+            if dependencies:
+                self.analysis["spm_dependencies"] = dependencies
+        except Exception:
+            # Silently fail if Swift detection has issues
+            pass
+
+    def _detect_spm_dependencies(self) -> list[str]:
+        """Detect Swift Package Manager dependencies."""
+        dependencies = []
+
+        # Try Package.swift first
+        if self._exists("Package.swift"):
+            content = self._read_file("Package.swift")
+            # Look for .package(url: "...", patterns
+            import re
+
+            urls = re.findall(r'\.package\s*\([^)]*url:\s*"([^"]+)"', content)
+            for url in urls:
+                # Extract package name from URL
+                name = url.rstrip("/").split("/")[-1].replace(".git", "")
+                if name:
+                    dependencies.append(name)
+
+        # Also check xcodeproj for XCRemoteSwiftPackageReference
+        for xcodeproj in self.path.glob("*.xcodeproj"):
+            pbxproj = xcodeproj / "project.pbxproj"
+            if pbxproj.exists():
+                try:
+                    content = pbxproj.read_text(encoding="utf-8", errors="ignore")
+                    import re
+
+                    # Match repositoryURL patterns
+                    urls = re.findall(r'repositoryURL\s*=\s*"([^"]+)"', content)
+                    for url in urls:
+                        name = url.rstrip("/").split("/")[-1].replace(".git", "")
+                        if name and name not in dependencies:
+                            dependencies.append(name)
+                except Exception:
+                    continue
+
+        return dependencies
+
     def _detect_node_package_manager(self) -> str:
         """Detect Node.js package manager."""
         if self._exists("pnpm-lock.yaml"):
             return "pnpm"
         elif self._exists("yarn.lock"):
             return "yarn"
-        elif self._exists("bun.lockb"):
+        elif self._exists("bun.lockb") or self._exists("bun.lock"):
             return "bun"
         return "npm"

apps/backend/analysis/analyzers/project_analyzer_module.py

@@ -31,6 +31,7 @@ class ProjectAnalyzer:
         """Run full project analysis."""
         self._detect_project_type()
         self._find_and_analyze_services()
+        self._aggregate_dependency_locations()
         self._analyze_infrastructure()
         self._detect_conventions()
         self._map_dependencies()
@@ -124,6 +125,63 @@ class ProjectAnalyzer:
 
         self.index["services"] = services
 
+    def _aggregate_dependency_locations(self) -> None:
+        """Aggregate dependency location metadata from all services.
+
+        Collects dependency_locations from each service and stores them as
+        paths relative to the project root (e.g., 'apps/backend/.venv'
+        instead of just '.venv').
+        """
+        aggregated: list[dict[str, Any]] = []
+
+        for service_name, service_info in self.index.get("services", {}).items():
+            service_deps = service_info.get("dependency_locations", [])
+            service_path = service_info.get("path", "")
+
+            # Compute service-relative prefix once per service
+            service_rel: Path | None = None
+            if service_path:
+                try:
+                    service_rel = Path(service_path).relative_to(self.project_dir)
+                except ValueError:
+                    # Service path is outside the project root — skip its deps
+                    # to avoid producing absolute paths that bypass containment
+                    continue
+
+            for dep in service_deps:
+                dep_path = dep.get("path")
+                if not dep_path:
+                    continue
+
+                # Build project-relative path from service path + dep path
+                if service_rel is not None:
+                    project_relative = str(service_rel / dep_path)
+                else:
+                    project_relative = dep_path
+
+                entry: dict[str, Any] = {
+                    "type": dep.get("type", "unknown"),
+                    "path": project_relative,
+                    "exists": dep.get("exists", False),
+                    "service": service_name,
+                }
+                if dep.get("requirements_file"):
+                    # Convert to project-relative path like we do for "path"
+                    if service_rel is not None:
+                        entry["requirements_file"] = str(
+                            service_rel / dep["requirements_file"]
+                        )
+                    else:
+                        entry["requirements_file"] = dep["requirements_file"]
+                pkg_mgr = dep.get("package_manager") or service_info.get(
+                    "package_manager"
+                )
+                if pkg_mgr:
+                    entry["package_manager"] = pkg_mgr
+                aggregated.append(entry)
+
+        self.index["dependency_locations"] = aggregated
+
     def _analyze_infrastructure(self) -> None:
         """Analyze infrastructure configuration."""
         infra = {}
@@ -287,6 +345,6 @@ class ProjectAnalyzer:
 
     def _read_file(self, path: str) -> str:
         try:
-            return (self.project_dir / path).read_text()
+            return (self.project_dir / path).read_text(encoding="utf-8")
         except (OSError, UnicodeDecodeError):
             return ""

apps/backend/analysis/analyzers/route_detector.py

@@ -66,7 +66,7 @@ class RouteDetector(BaseAnalyzer):
 
         for file_path in files_to_check:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -130,7 +130,7 @@ class RouteDetector(BaseAnalyzer):
 
         for file_path in files_to_check:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -179,7 +179,7 @@ class RouteDetector(BaseAnalyzer):
 
         for file_path in url_files:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -218,7 +218,7 @@ class RouteDetector(BaseAnalyzer):
         files_to_check = js_files + ts_files
         for file_path in files_to_check:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -283,7 +283,7 @@ class RouteDetector(BaseAnalyzer):
                 route_path = re.sub(r"\[([^\]]+)\]", r":\1", route_path)
 
                 try:
-                    content = route_file.read_text()
+                    content = route_file.read_text(encoding="utf-8")
                     # Detect exported methods: export async function GET(request)
                     methods = re.findall(
                         r"export\s+(?:async\s+)?function\s+(GET|POST|PUT|DELETE|PATCH)",
@@ -348,7 +348,7 @@ class RouteDetector(BaseAnalyzer):
 
         for file_path in go_files:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 
@@ -384,7 +384,7 @@ class RouteDetector(BaseAnalyzer):
 
         for file_path in rust_files:
             try:
-                content = file_path.read_text()
+                content = file_path.read_text(encoding="utf-8")
             except (OSError, UnicodeDecodeError):
                 continue
 

apps/backend/analysis/analyzers/service_analyzer.py

@@ -40,6 +40,8 @@ class ServiceAnalyzer(BaseAnalyzer):
         self._find_key_directories()
         self._find_entry_points()
         self._detect_dependencies()
+        self._detect_dependency_locations()
+        self._detect_package_manager()
         self._detect_testing()
         self._find_dockerfile()
 
@@ -209,6 +211,121 @@ class ServiceAnalyzer(BaseAnalyzer):
                         deps.append(match.group(1))
             self.analysis["dependencies"] = deps[:20]
 
+    def _detect_dependency_locations(self) -> None:
+        """Detect where dependencies live on disk for this service."""
+        locations: list[dict[str, Any]] = []
+
+        # Node.js: node_modules (only if package.json exists)
+        if self._exists("package.json"):
+            node_modules = self.path / "node_modules"
+            locations.append(
+                {
+                    "type": "node_modules",
+                    "path": "node_modules",
+                    "exists": node_modules.exists() and node_modules.is_dir(),
+                }
+            )
+
+        # Python: .venv or venv
+        for venv_dir in [".venv", "venv"]:
+            venv_path = self.path / venv_dir
+            if venv_path.exists() and venv_path.is_dir():
+                entry: dict[str, Any] = {
+                    "type": "venv",
+                    "path": venv_dir,
+                    "exists": True,
+                }
+                # Find requirements file
+                for req_file in ["requirements.txt", "pyproject.toml", "Pipfile"]:
+                    if self._exists(req_file):
+                        entry["requirements_file"] = req_file
+                        break
+                locations.append(entry)
+                break
+        else:
+            # No venv found, still record requirements file if present
+            for req_file in ["requirements.txt", "pyproject.toml", "Pipfile"]:
+                if self._exists(req_file):
+                    locations.append(
+                        {
+                            "type": "venv",
+                            "path": ".venv",
+                            "exists": False,
+                            "requirements_file": req_file,
+                        }
+                    )
+                    break
+
+        # PHP: vendor
+        vendor_path = self.path / "vendor"
+        if vendor_path.exists() and vendor_path.is_dir():
+            locations.append(
+                {
+                    "type": "vendor_php",
+                    "path": "vendor",
+                    "exists": True,
+                }
+            )
+
+        # Rust: target
+        target_path = self.path / "target"
+        if target_path.exists() and target_path.is_dir():
+            locations.append(
+                {
+                    "type": "cargo_target",
+                    "path": "target",
+                    "exists": True,
+                }
+            )
+
+        # Ruby: vendor/bundle
+        bundle_path = self.path / "vendor" / "bundle"
+        if bundle_path.exists() and bundle_path.is_dir():
+            locations.append(
+                {
+                    "type": "vendor_bundle",
+                    "path": "vendor/bundle",
+                    "exists": True,
+                }
+            )
+
+        self.analysis["dependency_locations"] = locations
+
+    def _detect_package_manager(self) -> None:
+        """Detect the package manager used by this service."""
+        # Node.js package managers
+        if self._exists("package-lock.json"):
+            self.analysis["package_manager"] = "npm"
+        elif self._exists("yarn.lock"):
+            self.analysis["package_manager"] = "yarn"
+        elif self._exists("pnpm-lock.yaml"):
+            self.analysis["package_manager"] = "pnpm"
+        elif self._exists("bun.lockb") or self._exists("bun.lock"):
+            self.analysis["package_manager"] = "bun"
+        # Python package managers
+        elif self._exists("Pipfile"):
+            self.analysis["package_manager"] = "pipenv"
+        elif self._exists("pyproject.toml"):
+            if self._exists("uv.lock"):
+                self.analysis["package_manager"] = "uv"
+            elif self._exists("poetry.lock"):
+                self.analysis["package_manager"] = "poetry"
+            else:
+                self.analysis["package_manager"] = "pip"
+        elif self._exists("requirements.txt"):
+            self.analysis["package_manager"] = "pip"
+        # Other
+        elif self._exists("Cargo.toml"):
+            self.analysis["package_manager"] = "cargo"
+        elif self._exists("go.mod"):
+            self.analysis["package_manager"] = "go_mod"
+        elif self._exists("Gemfile"):
+            self.analysis["package_manager"] = "gem"
+        elif self._exists("composer.json"):
+            self.analysis["package_manager"] = "composer"
+        else:
+            self.analysis["package_manager"] = None
+
     def _detect_testing(self) -> None:
         """Detect testing framework and configuration."""
         if self._exists("package.json"):

apps/backend/analysis/ci_discovery.py

@@ -163,7 +163,7 @@ class CIDiscovery:
             )
 
             try:
-                content = wf_file.read_text()
+                content = wf_file.read_text(encoding="utf-8")
                 workflow_data = self._parse_yaml(content)
 
                 if not workflow_data:
@@ -242,7 +242,7 @@ class CIDiscovery:
         )
 
         try:
-            content = config_file.read_text()
+            content = config_file.read_text(encoding="utf-8")
             data = self._parse_yaml(content)
 
             if not data:
@@ -312,7 +312,7 @@ class CIDiscovery:
         )
 
         try:
-            content = config_file.read_text()
+            content = config_file.read_text(encoding="utf-8")
             data = self._parse_yaml(content)
 
             if not data:
@@ -370,7 +370,7 @@ class CIDiscovery:
         )
 
         try:
-            content = jenkinsfile.read_text()
+            content = jenkinsfile.read_text(encoding="utf-8")
 
             # Extract sh commands using regex
             sh_pattern = re.compile(r'sh\s+[\'"]([^\'"]+)[\'"]')

apps/backend/analysis/insight_extractor.py

@@ -33,7 +33,9 @@ except ImportError:
 from core.auth import ensure_claude_code_oauth_token, get_auth_token
 
 # Default model for insight extraction (fast and cheap)
-DEFAULT_EXTRACTION_MODEL = "claude-3-5-haiku-latest"
+# Note: Using Haiku 4.5 for fast, cheap extraction. Haiku does not support
+# extended thinking, so thinking_default is set to "none" in models.py
+DEFAULT_EXTRACTION_MODEL = "claude-haiku-4-5-20251001"
 
 # Maximum diff size to send to the LLM (avoid context limits)
 MAX_DIFF_CHARS = 15000
@@ -235,7 +237,7 @@ def _get_subtask_description(spec_dir: Path, subtask_id: str) -> str:
         return f"Subtask: {subtask_id}"
 
     try:
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             plan = json.load(f)
 
         # Search through phases for the subtask
@@ -278,7 +280,7 @@ def _build_extraction_prompt(inputs: dict) -> str:
     prompt_file = Path(__file__).parent / "prompts" / "insight_extractor.md"
 
     if prompt_file.exists():
-        base_prompt = prompt_file.read_text()
+        base_prompt = prompt_file.read_text(encoding="utf-8")
     else:
         # Fallback if prompt file missing
         base_prompt = """Extract structured insights from this coding session.
@@ -366,19 +368,19 @@ async def run_insight_extraction(
     cwd = str(project_dir.resolve()) if project_dir else os.getcwd()
 
     try:
-        # Create a minimal SDK client for insight extraction
-        # No tools needed - just text generation
-        client = ClaudeSDKClient(
-            options=ClaudeAgentOptions(
-                model=model,
-                system_prompt=(
-                    "You are an expert code analyst. You extract structured insights from coding sessions. "
-                    "Always respond with valid JSON only, no markdown formatting or explanations."
-                ),
-                allowed_tools=[],  # No tools needed for extraction
-                max_turns=1,  # Single turn extraction
-                cwd=cwd,
-            )
+        # Use simple_client for insight extraction
+        from pathlib import Path
+
+        from core.simple_client import create_simple_client
+
+        client = create_simple_client(
+            agent_type="insights",
+            model=model,
+            system_prompt=(
+                "You are an expert code analyst. You extract structured insights from coding sessions. "
+                "Always respond with valid JSON only, no markdown formatting or explanations."
+            ),
+            cwd=Path(cwd) if cwd else None,
         )
 
         # Use async context manager
@@ -387,12 +389,40 @@ async def run_insight_extraction(
 
             # Collect the response
             response_text = ""
+            message_count = 0
+            text_blocks_found = 0
+
             async for msg in client.receive_response():
                 msg_type = type(msg).__name__
+                message_count += 1
+
                 if msg_type == "AssistantMessage" and hasattr(msg, "content"):
                     for block in msg.content:
-                        if hasattr(block, "text"):
-                            response_text += block.text
+                        # Must check block type - only TextBlock has .text attribute
+                        block_type = type(block).__name__
+                        if block_type == "TextBlock" and hasattr(block, "text"):
+                            text_blocks_found += 1
+                            if block.text:  # Only add non-empty text
+                                response_text += block.text
+                            else:
+                                logger.debug(
+                                    f"Found empty TextBlock in response (block #{text_blocks_found})"
+                                )
+
+            # Log response collection summary
+            logger.debug(
+                f"Insight extraction response: {message_count} messages, "
+                f"{text_blocks_found} text blocks, {len(response_text)} chars collected"
+            )
+
+            # Validate we received content before parsing
+            if not response_text.strip():
+                logger.warning(
+                    f"Insight extraction returned empty response. "
+                    f"Messages received: {message_count}, TextBlocks found: {text_blocks_found}. "
+                    f"This may indicate the AI model did not respond with text content."
+                )
+                return None
 
         # Parse JSON from response
         return parse_insights(response_text)
@@ -415,6 +445,11 @@ def parse_insights(response_text: str) -> dict | None:
     # Try to extract JSON from the response
     text = response_text.strip()
 
+    # Early validation - check for empty response
+    if not text:
+        logger.warning("Cannot parse insights: response text is empty")
+        return None
+
     # Handle markdown code blocks
     if text.startswith("```"):
         # Remove code block markers
@@ -422,17 +457,26 @@ def parse_insights(response_text: str) -> dict | None:
         # Remove first line (```json or ```)
         if lines[0].startswith("```"):
             lines = lines[1:]
-        # Remove last line if it's ``
+        # Remove last line if it's ```
         if lines and lines[-1].strip() == "```":
             lines = lines[:-1]
-        text = "\n".join(lines)
+        text = "\n".join(lines).strip()
+
+        # Check again after removing code blocks
+        if not text:
+            logger.warning(
+                "Cannot parse insights: response contained only markdown code block markers with no content"
+            )
+            return None
 
     try:
         insights = json.loads(text)
 
         # Validate structure
         if not isinstance(insights, dict):
-            logger.warning("Insights is not a dict")
+            logger.warning(
+                f"Insights is not a dict, got type: {type(insights).__name__}"
+            )
             return None
 
         # Ensure required keys exist with defaults
@@ -446,7 +490,13 @@ def parse_insights(response_text: str) -> dict | None:
 
     except json.JSONDecodeError as e:
         logger.warning(f"Failed to parse insights JSON: {e}")
-        logger.debug(f"Response text was: {text[:500]}")
+        # Show more context in the error message
+        preview_length = min(500, len(text))
+        logger.warning(
+            f"Response text preview (first {preview_length} chars): {text[:preview_length]}"
+        )
+        if len(text) > preview_length:
+            logger.warning(f"... (total length: {len(text)} chars)")
         return None
 
 

apps/backend/analysis/test_discovery.py

@@ -1,690 +0,0 @@
-#!/usr/bin/env python3
-"""
-Test Discovery Module
-=====================
-
-Detects test frameworks, test commands, and test directories in a project.
-This module analyzes project configuration files to discover how tests
-should be run.
-
-The test discovery results are used by:
-- QA Agent: To determine what test commands to run
-- Test Creator: To know what framework to use when creating tests
-- Planner: To include correct test commands in verification strategy
-
-Usage:
-    from test_discovery import TestDiscovery
-
-    discovery = TestDiscovery()
-    result = discovery.discover(project_dir)
-
-    print(f"Test frameworks: {result['frameworks']}")
-    print(f"Test command: {result['test_command']}")
-"""
-
-from __future__ import annotations
-
-import json
-from dataclasses import dataclass, field
-from pathlib import Path
-from typing import Any
-
-# =============================================================================
-# DATA CLASSES
-# =============================================================================
-
-
-@dataclass
-class TestFramework:
-    """
-    Represents a detected test framework.
-
-    Attributes:
-        name: Name of the framework (e.g., "pytest", "jest", "vitest")
-        type: Type of testing (unit, integration, e2e, all)
-        command: Command to run tests
-        config_file: Configuration file if found
-        version: Version if detected
-        coverage_command: Command for coverage if available
-    """
-
-    __test__ = False  # Prevent pytest from collecting this as a test class
-
-    name: str
-    type: str  # unit, integration, e2e, all
-    command: str
-    config_file: str | None = None
-    version: str | None = None
-    coverage_command: str | None = None
-
-
-@dataclass
-class TestDiscoveryResult:
-    """
-    Result of test framework discovery.
-
-    Attributes:
-        frameworks: List of detected test frameworks
-        test_command: Primary test command to run
-        test_directories: Discovered test directories
-        package_manager: Detected package manager
-        has_tests: Whether any test files were found
-        coverage_command: Command for coverage if available
-    """
-
-    __test__ = False  # Prevent pytest from collecting this as a test class
-
-    frameworks: list[TestFramework] = field(default_factory=list)
-    test_command: str = ""
-    test_directories: list[str] = field(default_factory=list)
-    package_manager: str = ""
-    has_tests: bool = False
-    coverage_command: str | None = None
-
-
-# =============================================================================
-# FRAMEWORK DETECTORS
-# =============================================================================
-
-
-# Pattern-based framework detection
-FRAMEWORK_PATTERNS = {
-    # JavaScript/TypeScript
-    "jest": {
-        "config_files": [
-            "jest.config.js",
-            "jest.config.ts",
-            "jest.config.mjs",
-            "jest.config.cjs",
-        ],
-        "package_key": "jest",
-        "type": "unit",
-        "command": "npx jest",
-        "coverage_command": "npx jest --coverage",
-    },
-    "vitest": {
-        "config_files": ["vitest.config.js", "vitest.config.ts", "vitest.config.mjs"],
-        "package_key": "vitest",
-        "type": "unit",
-        "command": "npx vitest run",
-        "coverage_command": "npx vitest run --coverage",
-    },
-    "mocha": {
-        "config_files": [
-            ".mocharc.js",
-            ".mocharc.json",
-            ".mocharc.yaml",
-            ".mocharc.yml",
-        ],
-        "package_key": "mocha",
-        "type": "unit",
-        "command": "npx mocha",
-        "coverage_command": "npx nyc mocha",
-    },
-    "playwright": {
-        "config_files": ["playwright.config.js", "playwright.config.ts"],
-        "package_key": "@playwright/test",
-        "type": "e2e",
-        "command": "npx playwright test",
-        "coverage_command": None,
-    },
-    "cypress": {
-        "config_files": ["cypress.config.js", "cypress.config.ts", "cypress.json"],
-        "package_key": "cypress",
-        "type": "e2e",
-        "command": "npx cypress run",
-        "coverage_command": None,
-    },
-    # Python
-    "pytest": {
-        "config_files": ["pytest.ini", "pyproject.toml", "setup.cfg", "conftest.py"],
-        "pyproject_key": "pytest",
-        "requirements_key": "pytest",
-        "type": "all",
-        "command": "pytest",
-        "coverage_command": "pytest --cov",
-    },
-    "unittest": {
-        "config_files": [],
-        "type": "unit",
-        "command": "python -m unittest discover",
-        "coverage_command": "coverage run -m unittest discover",
-    },
-    # Rust
-    "cargo_test": {
-        "config_files": ["Cargo.toml"],
-        "type": "all",
-        "command": "cargo test",
-        "coverage_command": "cargo tarpaulin",
-    },
-    # Go
-    "go_test": {
-        "config_files": ["go.mod"],
-        "type": "all",
-        "command": "go test ./...",
-        "coverage_command": "go test -cover ./...",
-    },
-    # Ruby
-    "rspec": {
-        "config_files": [".rspec", "spec/spec_helper.rb"],
-        "gemfile_key": "rspec",
-        "type": "all",
-        "command": "bundle exec rspec",
-        "coverage_command": "bundle exec rspec --format documentation",
-    },
-    "minitest": {
-        "config_files": [],
-        "gemfile_key": "minitest",
-        "type": "unit",
-        "command": "bundle exec rake test",
-        "coverage_command": None,
-    },
-}
-
-
-# =============================================================================
-# TEST DISCOVERY
-# =============================================================================
-
-
-class TestDiscovery:
-    """
-    Discovers test frameworks and configurations in a project.
-
-    Analyzes:
-    - Package files (package.json, pyproject.toml, Cargo.toml, etc.)
-    - Configuration files (jest.config.js, pytest.ini, etc.)
-    - Directory structure (tests/, spec/, __tests__/)
-    """
-
-    __test__ = False  # Prevent pytest from collecting this as a test class
-
-    def __init__(self) -> None:
-        """Initialize the test discovery."""
-        self._cache: dict[str, TestDiscoveryResult] = {}
-
-    def discover(self, project_dir: Path) -> TestDiscoveryResult:
-        """
-        Discover test frameworks and configuration in the project.
-
-        Args:
-            project_dir: Path to the project root
-
-        Returns:
-            TestDiscoveryResult with detected frameworks and commands
-        """
-        project_dir = Path(project_dir)
-        cache_key = str(project_dir.resolve())
-
-        if cache_key in self._cache:
-            return self._cache[cache_key]
-
-        result = TestDiscoveryResult()
-
-        # Detect package manager
-        result.package_manager = self._detect_package_manager(project_dir)
-
-        # Discover frameworks based on project type
-        if (project_dir / "package.json").exists():
-            self._discover_js_frameworks(project_dir, result)
-
-        # Check for Python project indicators
-        python_indicators = [
-            project_dir / "pyproject.toml",
-            project_dir / "requirements.txt",
-            project_dir / "setup.py",
-            project_dir / "pytest.ini",
-            project_dir / "conftest.py",
-            project_dir / "tests" / "conftest.py",
-        ]
-        if any(p.exists() for p in python_indicators):
-            self._discover_python_frameworks(project_dir, result)
-
-        if (project_dir / "Cargo.toml").exists():
-            self._discover_rust_frameworks(project_dir, result)
-        if (project_dir / "go.mod").exists():
-            self._discover_go_frameworks(project_dir, result)
-        if (project_dir / "Gemfile").exists():
-            self._discover_ruby_frameworks(project_dir, result)
-
-        # Find test directories
-        result.test_directories = self._find_test_directories(project_dir)
-
-        # Check if tests exist
-        result.has_tests = self._has_test_files(project_dir, result.test_directories)
-
-        # Set primary test command
-        if result.frameworks:
-            result.test_command = result.frameworks[0].command
-
-        # Set coverage command from first framework that has one
-        if not result.coverage_command:
-            for framework in result.frameworks:
-                if framework.coverage_command:
-                    result.coverage_command = framework.coverage_command
-                    break
-
-        self._cache[cache_key] = result
-        return result
-
-    def _detect_package_manager(self, project_dir: Path) -> str:
-        """Detect the package manager used by the project."""
-        if (project_dir / "pnpm-lock.yaml").exists():
-            return "pnpm"
-        if (project_dir / "yarn.lock").exists():
-            return "yarn"
-        if (project_dir / "package-lock.json").exists():
-            return "npm"
-        if (project_dir / "bun.lockb").exists():
-            return "bun"
-        if (project_dir / "uv.lock").exists():
-            return "uv"
-        if (project_dir / "poetry.lock").exists():
-            return "poetry"
-        if (project_dir / "Pipfile.lock").exists():
-            return "pipenv"
-        if (project_dir / "Cargo.lock").exists():
-            return "cargo"
-        if (project_dir / "go.sum").exists():
-            return "go"
-        if (project_dir / "Gemfile.lock").exists():
-            return "bundler"
-        return ""
-
-    def _discover_js_frameworks(
-        self, project_dir: Path, result: TestDiscoveryResult
-    ) -> None:
-        """Discover JavaScript/TypeScript test frameworks."""
-        package_json = project_dir / "package.json"
-        if not package_json.exists():
-            return
-
-        try:
-            with open(package_json, encoding="utf-8") as f:
-                pkg = json.load(f)
-        except (OSError, json.JSONDecodeError):
-            return
-
-        deps = pkg.get("dependencies", {})
-        dev_deps = pkg.get("devDependencies", {})
-        all_deps = {**deps, **dev_deps}
-        scripts = pkg.get("scripts", {})
-
-        # Check for test frameworks in dependencies
-        for name, pattern in FRAMEWORK_PATTERNS.items():
-            if "package_key" not in pattern:
-                continue
-
-            if pattern["package_key"] in all_deps:
-                # Check for config file
-                config_file = None
-                for cf in pattern.get("config_files", []):
-                    if (project_dir / cf).exists():
-                        config_file = cf
-                        break
-
-                # Get version
-                version = all_deps.get(pattern["package_key"], "")
-                if version.startswith("^") or version.startswith("~"):
-                    version = version[1:]
-
-                # Determine command - prefer npm scripts if available
-                command = pattern["command"]
-                if "test" in scripts and pattern["package_key"] in scripts.get(
-                    "test", ""
-                ):
-                    command = f"{result.package_manager or 'npm'} test"
-
-                result.frameworks.append(
-                    TestFramework(
-                        name=name,
-                        type=pattern["type"],
-                        command=command,
-                        config_file=config_file,
-                        version=version,
-                        coverage_command=pattern.get("coverage_command"),
-                    )
-                )
-
-        # Check npm scripts for test commands
-        if not result.frameworks and "test" in scripts:
-            test_script = scripts["test"]
-            if (
-                test_script
-                and test_script != 'echo "Error: no test specified" && exit 1'
-            ):
-                # Try to infer framework from script
-                framework_name = "npm_test"
-                framework_type = "unit"
-
-                if "jest" in test_script:
-                    framework_name = "jest"
-                elif "vitest" in test_script:
-                    framework_name = "vitest"
-                elif "mocha" in test_script:
-                    framework_name = "mocha"
-                elif "playwright" in test_script:
-                    framework_name = "playwright"
-                    framework_type = "e2e"
-                elif "cypress" in test_script:
-                    framework_name = "cypress"
-                    framework_type = "e2e"
-
-                result.frameworks.append(
-                    TestFramework(
-                        name=framework_name,
-                        type=framework_type,
-                        command=f"{result.package_manager or 'npm'} test",
-                        config_file=None,
-                    )
-                )
-
-    def _discover_python_frameworks(
-        self, project_dir: Path, result: TestDiscoveryResult
-    ) -> None:
-        """Discover Python test frameworks."""
-        # Check for pytest.ini first (explicit pytest config)
-        if (project_dir / "pytest.ini").exists():
-            if not any(f.name == "pytest" for f in result.frameworks):
-                result.frameworks.append(
-                    TestFramework(
-                        name="pytest",
-                        type="all",
-                        command="pytest",
-                        config_file="pytest.ini",
-                    )
-                )
-
-        # Check pyproject.toml
-        pyproject = project_dir / "pyproject.toml"
-        if pyproject.exists():
-            content = pyproject.read_text()
-
-            # Check for pytest
-            if "pytest" in content:
-                if not any(f.name == "pytest" for f in result.frameworks):
-                    config_file = (
-                        "pyproject.toml" if "[tool.pytest" in content else None
-                    )
-                    result.frameworks.append(
-                        TestFramework(
-                            name="pytest",
-                            type="all",
-                            command="pytest",
-                            config_file=config_file,
-                        )
-                    )
-
-        # Check requirements.txt
-        requirements = project_dir / "requirements.txt"
-        if requirements.exists():
-            content = requirements.read_text().lower()
-            if "pytest" in content and not any(
-                f.name == "pytest" for f in result.frameworks
-            ):
-                result.frameworks.append(
-                    TestFramework(
-                        name="pytest",
-                        type="all",
-                        command="pytest",
-                        config_file=None,
-                    )
-                )
-
-        # Check for conftest.py (pytest marker)
-        conftest_root = project_dir / "conftest.py"
-        conftest_tests = project_dir / "tests" / "conftest.py"
-        if conftest_root.exists() or conftest_tests.exists():
-            if not any(f.name == "pytest" for f in result.frameworks):
-                result.frameworks.append(
-                    TestFramework(
-                        name="pytest",
-                        type="all",
-                        command="pytest",
-                        config_file="conftest.py",
-                    )
-                )
-
-        # Fall back to unittest if test files exist but no framework detected
-        if not result.frameworks:
-            test_dirs = self._find_test_directories(project_dir)
-            if test_dirs:
-                result.frameworks.append(
-                    TestFramework(
-                        name="unittest",
-                        type="unit",
-                        command="python -m unittest discover",
-                        config_file=None,
-                    )
-                )
-
-    def _discover_rust_frameworks(
-        self, project_dir: Path, result: TestDiscoveryResult
-    ) -> None:
-        """Discover Rust test frameworks."""
-        cargo_toml = project_dir / "Cargo.toml"
-        if cargo_toml.exists():
-            result.frameworks.append(
-                TestFramework(
-                    name="cargo_test",
-                    type="all",
-                    command="cargo test",
-                    config_file="Cargo.toml",
-                )
-            )
-
-    def _discover_go_frameworks(
-        self, project_dir: Path, result: TestDiscoveryResult
-    ) -> None:
-        """Discover Go test frameworks."""
-        go_mod = project_dir / "go.mod"
-        if go_mod.exists():
-            result.frameworks.append(
-                TestFramework(
-                    name="go_test",
-                    type="all",
-                    command="go test ./...",
-                    config_file="go.mod",
-                )
-            )
-
-    def _discover_ruby_frameworks(
-        self, project_dir: Path, result: TestDiscoveryResult
-    ) -> None:
-        """Discover Ruby test frameworks."""
-        gemfile = project_dir / "Gemfile"
-        if not gemfile.exists():
-            return
-
-        content = gemfile.read_text().lower()
-
-        if "rspec" in content or (project_dir / ".rspec").exists():
-            result.frameworks.append(
-                TestFramework(
-                    name="rspec",
-                    type="all",
-                    command="bundle exec rspec",
-                    config_file=".rspec" if (project_dir / ".rspec").exists() else None,
-                )
-            )
-        elif "minitest" in content:
-            result.frameworks.append(
-                TestFramework(
-                    name="minitest",
-                    type="unit",
-                    command="bundle exec rake test",
-                    config_file=None,
-                )
-            )
-
-    def _find_test_directories(self, project_dir: Path) -> list[str]:
-        """Find test directories in the project."""
-        test_dir_patterns = [
-            "tests",
-            "test",
-            "spec",
-            "__tests__",
-            "specs",
-            "test_*",
-        ]
-
-        found_dirs = []
-        for pattern in test_dir_patterns:
-            if pattern.endswith("*"):
-                # Glob pattern
-                for d in project_dir.glob(pattern):
-                    if d.is_dir():
-                        found_dirs.append(str(d.relative_to(project_dir)))
-            else:
-                # Exact name
-                test_dir = project_dir / pattern
-                if test_dir.is_dir():
-                    found_dirs.append(pattern)
-
-        return found_dirs
-
-    def _has_test_files(self, project_dir: Path, test_directories: list[str]) -> bool:
-        """Check if any test files exist."""
-        test_file_patterns = [
-            "**/test_*.py",
-            "**/*_test.py",
-            "**/*.test.js",
-            "**/*.test.ts",
-            "**/*.test.tsx",
-            "**/*.spec.js",
-            "**/*.spec.ts",
-            "**/*.spec.tsx",
-            "**/test_*.go",
-            "**/*_test.go",
-            "**/*_test.rs",
-            "**/spec/**/*_spec.rb",
-        ]
-
-        # Check in test directories
-        for test_dir in test_directories:
-            test_path = project_dir / test_dir
-            if test_path.exists():
-                for pattern in test_file_patterns:
-                    if list(test_path.glob(pattern.replace("**/", ""))):
-                        return True
-
-        # Check project-wide
-        for pattern in test_file_patterns:
-            if list(project_dir.glob(pattern)):
-                return True
-
-        return False
-
-    def to_dict(self, result: TestDiscoveryResult) -> dict[str, Any]:
-        """Convert result to dictionary for JSON serialization."""
-        return {
-            "frameworks": [
-                {
-                    "name": f.name,
-                    "type": f.type,
-                    "command": f.command,
-                    "config_file": f.config_file,
-                    "version": f.version,
-                    "coverage_command": f.coverage_command,
-                }
-                for f in result.frameworks
-            ],
-            "test_command": result.test_command,
-            "test_directories": result.test_directories,
-            "package_manager": result.package_manager,
-            "has_tests": result.has_tests,
-            "coverage_command": result.coverage_command,
-        }
-
-    def clear_cache(self) -> None:
-        """Clear the internal cache."""
-        self._cache.clear()
-
-
-# =============================================================================
-# CONVENIENCE FUNCTIONS
-# =============================================================================
-
-
-def discover_tests(project_dir: Path) -> TestDiscoveryResult:
-    """
-    Convenience function to discover tests in a project.
-
-    Args:
-        project_dir: Path to project root
-
-    Returns:
-        TestDiscoveryResult with detected frameworks
-    """
-    discovery = TestDiscovery()
-    return discovery.discover(project_dir)
-
-
-def get_test_command(project_dir: Path) -> str:
-    """
-    Get the primary test command for a project.
-
-    Args:
-        project_dir: Path to project root
-
-    Returns:
-        Test command string, or empty string if not found
-    """
-    discovery = TestDiscovery()
-    result = discovery.discover(project_dir)
-    return result.test_command
-
-
-def get_test_frameworks(project_dir: Path) -> list[str]:
-    """
-    Get list of test framework names in a project.
-
-    Args:
-        project_dir: Path to project root
-
-    Returns:
-        List of framework names
-    """
-    discovery = TestDiscovery()
-    result = discovery.discover(project_dir)
-    return [f.name for f in result.frameworks]
-
-
-# =============================================================================
-# CLI
-# =============================================================================
-
-
-def main() -> None:
-    """CLI entry point for testing."""
-    import argparse
-
-    parser = argparse.ArgumentParser(description="Discover test frameworks")
-    parser.add_argument("project_dir", type=Path, help="Path to project root")
-    parser.add_argument("--json", action="store_true", help="Output as JSON")
-
-    args = parser.parse_args()
-
-    discovery = TestDiscovery()
-    result = discovery.discover(args.project_dir)
-
-    if args.json:
-        print(json.dumps(discovery.to_dict(result), indent=2))
-    else:
-        print(f"Package Manager: {result.package_manager or 'unknown'}")
-        print(f"Has Tests: {result.has_tests}")
-        print(f"Test Command: {result.test_command or 'none'}")
-        print(f"Test Directories: {', '.join(result.test_directories) or 'none'}")
-        print(f"Coverage Command: {result.coverage_command or 'none'}")
-        print(f"\nFrameworks ({len(result.frameworks)}):")
-        for f in result.frameworks:
-            print(f"  - {f.name} ({f.type})")
-            print(f"    Command: {f.command}")
-            if f.config_file:
-                print(f"    Config: {f.config_file}")
-            if f.version:
-                print(f"    Version: {f.version}")
-
-
-if __name__ == "__main__":
-    main()

apps/backend/cli/batch_commands.py

@@ -6,8 +6,11 @@ Commands for creating and managing multiple tasks from batch files.
 """
 
 import json
+import shutil
+import subprocess
 from pathlib import Path
 
+from qa.criteria import is_fixes_applied, is_qa_approved, is_qa_rejected
 from ui import highlight, print_status
 
 
@@ -29,7 +32,7 @@ def handle_batch_create_command(batch_file: str, project_dir: str) -> bool:
         return False
 
     try:
-        with open(batch_path) as f:
+        with open(batch_path, encoding="utf-8") as f:
             batch_data = json.load(f)
     except json.JSONDecodeError as e:
         print_status(f"Invalid JSON in batch file: {e}", "error")
@@ -79,7 +82,7 @@ def handle_batch_create_command(batch_file: str, project_dir: str) -> bool:
         }
 
         req_file = spec_dir / "requirements.json"
-        with open(req_file, "w") as f:
+        with open(req_file, "w", encoding="utf-8") as f:
             json.dump(requirements, f, indent=2, default=str)
 
         created_specs.append(
@@ -143,19 +146,28 @@ def handle_batch_status_command(project_dir: str) -> bool:
 
         if req_file.exists():
             try:
-                with open(req_file) as f:
+                with open(req_file, encoding="utf-8") as f:
                     req = json.load(f)
                     title = req.get("task_description", title)
             except json.JSONDecodeError:
                 pass
 
-        # Determine status
-        if (spec_dir / "spec.md").exists():
-            status = "spec_created"
-        elif (spec_dir / "implementation_plan.json").exists():
-            status = "building"
-        elif (spec_dir / "qa_report.md").exists():
+        # Determine status (highest priority first)
+        # Use authoritative QA status check, not just file existence
+        if is_qa_approved(spec_dir):
             status = "qa_approved"
+        elif is_qa_rejected(spec_dir):
+            status = "qa_rejected"
+        elif is_fixes_applied(spec_dir):
+            status = "fixes_applied"
+        elif (spec_dir / "implementation_plan.json").exists():
+            # Check if there's a qa_report.md but no approval yet (QA in progress)
+            if (spec_dir / "qa_report.md").exists():
+                status = "qa_in_progress"
+            else:
+                status = "building"
+        elif (spec_dir / "spec.md").exists():
+            status = "spec_created"
         else:
             status = "pending_spec"
 
@@ -163,7 +175,10 @@ def handle_batch_status_command(project_dir: str) -> bool:
             "pending_spec": "⏳",
             "spec_created": "📋",
             "building": "⚙️",
+            "qa_in_progress": "🔍",
             "qa_approved": "✅",
+            "qa_rejected": "❌",
+            "fixes_applied": "🔧",
             "unknown": "❓",
         }.get(status, "❓")
 
@@ -184,16 +199,16 @@ def handle_batch_cleanup_command(project_dir: str, dry_run: bool = True) -> bool
         True if successful
     """
     specs_dir = Path(project_dir) / ".auto-claude" / "specs"
-    worktrees_dir = Path(project_dir) / ".worktrees"
+    worktrees_dir = Path(project_dir) / ".auto-claude" / "worktrees" / "tasks"
 
     if not specs_dir.exists():
         print_status("No specs directory found", "info")
         return True
 
-    # Find completed specs
+    # Find completed specs (only QA-approved, matching status display logic)
     completed = []
     for spec_dir in specs_dir.iterdir():
-        if spec_dir.is_dir() and (spec_dir / "qa_report.md").exists():
+        if spec_dir.is_dir() and is_qa_approved(spec_dir):
             completed.append(spec_dir.name)
 
     if not completed:
@@ -209,8 +224,56 @@ def handle_batch_cleanup_command(project_dir: str, dry_run: bool = True) -> bool
             print(f"  - {spec_name}")
             wt_path = worktrees_dir / spec_name
             if wt_path.exists():
-                print(f"    └─ .worktrees/{spec_name}/")
+                print(f"    └─ .auto-claude/worktrees/tasks/{spec_name}/")
         print()
         print("Run with --no-dry-run to actually delete")
+    else:
+        # Actually delete specs and worktrees
+        deleted_count = 0
+        for spec_name in completed:
+            spec_path = specs_dir / spec_name
+            wt_path = worktrees_dir / spec_name
+
+            # Remove worktree first (if exists)
+            if wt_path.exists():
+                try:
+                    result = subprocess.run(
+                        ["git", "worktree", "remove", "--force", str(wt_path)],
+                        cwd=project_dir,
+                        capture_output=True,
+                        text=True,
+                        timeout=30,
+                    )
+                    if result.returncode == 0:
+                        print_status(f"Removed worktree: {spec_name}", "success")
+                    else:
+                        # Fallback: remove directory manually if git fails
+                        shutil.rmtree(wt_path, ignore_errors=True)
+                        print_status(
+                            f"Removed worktree directory: {spec_name}", "success"
+                        )
+                except subprocess.TimeoutExpired:
+                    # Timeout: fall back to manual removal
+                    shutil.rmtree(wt_path, ignore_errors=True)
+                    print_status(
+                        f"Worktree removal timed out, removed directory: {spec_name}",
+                        "warning",
+                    )
+                except Exception as e:
+                    print_status(
+                        f"Failed to remove worktree {spec_name}: {e}", "warning"
+                    )
+
+            # Remove spec directory
+            if spec_path.exists():
+                try:
+                    shutil.rmtree(spec_path)
+                    print_status(f"Removed spec: {spec_name}", "success")
+                    deleted_count += 1
+                except Exception as e:
+                    print_status(f"Failed to remove spec {spec_name}: {e}", "error")
+
+        print()
+        print_status(f"Cleaned up {deleted_count} spec(s)", "info")
 
     return True

apps/backend/cli/build_commands.py

@@ -61,6 +61,8 @@ def handle_build_command(
     skip_qa: bool,
     force_bypass_approval: bool,
     base_branch: str | None = None,
+    issue_workflow: bool = False,
+    issue_number: int | None = None,
 ) -> None:
     """
     Handle the main build command.
@@ -77,9 +79,11 @@ def handle_build_command(
         skip_qa: Skip automatic QA validation
         force_bypass_approval: Force bypass approval check
         base_branch: Base branch for worktree creation (default: current branch)
+        issue_workflow: If True, run from a GitHub issue investigation
+        issue_number: GitHub issue number (required when issue_workflow=True)
     """
     # Lazy imports to avoid loading heavy modules
-    from agent import run_autonomous_agent, sync_plan_to_source
+    from agent import run_autonomous_agent, sync_spec_to_source
     from debug import (
         debug,
         debug_info,
@@ -87,10 +91,38 @@ def handle_build_command(
         debug_success,
     )
     from phase_config import get_phase_model
+    from prompts_pkg.prompts import (
+        get_base_branch_from_metadata,
+        get_use_local_branch_from_metadata,
+    )
     from qa_loop import run_qa_validation_loop, should_run_qa
 
     from .utils import print_banner, validate_environment
 
+    # Handle issue workflow: load investigation report and inject context
+    if issue_workflow:
+        if not issue_number:
+            print("\nError: --issue-number is required with --issue-workflow")
+            sys.exit(1)
+
+        pipeline_mode = _get_investigation_pipeline_mode(project_dir)
+        _inject_issue_workflow_context(project_dir, spec_dir, issue_number)
+
+        # pipelineMode controls which phases to skip:
+        # - "full": run complete spec + planning + coding + QA pipeline (default)
+        # - "skip_to_planning": skip spec creation, go to planning (investigation = spec)
+        # - "minimal": skip spec + planning, go straight to coding
+        if pipeline_mode == "skip_to_planning":
+            # Investigation report serves as the spec; bypass approval since
+            # the investigation was already reviewed.
+            force_bypass_approval = True
+        elif pipeline_mode == "minimal":
+            # Skip everything: create a minimal plan so the planner is bypassed
+            # and the coder starts immediately from the investigation context.
+            force_bypass_approval = True
+            skip_qa = True
+            _create_minimal_plan_for_issue(spec_dir, issue_number)
+
     # Get the resolved model for the planning phase (first phase of build)
     # This respects task_metadata.json phase configuration from the UI
     planning_model = get_phase_model(spec_dir, "planning", model)
@@ -194,6 +226,17 @@ def handle_build_command(
         auto_continue=auto_continue,
     )
 
+    # If base_branch not provided via CLI, try to read from task_metadata.json
+    # This ensures the backend uses the branch configured in the frontend
+    if base_branch is None:
+        metadata_branch = get_base_branch_from_metadata(spec_dir)
+        if metadata_branch:
+            base_branch = metadata_branch
+            debug("run.py", f"Using base branch from task metadata: {base_branch}")
+
+    # Check if user requested local branch (preserves gitignored files like .env)
+    use_local_branch = get_use_local_branch_from_metadata(spec_dir)
+
     if workspace_mode == WorkspaceMode.ISOLATED:
         # Keep reference to original spec directory for syncing progress back
         source_spec_dir = spec_dir
@@ -204,6 +247,7 @@ def handle_build_command(
             workspace_mode,
             source_spec_dir=spec_dir,
             base_branch=base_branch,
+            use_local_branch=use_local_branch,
         )
         # Use the localized spec directory (inside worktree) for AI access
         if localized_spec_dir:
@@ -274,7 +318,7 @@ def handle_build_command(
 
                 # Sync implementation plan to main project after QA
                 # This ensures the main project has the latest status (human_review)
-                if sync_plan_to_source(spec_dir, source_spec_dir):
+                if sync_spec_to_source(spec_dir, source_spec_dir):
                     debug_info(
                         "run.py", "Implementation plan synced to main project after QA"
                     )
@@ -412,7 +456,7 @@ def _handle_build_interrupt(
         if human_input:
             # Save to HUMAN_INPUT.md
             input_file = spec_dir / "HUMAN_INPUT.md"
-            input_file.write_text(human_input)
+            input_file.write_text(human_input, encoding="utf-8")
 
             content = [
                 success(f"{icon(Icons.SUCCESS)} INSTRUCTIONS SAVED"),
@@ -433,7 +477,7 @@ def _handle_build_interrupt(
         if choice == "skip":
             print()
             print_status("Resuming build...", "info")
-            status_manager.update(state=BuildState.RUNNING)
+            status_manager.update(state=BuildState.BUILDING)
             asyncio.run(
                 run_autonomous_agent(
                     project_dir=working_dir,
@@ -469,3 +513,228 @@ def _handle_build_interrupt(
         content.append(muted("Your build is in a separate workspace and is safe."))
     print(box(content, width=70, style="light"))
     print()
+
+
+def _create_minimal_plan_for_issue(spec_dir: Path, issue_number: int) -> None:
+    """Create a minimal implementation plan so the planner phase is skipped.
+
+    Used in "minimal" pipeline mode where the investigation context is
+    sufficient and we want the coder to start immediately.
+
+    Args:
+        spec_dir: Spec directory path
+        issue_number: GitHub issue number for context
+    """
+    from datetime import datetime
+
+    plan_file = spec_dir / "implementation_plan.json"
+    if plan_file.exists():
+        # Don't overwrite an existing plan (e.g. if resuming)
+        return
+
+    plan = {
+        "phases": [
+            {
+                "phase": 1,
+                "name": "Implementation",
+                "description": f"Implement fix for issue #{issue_number} based on investigation findings",
+                "depends_on": [],
+                "subtasks": [
+                    {
+                        "id": "subtask-1-1",
+                        "description": (
+                            f"Implement the fix for issue #{issue_number}. "
+                            "Follow the investigation context in HUMAN_INPUT.md "
+                            "for root cause analysis, recommended fix approach, "
+                            "and files to modify."
+                        ),
+                        "service": "main",
+                        "status": "pending",
+                        "files_to_create": [],
+                        "files_to_modify": [],
+                        "patterns_from": [],
+                        "verification": {
+                            "type": "manual",
+                            "run": "Verify the fix resolves the issue",
+                        },
+                    }
+                ],
+            }
+        ],
+        "metadata": {
+            "created_at": datetime.now().isoformat(),
+            "complexity": "simple",
+            "estimated_sessions": 1,
+            "pipeline_mode": "minimal",
+            "source_issue": issue_number,
+        },
+    }
+
+    from core.file_utils import write_json_atomic
+
+    write_json_atomic(plan_file, plan)
+    print("  Pipeline mode: minimal (skipping planner, created single-subtask plan)")
+
+
+def _get_investigation_pipeline_mode(project_dir: Path) -> str:
+    """Read the pipelineMode from investigation settings.
+
+    Reads from .auto-claude/github/config.json -> investigation_settings.pipelineMode.
+    Defaults to "full" if not configured.
+
+    Args:
+        project_dir: Project root directory
+
+    Returns:
+        Pipeline mode string: "full", "skip_to_planning", or "minimal"
+    """
+    import json
+
+    config_path = project_dir / ".auto-claude" / "github" / "config.json"
+    if not config_path.exists():
+        return "full"
+
+    try:
+        data = json.loads(config_path.read_text(encoding="utf-8"))
+        settings = data.get("investigation_settings", {})
+        mode = settings.get("pipelineMode", "full")
+        if mode in ("full", "skip_to_planning", "minimal"):
+            return mode
+        return "full"
+    except (json.JSONDecodeError, OSError):
+        return "full"
+
+
+def _inject_issue_workflow_context(
+    project_dir: Path,
+    spec_dir: Path,
+    issue_number: int,
+) -> None:
+    """Inject investigation context into the build workflow.
+
+    Loads the investigation report for the given issue and writes a
+    HUMAN_INPUT.md file in the spec directory with root cause analysis,
+    fix advice, and other investigation context. This is read by the
+    coder agent as additional guidance.
+
+    Also updates the investigation state to "building".
+
+    Args:
+        project_dir: Project root directory
+        spec_dir: Spec directory path
+        issue_number: GitHub issue number
+    """
+
+    # Use try/except for imports matching the codebase pattern
+    try:
+        from runners.github.services.investigation_persistence import (
+            load_investigation_report,
+            save_investigation_state,
+        )
+    except (ImportError, ValueError, SystemError):
+        # Add parent to path if needed
+        _backend = Path(__file__).parent.parent
+        if str(_backend) not in sys.path:
+            sys.path.insert(0, str(_backend))
+        from runners.github.services.investigation_persistence import (
+            load_investigation_report,
+            save_investigation_state,
+        )
+
+    report = load_investigation_report(project_dir, issue_number)
+    if report is None:
+        print(f"\nWarning: No investigation report found for issue #{issue_number}")
+        print("Proceeding without investigation context.")
+        return
+
+    # Build context string for the coder agent
+    context_parts: list[str] = []
+    context_parts.append(f"# Investigation Context for Issue #{issue_number}")
+    context_parts.append("")
+    context_parts.append(f"## {report.issue_title}")
+    context_parts.append("")
+    context_parts.append(f"**Severity:** {report.severity}")
+    context_parts.append("")
+
+    # AI summary
+    context_parts.append("## Summary")
+    context_parts.append(report.ai_summary)
+    context_parts.append("")
+
+    # Root cause
+    context_parts.append("## Root Cause")
+    context_parts.append(report.root_cause.identified_root_cause)
+    context_parts.append("")
+
+    if report.root_cause.code_paths:
+        context_parts.append("### Code Paths")
+        for cp in report.root_cause.code_paths:
+            end = cp.end_line if cp.end_line else cp.start_line
+            context_parts.append(
+                f"- `{cp.file}:{cp.start_line}-{end}`: {cp.description}"
+            )
+        context_parts.append("")
+
+    # Fix advice
+    if report.fix_advice.approaches:
+        rec_idx = report.fix_advice.recommended_approach
+        context_parts.append("## Recommended Fix")
+        if 0 <= rec_idx < len(report.fix_advice.approaches):
+            approach = report.fix_advice.approaches[rec_idx]
+            context_parts.append(approach.description)
+            context_parts.append("")
+            if approach.files_affected:
+                context_parts.append("**Files to modify:**")
+                for f in approach.files_affected:
+                    context_parts.append(f"- `{f}`")
+                context_parts.append("")
+
+    # Gotchas
+    if report.fix_advice.gotchas:
+        context_parts.append("## Gotchas")
+        for gotcha in report.fix_advice.gotchas:
+            context_parts.append(f"- {gotcha}")
+        context_parts.append("")
+
+    # Patterns
+    if report.fix_advice.patterns_to_follow:
+        context_parts.append("## Patterns to Follow")
+        for pat in report.fix_advice.patterns_to_follow:
+            context_parts.append(f"- `{pat.file}`: {pat.description}")
+        context_parts.append("")
+
+    context = "\n".join(context_parts)
+
+    # Write as HUMAN_INPUT.md (existing mechanism for agent guidance injection)
+    input_file = spec_dir / "HUMAN_INPUT.md"
+    existing = ""
+    if input_file.exists():
+        existing = input_file.read_text(encoding="utf-8")
+
+    if existing:
+        # Append investigation context to existing human input
+        combined = existing + "\n\n" + context
+    else:
+        combined = context
+
+    input_file.write_text(combined, encoding="utf-8")
+
+    # Update investigation state to "building" (note: we use the broader
+    # "task_created" status since "building" isn't a valid InvestigationState status)
+    from datetime import datetime, timezone
+
+    save_investigation_state(
+        project_dir,
+        issue_number,
+        {
+            "issue_number": issue_number,
+            "status": "task_created",
+            "started_at": datetime.now(timezone.utc).isoformat(),
+            "linked_spec_id": spec_dir.name,
+        },
+    )
+
+    print(f"\nIssue workflow: Injected investigation context for #{issue_number}")
+    print(f"  Root cause: {report.root_cause.identified_root_cause[:80]}...")
+    print(f"  Severity: {report.severity}")
+    print()

apps/backend/cli/followup_commands.py

@@ -121,7 +121,7 @@ def collect_followup_task(spec_dir: Path, max_retries: int = 3) -> str | None:
                 # Expand ~ and resolve path
                 file_path = Path(file_path_str).expanduser().resolve()
                 if file_path.exists():
-                    followup_task = file_path.read_text().strip()
+                    followup_task = file_path.read_text(encoding="utf-8").strip()
                     if followup_task:
                         print_status(
                             f"Loaded {len(followup_task)} characters from file",
@@ -195,7 +195,7 @@ def collect_followup_task(spec_dir: Path, max_retries: int = 3) -> str | None:
 
         # Save to FOLLOWUP_REQUEST.md
         request_file = spec_dir / "FOLLOWUP_REQUEST.md"
-        request_file.write_text(followup_task)
+        request_file.write_text(followup_task, encoding="utf-8")
 
         # Show confirmation
         content = [
@@ -285,7 +285,7 @@ def handle_followup_command(
     # Check for prior follow-ups (for sequential follow-up context)
     prior_followup_count = 0
     try:
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             plan_data = json.load(f)
         phases = plan_data.get("phases", [])
         # Count phases that look like follow-up phases (name contains "Follow" or high phase number)

apps/backend/cli/input_handlers.py

@@ -149,7 +149,7 @@ def read_from_file() -> str | None:
         # Expand ~ and resolve path
         file_path = Path(file_path_input).expanduser().resolve()
         if file_path.exists():
-            content = file_path.read_text().strip()
+            content = file_path.read_text(encoding="utf-8").strip()
             if content:
                 print_status(
                     f"Loaded {len(content)} characters from file",

apps/backend/cli/main.py

@@ -15,10 +15,6 @@ _PARENT_DIR = Path(__file__).parent.parent
 if str(_PARENT_DIR) not in sys.path:
     sys.path.insert(0, str(_PARENT_DIR))
 
-from ui import (
-    Icons,
-    icon,
-)
 
 from .batch_commands import (
     handle_batch_cleanup_command,
@@ -42,6 +38,7 @@ from .utils import (
 )
 from .workspace_commands import (
     handle_cleanup_worktrees_command,
+    handle_create_pr_command,
     handle_discard_command,
     handle_list_worktrees_command,
     handle_merge_command,
@@ -77,12 +74,12 @@ Examples:
   python auto-claude/run.py --spec 001 --qa-status      # Check QA validation status
 
 Prerequisites:
-  1. Create a spec first: claude /spec
-  2. Run 'claude setup-token' and set CLAUDE_CODE_OAUTH_TOKEN
+  1. Authenticate: Run 'claude' and type '/login'
+  2. Create a spec first: claude /spec
 
 Environment Variables:
-  CLAUDE_CODE_OAUTH_TOKEN  Your Claude Code OAuth token (required)
-                           Get it by running: claude setup-token
+  CLAUDE_CODE_OAUTH_TOKEN  Your Claude Code OAuth token (auto-detected from Keychain)
+                           Or authenticate via: claude → /login
   AUTO_BUILD_MODEL         Override default model (optional)
         """,
     )
@@ -157,6 +154,30 @@ Environment Variables:
         action="store_true",
         help="Discard an existing build (requires confirmation)",
     )
+    build_group.add_argument(
+        "--create-pr",
+        action="store_true",
+        help="Push branch and create a GitHub Pull Request",
+    )
+
+    # PR options
+    parser.add_argument(
+        "--pr-target",
+        type=str,
+        metavar="BRANCH",
+        help="With --create-pr: target branch for PR (default: auto-detect)",
+    )
+    parser.add_argument(
+        "--pr-title",
+        type=str,
+        metavar="TITLE",
+        help="With --create-pr: custom PR title (default: generated from spec name)",
+    )
+    parser.add_argument(
+        "--pr-draft",
+        action="store_true",
+        help="With --create-pr: create as draft PR",
+    )
 
     # Merge options
     parser.add_argument(
@@ -201,13 +222,6 @@ Environment Variables:
         help="Show human review/approval status for a spec",
     )
 
-    # Dev mode (deprecated)
-    parser.add_argument(
-        "--dev",
-        action="store_true",
-        help="[Deprecated] No longer has any effect - kept for compatibility",
-    )
-
     # Non-interactive mode (for UI/automation)
     parser.add_argument(
         "--auto-continue",
@@ -266,6 +280,19 @@ Environment Variables:
         help="Actually delete files in cleanup (not just preview)",
     )
 
+    # Issue workflow
+    parser.add_argument(
+        "--issue-workflow",
+        action="store_true",
+        help="Run build from a GitHub issue investigation (requires --issue-number)",
+    )
+    parser.add_argument(
+        "--issue-number",
+        type=int,
+        default=None,
+        help="GitHub issue number for --issue-workflow",
+    )
+
     return parser.parse_args()
 
 
@@ -274,6 +301,28 @@ def main() -> None:
     # Set up environment first
     setup_environment()
 
+    # Initialize Sentry early to capture any startup errors
+    from core.sentry import capture_exception, init_sentry
+
+    init_sentry(component="cli")
+
+    try:
+        _run_cli()
+    except KeyboardInterrupt:
+        # Clean exit on Ctrl+C
+        sys.exit(130)
+    except Exception as e:
+        # Capture unexpected errors to Sentry
+        capture_exception(e)
+        print(f"\nUnexpected error: {e}")
+        sys.exit(1)
+
+
+def _run_cli() -> None:
+    """Run the CLI logic (extracted for error handling)."""
+    # Import here to avoid import errors during startup
+    from core.sentry import set_context
+
     # Parse arguments
     args = parse_args()
 
@@ -287,19 +336,14 @@ def main() -> None:
     project_dir = get_project_dir(args.project_dir)
     debug("run.py", f"Using project directory: {project_dir}")
 
-    # Get model (with env var fallback)
-    model = args.model or os.environ.get("AUTO_BUILD_MODEL", DEFAULT_MODEL)
-
-    # Note: --dev flag is deprecated but kept for API compatibility
-    if args.dev:
-        print(
-            f"\n{icon(Icons.GEAR)} Note: --dev flag is deprecated. All specs now use .auto-claude/specs/\n"
-        )
+    # Get model from CLI arg or env var (None if not explicitly set)
+    # This allows get_phase_model() to fall back to task_metadata.json
+    model = args.model or os.environ.get("AUTO_BUILD_MODEL")
 
     # Handle --list command
     if args.list:
         print_banner()
-        print_specs_list(project_dir, args.dev)
+        print_specs_list(project_dir)
         return
 
     # Handle --list-worktrees command
@@ -337,18 +381,27 @@ def main() -> None:
         sys.exit(1)
 
     # Find the spec
-    debug("run.py", "Finding spec", spec_identifier=args.spec, dev_mode=args.dev)
-    spec_dir = find_spec(project_dir, args.spec, args.dev)
+    debug("run.py", "Finding spec", spec_identifier=args.spec)
+    spec_dir = find_spec(project_dir, args.spec)
     if not spec_dir:
         debug_error("run.py", "Spec not found", spec=args.spec)
         print_banner()
         print(f"\nError: Spec '{args.spec}' not found")
         print("\nAvailable specs:")
-        print_specs_list(project_dir, args.dev)
+        print_specs_list(project_dir)
         sys.exit(1)
 
     debug_success("run.py", "Spec found", spec_dir=str(spec_dir))
 
+    # Set Sentry context for error tracking
+    set_context(
+        "spec",
+        {
+            "name": spec_dir.name,
+            "project": str(project_dir),
+        },
+    )
+
     # Handle build management commands
     if args.merge_preview:
         from cli.workspace_commands import handle_merge_preview_command
@@ -381,6 +434,21 @@ def main() -> None:
         handle_discard_command(project_dir, spec_dir.name)
         return
 
+    if args.create_pr:
+        # Pass args.pr_target directly - WorktreeManager._detect_base_branch
+        # handles base branch detection internally when target_branch is None
+        result = handle_create_pr_command(
+            project_dir=project_dir,
+            spec_name=spec_dir.name,
+            target_branch=args.pr_target,
+            title=args.pr_title,
+            draft=args.pr_draft,
+        )
+        # JSON output is already printed by handle_create_pr_command
+        if not result.get("success"):
+            sys.exit(1)
+        return
+
     # Handle QA commands
     if args.qa_status:
         handle_qa_status_command(spec_dir)
@@ -422,6 +490,8 @@ def main() -> None:
         skip_qa=args.skip_qa,
         force_bypass_approval=args.force,
         base_branch=args.base_branch,
+        issue_workflow=args.issue_workflow,
+        issue_number=args.issue_number,
     )
 
 

apps/backend/cli/recovery.py

@@ -0,0 +1,217 @@
+#!/usr/bin/env python3
+"""
+JSON Recovery Utility
+=====================
+
+Detects and repairs corrupted JSON files in specs directories.
+
+Usage:
+    python -m cli.recovery --project-dir /path/to/project --detect
+    python -m cli.recovery --project-dir /path/to/project --spec-id 004-feature --delete
+    python -m cli.recovery --project-dir /path/to/project --all --delete
+"""
+
+import argparse
+import json
+import sys
+import uuid
+from pathlib import Path
+
+from cli.utils import find_specs_dir
+
+
+def check_json_file(filepath: Path) -> tuple[bool, str | None]:
+    """
+    Check if a JSON file is valid.
+
+    Returns:
+        (is_valid, error_message)
+    """
+    try:
+        with open(filepath, encoding="utf-8") as f:
+            json.load(f)
+        return True, None
+    except json.JSONDecodeError as e:
+        return False, str(e)
+    except Exception as e:
+        return False, str(e)
+
+
+def detect_corrupted_files(specs_dir: Path) -> list[tuple[Path, str]]:
+    """
+    Scan specs directory recursively for corrupted JSON files.
+
+    Returns:
+        List of (filepath, error_message) tuples
+    """
+    corrupted = []
+
+    if not specs_dir.exists():
+        return corrupted
+
+    # Recursively scan for JSON files (includes nested files like memory/*.json)
+    for json_file in specs_dir.rglob("*.json"):
+        is_valid, error = check_json_file(json_file)
+        if not is_valid:
+            # Type narrowing: error is str when is_valid is False
+            assert error is not None
+            corrupted.append((json_file, error))
+
+    return corrupted
+
+
+def backup_corrupted_file(filepath: Path) -> bool:
+    """
+    Backup a corrupted file by renaming it with a .corrupted suffix.
+
+    Args:
+        filepath: Path to the corrupted file
+
+    Returns:
+        True if backed up successfully, False otherwise
+    """
+    try:
+        # Create backup before deleting
+        base_backup_path = filepath.with_suffix(f"{filepath.suffix}.corrupted")
+        backup_path = base_backup_path
+
+        # Handle existing backup files by generating unique name with UUID
+        if backup_path.exists():
+            # Use UUID for unique naming to avoid races
+            unique_suffix = uuid.uuid4().hex[:8]
+            backup_path = filepath.with_suffix(
+                f"{filepath.suffix}.corrupted.{unique_suffix}"
+            )
+
+        filepath.rename(backup_path)
+        print(f"  [BACKUP] Moved corrupted file to: {backup_path}")
+        return True
+    except Exception as e:
+        print(f"  [ERROR] Failed to backup file: {e}")
+        return False
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(
+        description="Detect and repair corrupted JSON files in specs directories"
+    )
+    parser.add_argument(
+        "--project-dir",
+        type=Path,
+        default=Path.cwd(),
+        help="Project directory (default: current directory)",
+    )
+    parser.add_argument(
+        "--specs-dir",
+        type=Path,
+        help="Specs directory path (overrides auto-detection)",
+    )
+    parser.add_argument(
+        "--detect",
+        action="store_true",
+        help="Detect corrupted JSON files",
+    )
+    parser.add_argument(
+        "--spec-id",
+        type=str,
+        help="Specific spec ID to fix (e.g., 004-feature)",
+    )
+    parser.add_argument(
+        "--delete",
+        action="store_true",
+        help="Delete corrupted files (creates .corrupted backup)",
+    )
+    parser.add_argument(
+        "--all",
+        action="store_true",
+        help="Fix all corrupted files (requires --delete)",
+    )
+
+    args = parser.parse_args()
+
+    # Validate --all requires --delete
+    if args.all and not args.delete:
+        parser.error("--all requires --delete")
+
+    # Find specs directory
+    if args.specs_dir:
+        specs_dir = args.specs_dir
+    else:
+        specs_dir = find_specs_dir(args.project_dir)
+
+    print(f"[INFO] Scanning specs directory: {specs_dir}")
+
+    # Default to detect mode if no flags provided
+    if not args.detect and not args.delete:
+        args.detect = True
+
+    # Detect corrupted files (dry-run when detect-only, otherwise for deletion)
+    corrupted = detect_corrupted_files(specs_dir)
+
+    # Detect-only mode: show results and exit
+    if args.detect and not args.delete:
+        if not corrupted:
+            print("[OK] No corrupted JSON files found")
+            sys.exit(0)
+
+        print(f"\n[FOUND] {len(corrupted)} corrupted file(s):\n")
+        for filepath, error in corrupted:
+            print(f"  - {filepath.relative_to(specs_dir.parent)}")
+            print(f"    Error: {error}")
+        print()
+        # Exit with error code when corrupted files are found
+        sys.exit(1)
+
+    # Delete corrupted files
+    if args.delete:
+        if args.spec_id:
+            # Delete specific spec
+            spec_dir = (specs_dir / args.spec_id).resolve()
+            specs_dir_resolved = specs_dir.resolve()
+            # Validate path doesn't escape specs directory
+            if not spec_dir.is_relative_to(specs_dir_resolved):
+                print("[ERROR] Invalid spec ID: path traversal detected")
+                sys.exit(1)
+
+            if not spec_dir.exists():
+                print(f"[ERROR] Spec directory not found: {spec_dir}")
+                sys.exit(1)
+
+            print(f"[INFO] Processing spec: {args.spec_id}")
+            has_failures = False
+            for json_file in spec_dir.rglob("*.json"):
+                is_valid, error = check_json_file(json_file)
+                if not is_valid:
+                    print(f"  [CORRUPTED] {json_file.name}")
+                    if not backup_corrupted_file(json_file):
+                        has_failures = True
+
+            if has_failures:
+                sys.exit(1)
+
+        elif args.all:
+            # Delete all corrupted files
+            # Use the already-detected corrupted list, or re-scan if needed
+            if not corrupted:
+                corrupted = detect_corrupted_files(specs_dir)
+            if not corrupted:
+                print("[OK] No corrupted files to delete")
+                sys.exit(0)
+
+            print(f"\n[INFO] Backing up {len(corrupted)} corrupted file(s):\n")
+            has_failures = False
+            for filepath, _ in corrupted:
+                # backup_corrupted_file prints its own [BACKUP] message
+                if not backup_corrupted_file(filepath):
+                    has_failures = True
+
+            if has_failures:
+                sys.exit(1)
+
+        else:
+            print("[ERROR] Must specify --spec-id or --all with --delete")
+            sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

apps/backend/cli/spec_commands.py

@@ -19,18 +19,17 @@ from workspace import get_existing_build_worktree
 from .utils import get_specs_dir
 
 
-def list_specs(project_dir: Path, dev_mode: bool = False) -> list[dict]:
+def list_specs(project_dir: Path) -> list[dict]:
     """
     List all specs in the project.
 
     Args:
         project_dir: Project root directory
-        dev_mode: If True, use dev/auto-claude/specs/
 
     Returns:
         List of spec info dicts with keys: number, name, path, status, progress
     """
-    specs_dir = get_specs_dir(project_dir, dev_mode)
+    specs_dir = get_specs_dir(project_dir)
     specs = []
 
     if not specs_dir.exists():
@@ -93,19 +92,16 @@ def list_specs(project_dir: Path, dev_mode: bool = False) -> list[dict]:
     return specs
 
 
-def print_specs_list(
-    project_dir: Path, dev_mode: bool = False, auto_create: bool = True
-) -> None:
+def print_specs_list(project_dir: Path, auto_create: bool = True) -> None:
     """Print a formatted list of all specs.
 
     Args:
         project_dir: Project root directory
-        dev_mode: If True, use dev/auto-claude/specs/
         auto_create: If True and no specs exist, automatically launch spec creation
     """
     import subprocess
 
-    specs = list_specs(project_dir, dev_mode)
+    specs = list_specs(project_dir)
 
     if not specs:
         print("\nNo specs found.")

apps/backend/cli/utils.py

@@ -15,8 +15,50 @@ if str(_PARENT_DIR) not in sys.path:
     sys.path.insert(0, str(_PARENT_DIR))
 
 from core.auth import get_auth_token, get_auth_token_source
-from dotenv import load_dotenv
-from graphiti_config import get_graphiti_status
+from core.dependency_validator import validate_platform_dependencies
+
+
+def import_dotenv():
+    """
+    Import and return load_dotenv with helpful error message if not installed.
+
+    This centralized function ensures consistent error messaging across all
+    runner scripts when python-dotenv is not available.
+
+    Returns:
+        The load_dotenv function
+
+    Raises:
+        SystemExit: If dotenv cannot be imported, with helpful installation instructions.
+    """
+    try:
+        from dotenv import load_dotenv as _load_dotenv
+
+        return _load_dotenv
+    except ImportError:
+        sys.exit(
+            "Error: Required Python package 'python-dotenv' is not installed.\n"
+            "\n"
+            "This usually means you're not using the virtual environment.\n"
+            "\n"
+            "To fix this:\n"
+            "1. From the 'apps/backend/' directory, activate the venv:\n"
+            "   source .venv/bin/activate  # Linux/macOS\n"
+            "   .venv\\Scripts\\activate   # Windows\n"
+            "\n"
+            "2. Or install dependencies directly:\n"
+            "   pip install python-dotenv\n"
+            "   pip install -r requirements.txt\n"
+            "\n"
+            f"Current Python: {sys.executable}\n"
+        )
+
+
+# Load .env with helpful error if dependencies not installed
+load_dotenv = import_dotenv()
+# NOTE: graphiti_config is imported lazily in validate_environment() to avoid
+# triggering graphiti_core -> real_ladybug -> pywintypes import chain before
+# platform dependency validation can run. See ACS-253.
 from linear_integration import LinearManager
 from linear_updater import is_linear_enabled
 from spec.pipeline import get_specs_dir
@@ -28,8 +70,8 @@ from ui import (
     muted,
 )
 
-# Configuration
-DEFAULT_MODEL = "claude-opus-4-5-20251101"
+# Configuration - uses shorthand that resolves via API Profile if configured
+DEFAULT_MODEL = "sonnet"  # Changed from "opus" (fix #433)
 
 
 def setup_environment() -> Path:
@@ -54,35 +96,56 @@ def setup_environment() -> Path:
     return script_dir
 
 
-def find_spec(
-    project_dir: Path, spec_identifier: str, dev_mode: bool = False
-) -> Path | None:
+def find_spec(project_dir: Path, spec_identifier: str) -> Path | None:
     """
     Find a spec by number or full name.
 
     Args:
         project_dir: Project root directory
         spec_identifier: Either "001" or "001-feature-name"
-        dev_mode: If True, use dev/auto-claude/specs/
 
     Returns:
         Path to spec folder, or None if not found
     """
-    specs_dir = get_specs_dir(project_dir, dev_mode)
+    specs_dir = get_specs_dir(project_dir)
 
-    if not specs_dir.exists():
-        return None
+    if specs_dir.exists():
+        # Try exact match first
+        exact_path = specs_dir / spec_identifier
+        if exact_path.exists() and (exact_path / "spec.md").exists():
+            return exact_path
 
-    # Try exact match first
-    exact_path = specs_dir / spec_identifier
-    if exact_path.exists() and (exact_path / "spec.md").exists():
-        return exact_path
+        # Try matching by number prefix
+        for spec_folder in specs_dir.iterdir():
+            if spec_folder.is_dir() and spec_folder.name.startswith(
+                spec_identifier + "-"
+            ):
+                if (spec_folder / "spec.md").exists():
+                    return spec_folder
 
-    # Try matching by number prefix
-    for spec_folder in specs_dir.iterdir():
-        if spec_folder.is_dir() and spec_folder.name.startswith(spec_identifier + "-"):
-            if (spec_folder / "spec.md").exists():
-                return spec_folder
+    # Check worktree specs (for merge-preview, merge, review, discard operations)
+    worktree_base = project_dir / ".auto-claude" / "worktrees" / "tasks"
+    if worktree_base.exists():
+        # Try exact match in worktree
+        worktree_spec = (
+            worktree_base / spec_identifier / ".auto-claude" / "specs" / spec_identifier
+        )
+        if worktree_spec.exists() and (worktree_spec / "spec.md").exists():
+            return worktree_spec
+
+        # Try matching by prefix in worktrees
+        for worktree_dir in worktree_base.iterdir():
+            if worktree_dir.is_dir() and worktree_dir.name.startswith(
+                spec_identifier + "-"
+            ):
+                spec_in_worktree = (
+                    worktree_dir / ".auto-claude" / "specs" / worktree_dir.name
+                )
+                if (
+                    spec_in_worktree.exists()
+                    and (spec_in_worktree / "spec.md").exists()
+                ):
+                    return spec_in_worktree
 
     return None
 
@@ -94,6 +157,9 @@ def validate_environment(spec_dir: Path) -> bool:
     Returns:
         True if valid, False otherwise (with error messages printed)
     """
+    # Validate platform-specific dependencies first (exits if missing)
+    validate_platform_dependencies()
+
     valid = True
 
     # Check for OAuth token (API keys are not supported)
@@ -141,6 +207,9 @@ def validate_environment(spec_dir: Path) -> bool:
         print("Linear integration: DISABLED (set LINEAR_API_KEY to enable)")
 
     # Check Graphiti integration (optional but show status)
+    # Lazy import to avoid triggering pywintypes import before validation (ACS-253)
+    from graphiti_config import get_graphiti_status
+
     graphiti_status = get_graphiti_status()
     if graphiti_status["available"]:
         print("Graphiti memory: ENABLED")
@@ -191,3 +260,19 @@ def get_project_dir(provided_dir: Path | None) -> Path:
         project_dir = project_dir.parent.parent
 
     return project_dir
+
+
+def find_specs_dir(project_dir: Path) -> Path:
+    """
+    Find the specs directory for a project.
+
+    Returns the '.auto-claude/specs' directory path.
+    The directory is guaranteed to exist (get_specs_dir calls init_auto_claude_dir).
+
+    Args:
+        project_dir: Project root directory
+
+    Returns:
+        Path to specs directory (always returns a valid Path)
+    """
+    return get_specs_dir(project_dir)

apps/backend/cli/workspace_commands.py

@@ -5,6 +5,7 @@ Workspace Commands
 CLI commands for workspace management (merge, review, discard, list, cleanup)
 """
 
+import json
 import subprocess
 import sys
 from pathlib import Path
@@ -14,7 +15,16 @@ _PARENT_DIR = Path(__file__).parent.parent
 if str(_PARENT_DIR) not in sys.path:
     sys.path.insert(0, str(_PARENT_DIR))
 
-from core.workspace.git_utils import _is_auto_claude_file, is_lock_file
+from core.workspace.git_utils import (
+    _is_auto_claude_file,
+    apply_path_mapping,
+    detect_file_renames,
+    get_file_content_from_ref,
+    get_merge_base,
+    is_lock_file,
+)
+from core.worktree import PushAndCreatePRResult as CreatePRResult
+from core.worktree import WorktreeManager
 from debug import debug_warning
 from ui import (
     Icons,
@@ -23,6 +33,7 @@ from ui import (
 from workspace import (
     cleanup_all_worktrees,
     discard_existing_build,
+    get_existing_build_worktree,
     list_all_worktrees,
     merge_existing_build,
     review_existing_build,
@@ -60,6 +71,7 @@ def _detect_default_branch(project_dir: Path) -> str:
             cwd=project_dir,
             capture_output=True,
             text=True,
+            timeout=5,
         )
         if result.returncode == 0:
             return env_branch
@@ -71,6 +83,7 @@ def _detect_default_branch(project_dir: Path) -> str:
             cwd=project_dir,
             capture_output=True,
             text=True,
+            timeout=5,
         )
         if result.returncode == 0:
             return branch
@@ -83,18 +96,32 @@ def _get_changed_files_from_git(
     worktree_path: Path, base_branch: str = "main"
 ) -> list[str]:
     """
-    Get list of changed files from git diff between base branch and HEAD.
+    Get list of files changed by the task (not files changed on base branch).
+
+    Uses merge-base to accurately identify only the files modified in the worktree,
+    not files that changed on the base branch since the worktree was created.
 
     Args:
         worktree_path: Path to the worktree
         base_branch: Base branch to compare against (default: main)
 
     Returns:
-        List of changed file paths
+        List of changed file paths (task changes only)
     """
     try:
+        # First, get the merge-base (the point where the worktree branched)
+        merge_base_result = subprocess.run(
+            ["git", "merge-base", base_branch, "HEAD"],
+            cwd=worktree_path,
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+        merge_base = merge_base_result.stdout.strip()
+
+        # Use two-dot diff from merge-base to get only task's changes
         result = subprocess.run(
-            ["git", "diff", "--name-only", f"{base_branch}...HEAD"],
+            ["git", "diff", "--name-only", f"{merge_base}..HEAD"],
             cwd=worktree_path,
             capture_output=True,
             text=True,
@@ -106,10 +133,10 @@ def _get_changed_files_from_git(
         # Log the failure before trying fallback
         debug_warning(
             "workspace_commands",
-            f"git diff (three-dot) failed: returncode={e.returncode}, "
+            f"git diff with merge-base failed: returncode={e.returncode}, "
             f"stderr={e.stderr.strip() if e.stderr else 'N/A'}",
         )
-        # Fallback: try without the three-dot notation
+        # Fallback: try direct two-arg diff (less accurate but works)
         try:
             result = subprocess.run(
                 ["git", "diff", "--name-only", base_branch, "HEAD"],
@@ -124,12 +151,176 @@ def _get_changed_files_from_git(
             # Log the failure before returning empty list
             debug_warning(
                 "workspace_commands",
-                f"git diff (two-arg) failed: returncode={e.returncode}, "
+                f"git diff (fallback) failed: returncode={e.returncode}, "
                 f"stderr={e.stderr.strip() if e.stderr else 'N/A'}",
             )
             return []
 
 
+def _detect_worktree_base_branch(
+    project_dir: Path,
+    worktree_path: Path,
+    spec_name: str,
+) -> str | None:
+    """
+    Detect which branch a worktree was created from.
+
+    Tries multiple strategies:
+    1. Check worktree config file (.auto-claude/worktree-config.json)
+    2. Find merge-base with known branches (develop, main, master)
+    3. Return None if unable to detect
+
+    Args:
+        project_dir: Project root directory
+        worktree_path: Path to the worktree
+        spec_name: Name of the spec
+
+    Returns:
+        The detected base branch name, or None if unable to detect
+    """
+    # Strategy 1: Check for worktree config file
+    config_path = worktree_path / ".auto-claude" / "worktree-config.json"
+    if config_path.exists():
+        try:
+            config = json.loads(config_path.read_text(encoding="utf-8"))
+            if config.get("base_branch"):
+                debug(
+                    MODULE,
+                    f"Found base branch in worktree config: {config['base_branch']}",
+                )
+                return config["base_branch"]
+        except Exception as e:
+            debug_warning(MODULE, f"Failed to read worktree config: {e}")
+
+    # Strategy 2: Find which branch has the closest merge-base
+    # Check common branches: develop, main, master
+    spec_branch = f"auto-claude/{spec_name}"
+    candidate_branches = ["develop", "main", "master"]
+
+    best_branch = None
+    best_commits_behind = float("inf")
+
+    for branch in candidate_branches:
+        try:
+            # Check if branch exists
+            check = subprocess.run(
+                ["git", "rev-parse", "--verify", branch],
+                cwd=project_dir,
+                capture_output=True,
+                text=True,
+            )
+            if check.returncode != 0:
+                continue
+
+            # Get merge base
+            merge_base_result = subprocess.run(
+                ["git", "merge-base", branch, spec_branch],
+                cwd=project_dir,
+                capture_output=True,
+                text=True,
+            )
+            if merge_base_result.returncode != 0:
+                continue
+
+            merge_base = merge_base_result.stdout.strip()
+
+            # Count commits between merge-base and branch tip
+            # The branch with fewer commits ahead is likely the one we branched from
+            ahead_result = subprocess.run(
+                ["git", "rev-list", "--count", f"{merge_base}..{branch}"],
+                cwd=project_dir,
+                capture_output=True,
+                text=True,
+            )
+            if ahead_result.returncode == 0:
+                commits_ahead = int(ahead_result.stdout.strip())
+                debug(
+                    MODULE,
+                    f"Branch {branch} is {commits_ahead} commits ahead of merge-base",
+                )
+                if commits_ahead < best_commits_behind:
+                    best_commits_behind = commits_ahead
+                    best_branch = branch
+        except Exception as e:
+            debug_warning(MODULE, f"Error checking branch {branch}: {e}")
+            continue
+
+    if best_branch:
+        debug(
+            MODULE,
+            f"Detected base branch from git history: {best_branch} (commits ahead: {best_commits_behind})",
+        )
+        return best_branch
+
+    return None
+
+
+def _detect_parallel_task_conflicts(
+    project_dir: Path,
+    current_task_id: str,
+    current_task_files: list[str],
+) -> list[dict]:
+    """
+    Detect potential conflicts between this task and other active tasks.
+
+    Uses existing evolution data to check if any of this task's files
+    have been modified by other active tasks. This is a lightweight check
+    that doesn't require re-processing all files.
+
+    Args:
+        project_dir: Project root directory
+        current_task_id: ID of the current task
+        current_task_files: Files modified by this task (from git diff)
+
+    Returns:
+        List of conflict dictionaries with 'file' and 'tasks' keys
+    """
+    try:
+        from merge import MergeOrchestrator
+
+        # Initialize orchestrator just to access evolution data
+        orchestrator = MergeOrchestrator(
+            project_dir,
+            enable_ai=False,
+            dry_run=True,
+        )
+
+        # Get all active tasks from evolution data
+        active_tasks = orchestrator.evolution_tracker.get_active_tasks()
+
+        # Remove current task from active tasks
+        other_active_tasks = active_tasks - {current_task_id}
+
+        if not other_active_tasks:
+            return []
+
+        # Convert current task files to a set for fast lookup
+        current_files_set = set(current_task_files)
+
+        # Get files modified by other active tasks
+        conflicts = []
+        other_task_files = orchestrator.evolution_tracker.get_files_modified_by_tasks(
+            list(other_active_tasks)
+        )
+
+        # Find intersection - files modified by both this task and other tasks
+        for file_path, tasks in other_task_files.items():
+            if file_path in current_files_set:
+                # This file was modified by both current task and other task(s)
+                all_tasks = [current_task_id] + tasks
+                conflicts.append({"file": file_path, "tasks": all_tasks})
+
+        return conflicts
+
+    except Exception as e:
+        # If anything fails, just return empty - parallel task detection is optional
+        debug_warning(
+            "workspace_commands",
+            f"Parallel task conflict detection failed: {e}",
+        )
+        return []
+
+
 # Import debug utilities
 try:
     from debug import (
@@ -345,7 +536,178 @@ def handle_cleanup_worktrees_command(project_dir: Path) -> None:
     cleanup_all_worktrees(project_dir, confirm=True)
 
 
-def _check_git_merge_conflicts(project_dir: Path, spec_name: str) -> dict:
+def _detect_conflict_scenario(
+    project_dir: Path,
+    conflicting_files: list[str],
+    spec_branch: str,
+    base_branch: str,
+) -> dict:
+    """
+    Analyze conflicting files to determine the conflict scenario.
+
+    This helps distinguish between:
+    - 'already_merged': Task changes already identical in target branch
+    - 'superseded': Target has newer version of same feature
+    - 'diverged': Standard diverged branches (AI can resolve)
+    - 'normal_conflict': Actual conflicting changes
+
+    Returns dict with:
+    - scenario: 'already_merged' | 'superseded' | 'diverged' | 'normal_conflict'
+    - already_merged_files: files identical in task and target
+    - details: additional context
+    """
+    if not conflicting_files:
+        return {
+            "scenario": "normal_conflict",
+            "already_merged_files": [],
+            "details": "No conflicting files to analyze",
+        }
+
+    already_merged_files = []
+    superseded_files = []
+    diverged_files = []
+
+    try:
+        # Get the merge-base commit
+        merge_base_result = subprocess.run(
+            ["git", "merge-base", base_branch, spec_branch],
+            cwd=project_dir,
+            capture_output=True,
+            text=True,
+        )
+        if merge_base_result.returncode != 0:
+            debug_warning(
+                MODULE, "Could not find merge base for conflict scenario detection"
+            )
+            return {
+                "scenario": "normal_conflict",
+                "already_merged_files": [],
+                "details": "Could not determine merge base",
+            }
+
+        merge_base = merge_base_result.stdout.strip()
+
+        for file_path in conflicting_files:
+            try:
+                # Get content from spec branch (task's changes)
+                spec_content_result = subprocess.run(
+                    ["git", "show", f"{spec_branch}:{file_path}"],
+                    cwd=project_dir,
+                    capture_output=True,
+                    text=True,
+                )
+                # Get content from base branch (target)
+                base_content_result = subprocess.run(
+                    ["git", "show", f"{base_branch}:{file_path}"],
+                    cwd=project_dir,
+                    capture_output=True,
+                    text=True,
+                )
+                # Get content from merge-base (original state)
+                merge_base_content_result = subprocess.run(
+                    ["git", "show", f"{merge_base}:{file_path}"],
+                    cwd=project_dir,
+                    capture_output=True,
+                    text=True,
+                )
+
+                # Check file existence in each ref
+                spec_exists = spec_content_result.returncode == 0
+                base_exists = base_content_result.returncode == 0
+                merge_base_exists = merge_base_content_result.returncode == 0
+
+                if spec_exists and base_exists:
+                    spec_content = spec_content_result.stdout
+                    base_content = base_content_result.stdout
+
+                    # If contents are identical, the changes are already merged
+                    if spec_content == base_content:
+                        already_merged_files.append(file_path)
+                        debug(
+                            MODULE,
+                            f"File {file_path}: already merged (identical content)",
+                        )
+                    elif merge_base_exists:
+                        merge_base_content = merge_base_content_result.stdout
+                        # If base has changed from merge_base but spec matches merge_base,
+                        # the task's changes are superseded by newer changes
+                        if spec_content == merge_base_content:
+                            superseded_files.append(file_path)
+                            debug(
+                                MODULE,
+                                f"File {file_path}: superseded (base has newer changes)",
+                            )
+                        else:
+                            diverged_files.append(file_path)
+                            debug(
+                                MODULE,
+                                f"File {file_path}: diverged (both branches modified)",
+                            )
+                    else:
+                        diverged_files.append(file_path)
+                else:
+                    diverged_files.append(file_path)
+
+            except Exception as e:
+                debug_warning(
+                    MODULE, f"Error analyzing file {file_path} for scenario: {e}"
+                )
+                diverged_files.append(file_path)
+
+        # Determine overall scenario based on dominant pattern
+        total_files = len(conflicting_files)
+
+        if len(already_merged_files) == total_files:
+            scenario = "already_merged"
+            details = "All conflicting files have identical content in both branches"
+        elif len(already_merged_files) > total_files / 2:
+            scenario = "already_merged"
+            details = f"{len(already_merged_files)} of {total_files} files already have the same content"
+        elif len(superseded_files) == total_files:
+            scenario = "superseded"
+            details = "All task changes have been superseded by newer changes in the target branch"
+        elif len(superseded_files) > total_files / 2:
+            scenario = "superseded"
+            details = (
+                f"{len(superseded_files)} of {total_files} files have been superseded"
+            )
+        elif diverged_files:
+            scenario = "diverged"
+            details = f"{len(diverged_files)} files have diverged and need AI merge"
+        else:
+            scenario = "normal_conflict"
+            details = "Standard merge conflicts detected"
+
+        debug(
+            MODULE,
+            f"Conflict scenario: {scenario}",
+            already_merged=len(already_merged_files),
+            superseded=len(superseded_files),
+            diverged=len(diverged_files),
+        )
+
+        return {
+            "scenario": scenario,
+            "already_merged_files": already_merged_files,
+            "superseded_files": superseded_files,
+            "diverged_files": diverged_files,
+            "details": details,
+        }
+
+    except Exception as e:
+        debug_error(MODULE, f"Error detecting conflict scenario: {e}")
+        return {
+            "scenario": "normal_conflict",
+            "already_merged_files": [],
+            "superseded_files": [],
+            "diverged_files": [],
+            "details": f"Error during analysis: {e}",
+        }
+
+
+def _check_git_merge_conflicts(
+    project_dir: Path, spec_name: str, base_branch: str | None = None
+) -> dict:
     """
     Check for git-level merge conflicts WITHOUT modifying the working directory.
 
@@ -355,6 +717,7 @@ def _check_git_merge_conflicts(project_dir: Path, spec_name: str) -> dict:
     Args:
         project_dir: Project root directory
         spec_name: Name of the spec
+        base_branch: Branch the task was created from (default: auto-detect)
 
     Returns:
         Dictionary with git conflict information:
@@ -373,21 +736,25 @@ def _check_git_merge_conflicts(project_dir: Path, spec_name: str) -> dict:
         "has_conflicts": False,
         "conflicting_files": [],
         "needs_rebase": False,
-        "base_branch": "main",
+        "base_branch": base_branch or "main",
         "spec_branch": spec_branch,
         "commits_behind": 0,
     }
 
     try:
-        # Get the current branch (base branch)
-        base_result = subprocess.run(
-            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
-            cwd=project_dir,
-            capture_output=True,
-            text=True,
-        )
-        if base_result.returncode == 0:
-            result["base_branch"] = base_result.stdout.strip()
+        # Use provided base_branch, or detect from current HEAD
+        if not base_branch:
+            base_result = subprocess.run(
+                ["git", "rev-parse", "--abbrev-ref", "HEAD"],
+                cwd=project_dir,
+                capture_output=True,
+                text=True,
+            )
+            if base_result.returncode == 0:
+                result["base_branch"] = base_result.stdout.strip()
+        else:
+            result["base_branch"] = base_branch
+            debug(MODULE, f"Using provided base branch: {base_branch}")
 
         # Get the merge base commit
         merge_base_result = subprocess.run(
@@ -546,7 +913,6 @@ def handle_merge_preview_command(
         spec_name=spec_name,
     )
 
-    from merge import MergeOrchestrator
     from workspace import get_existing_build_worktree
 
     worktree_path = get_existing_build_worktree(project_dir, spec_name)
@@ -573,16 +939,32 @@ def handle_merge_preview_command(
         }
 
     try:
-        # First, check for git-level conflicts (diverged branches)
-        git_conflicts = _check_git_merge_conflicts(project_dir, spec_name)
-
         # Determine the task's source branch (where the task was created from)
-        # Use provided base_branch (from task metadata), or fall back to detected default
+        # Priority:
+        # 1. Provided base_branch (from task metadata)
+        # 2. Detect from worktree's git history (find which branch it diverged from)
+        # 3. Fall back to default branch detection (main/master)
         task_source_branch = base_branch
         if not task_source_branch:
-            # Auto-detect the default branch (main/master) that worktrees are typically created from
+            # Try to detect from worktree's git history
+            task_source_branch = _detect_worktree_base_branch(
+                project_dir, worktree_path, spec_name
+            )
+        if not task_source_branch:
+            # Fall back to auto-detecting main/master
             task_source_branch = _detect_default_branch(project_dir)
 
+        debug(
+            MODULE,
+            f"Using task source branch: {task_source_branch}",
+            provided=base_branch is not None,
+        )
+
+        # Check for git-level conflicts (diverged branches) using the task's source branch
+        git_conflicts = _check_git_merge_conflicts(
+            project_dir, spec_name, base_branch=task_source_branch
+        )
+
         # Get actual changed files from git diff (this is the authoritative count)
         all_changed_files = _get_changed_files_from_git(
             worktree_path, task_source_branch
@@ -593,49 +975,39 @@ def handle_merge_preview_command(
             changed_files=all_changed_files[:10],  # Log first 10
         )
 
-        debug(MODULE, "Initializing MergeOrchestrator for preview...")
+        # OPTIMIZATION: Skip expensive refresh_from_git() and preview_merge() calls
+        # For merge-preview, we only need to detect:
+        # 1. Git conflicts (task vs base branch) - already calculated in _check_git_merge_conflicts()
+        # 2. Parallel task conflicts (this task vs other active tasks)
+        #
+        # For parallel task detection, we just check if this task's files overlap
+        # with files OTHER tasks have already recorded - no need to re-process all files.
 
-        # Initialize the orchestrator
-        orchestrator = MergeOrchestrator(
-            project_dir,
-            enable_ai=False,  # Don't use AI for preview
-            dry_run=True,  # Don't write anything
+        debug(MODULE, "Checking for parallel task conflicts (lightweight)...")
+
+        # Check for parallel task conflicts by looking at existing evolution data
+        parallel_conflicts = _detect_parallel_task_conflicts(
+            project_dir, spec_name, all_changed_files
         )
-
-        # Refresh evolution data from the worktree
-        # Compare against the task's source branch (where the task was created from)
         debug(
             MODULE,
-            f"Refreshing evolution data from worktree: {worktree_path}",
-            task_source_branch=task_source_branch,
-        )
-        orchestrator.evolution_tracker.refresh_from_git(
-            spec_name, worktree_path, target_branch=task_source_branch
+            f"Parallel task conflicts detected: {len(parallel_conflicts)}",
+            conflicts=parallel_conflicts[:5] if parallel_conflicts else [],
         )
 
-        # Get merge preview (semantic conflicts between parallel tasks)
-        debug(MODULE, "Generating merge preview...")
-        preview = orchestrator.preview_merge([spec_name])
-
-        # Transform semantic conflicts to UI-friendly format
+        # Build conflict list - start with parallel task conflicts
         conflicts = []
-        for c in preview.get("conflicts", []):
-            debug_verbose(
-                MODULE,
-                "Processing semantic conflict",
-                file=c.get("file", ""),
-                severity=c.get("severity", "unknown"),
-            )
+        for pc in parallel_conflicts:
             conflicts.append(
                 {
-                    "file": c.get("file", ""),
-                    "location": c.get("location", ""),
-                    "tasks": c.get("tasks", []),
-                    "severity": c.get("severity", "unknown"),
-                    "canAutoMerge": c.get("can_auto_merge", False),
-                    "strategy": c.get("strategy"),
-                    "reason": c.get("reason", ""),
-                    "type": "semantic",
+                    "file": pc["file"],
+                    "location": "file-level",
+                    "tasks": pc["tasks"],
+                    "severity": "medium",
+                    "canAutoMerge": False,
+                    "strategy": None,
+                    "reason": f"File modified by multiple active tasks: {', '.join(pc['tasks'])}",
+                    "type": "parallel",
                 }
             )
 
@@ -662,24 +1034,95 @@ def handle_merge_preview_command(
                 }
             )
 
-        summary = preview.get("summary", {})
         # Count only non-lock-file conflicts
         git_conflict_count = len(git_conflicts.get("conflicting_files", [])) - len(
             lock_files_excluded
         )
-        total_conflicts = summary.get("total_conflicts", 0) + git_conflict_count
-        conflict_files = summary.get("conflict_files", 0) + git_conflict_count
+        # Calculate totals from our conflict lists (git conflicts + parallel conflicts)
+        parallel_conflict_count = len(parallel_conflicts)
+        total_conflicts = git_conflict_count + parallel_conflict_count
+        conflict_files = git_conflict_count + parallel_conflict_count
 
         # Filter lock files from the git conflicts list for the response
         non_lock_conflicting_files = [
             f for f in git_conflicts.get("conflicting_files", []) if not is_lock_file(f)
         ]
 
+        # Detect conflict scenario (already_merged, superseded, diverged, normal_conflict)
+        # This helps the UI show appropriate messaging and actions
+        conflict_scenario = None
+        if non_lock_conflicting_files:
+            conflict_scenario = _detect_conflict_scenario(
+                project_dir,
+                non_lock_conflicting_files,
+                git_conflicts["spec_branch"],
+                git_conflicts["base_branch"],
+            )
+            debug(
+                MODULE,
+                f"Conflict scenario detected: {conflict_scenario.get('scenario')}",
+                already_merged_files=len(
+                    conflict_scenario.get("already_merged_files", [])
+                ),
+            )
+
         # Use git diff file count as the authoritative totalFiles count
         # The semantic tracker may not track all files (e.g., test files, config files)
         # but we want to show the user all files that will be merged
         total_files_from_git = len(all_changed_files)
 
+        # Detect files that need AI merge due to path mappings (file renames)
+        # This happens when the target branch has renamed/moved files that the
+        # worktree modified at their old locations
+        path_mapped_ai_merges: list[dict] = []
+        path_mappings: dict[str, str] = {}
+
+        if git_conflicts["needs_rebase"] and git_conflicts["commits_behind"] > 0:
+            # Get the merge-base between the branches
+            spec_branch = git_conflicts["spec_branch"]
+            base_branch = git_conflicts["base_branch"]
+            merge_base = get_merge_base(project_dir, spec_branch, base_branch)
+
+            if merge_base:
+                # Detect file renames between merge-base and current base branch
+                path_mappings = detect_file_renames(
+                    project_dir, merge_base, base_branch
+                )
+
+                if path_mappings:
+                    debug(
+                        MODULE,
+                        f"Detected {len(path_mappings)} file rename(s) between merge-base and target",
+                        sample_mappings={
+                            k: v for k, v in list(path_mappings.items())[:3]
+                        },
+                    )
+
+                    # Check which changed files have path mappings and need AI merge
+                    for file_path in all_changed_files:
+                        mapped_path = apply_path_mapping(file_path, path_mappings)
+                        if mapped_path != file_path:
+                            # File was renamed - check if both versions exist
+                            worktree_content = get_file_content_from_ref(
+                                project_dir, spec_branch, file_path
+                            )
+                            target_content = get_file_content_from_ref(
+                                project_dir, base_branch, mapped_path
+                            )
+
+                            if worktree_content and target_content:
+                                path_mapped_ai_merges.append(
+                                    {
+                                        "oldPath": file_path,
+                                        "newPath": mapped_path,
+                                        "reason": "File was renamed/moved and modified in both branches",
+                                    }
+                                )
+                                debug(
+                                    MODULE,
+                                    f"Path-mapped file needs AI merge: {file_path} -> {mapped_path}",
+                                )
+
         result = {
             "success": True,
             # Use git diff files as the authoritative list of files to merge
@@ -693,15 +1136,30 @@ def handle_merge_preview_command(
                 "commitsBehind": git_conflicts["commits_behind"],
                 "baseBranch": git_conflicts["base_branch"],
                 "specBranch": git_conflicts["spec_branch"],
+                # Path-mapped files that need AI merge due to renames
+                "pathMappedAIMerges": path_mapped_ai_merges,
+                "totalRenames": len(path_mappings),
+                # Conflict scenario detection for better UX messaging
+                "scenario": conflict_scenario.get("scenario")
+                if conflict_scenario
+                else None,
+                "alreadyMergedFiles": conflict_scenario.get("already_merged_files", [])
+                if conflict_scenario
+                else [],
+                "scenarioMessage": conflict_scenario.get("details")
+                if conflict_scenario
+                else None,
             },
             "summary": {
                 # Use git diff count, not semantic tracker count
                 "totalFiles": total_files_from_git,
                 "conflictFiles": conflict_files,
                 "totalConflicts": total_conflicts,
-                "autoMergeable": summary.get("auto_mergeable", 0),
+                "autoMergeable": 0,  # Not tracking auto-merge in lightweight mode
                 "hasGitConflicts": git_conflicts["has_conflicts"]
                 and len(non_lock_conflicting_files) > 0,
+                # Include path-mapped AI merge count for UI display
+                "pathMappedAIMergeCount": len(path_mapped_ai_merges),
             },
             # Include lock files info so UI can optionally show them
             "lockFilesExcluded": lock_files_excluded,
@@ -712,10 +1170,11 @@ def handle_merge_preview_command(
             "Merge preview complete",
             total_files=result["summary"]["totalFiles"],
             total_files_source="git_diff",
-            semantic_tracked_files=summary.get("total_files", 0),
             total_conflicts=result["summary"]["totalConflicts"],
             has_git_conflicts=git_conflicts["has_conflicts"],
-            auto_mergeable=result["summary"]["autoMergeable"],
+            parallel_conflicts=parallel_conflict_count,
+            path_mapped_ai_merges=len(path_mapped_ai_merges),
+            total_renames=len(path_mappings),
         )
 
         return result
@@ -736,5 +1195,223 @@ def handle_merge_preview_command(
                 "conflictFiles": 0,
                 "totalConflicts": 0,
                 "autoMergeable": 0,
+                "pathMappedAIMergeCount": 0,
             },
         }
+
+
+def handle_create_pr_command(
+    project_dir: Path,
+    spec_name: str,
+    target_branch: str | None = None,
+    title: str | None = None,
+    draft: bool = False,
+) -> CreatePRResult:
+    """
+    Handle the --create-pr command: push branch and create a GitHub PR.
+
+    Args:
+        project_dir: Path to the project directory
+        spec_name: Name of the spec (e.g., "001-feature-name")
+        target_branch: Target branch for PR (defaults to base branch)
+        title: Custom PR title (defaults to spec name)
+        draft: Whether to create as draft PR
+
+    Returns:
+        CreatePRResult with success status, pr_url, and any errors
+    """
+    from core.worktree import WorktreeManager
+
+    print_banner()
+    print("\n" + "=" * 70)
+    print("  CREATE PULL REQUEST")
+    print("=" * 70)
+
+    # Check if worktree exists
+    worktree_path = get_existing_build_worktree(project_dir, spec_name)
+    if not worktree_path:
+        print(f"\n{icon(Icons.ERROR)} No build found for spec: {spec_name}")
+        print("\nA completed build worktree is required to create a PR.")
+        print("Run your build first, then use --create-pr.")
+        error_result: CreatePRResult = {
+            "success": False,
+            "error": "No build found for this spec",
+        }
+        return error_result
+
+    # Create worktree manager
+    manager = WorktreeManager(project_dir, base_branch=target_branch)
+
+    print(f"\n{icon(Icons.BRANCH)} Pushing branch and creating PR...")
+    print(f"   Spec: {spec_name}")
+    print(f"   Target: {target_branch or manager.base_branch}")
+    if title:
+        print(f"   Title: {title}")
+    if draft:
+        print("   Mode: Draft PR")
+
+    # Push and create PR with exception handling for clean JSON output
+    try:
+        raw_result = manager.push_and_create_pr(
+            spec_name=spec_name,
+            target_branch=target_branch,
+            title=title,
+            draft=draft,
+        )
+    except Exception as e:
+        debug_error(MODULE, f"Exception during PR creation: {e}")
+        error_result: CreatePRResult = {
+            "success": False,
+            "error": str(e),
+            "message": "Failed to create PR",
+        }
+        print(f"\n{icon(Icons.ERROR)} Failed to create PR: {e}")
+        print(json.dumps(error_result))
+        return error_result
+
+    # Convert PushAndCreatePRResult to CreatePRResult
+    result: CreatePRResult = {
+        "success": raw_result.get("success", False),
+        "pr_url": raw_result.get("pr_url"),
+        "already_exists": raw_result.get("already_exists", False),
+        "error": raw_result.get("error"),
+        "message": raw_result.get("message"),
+        "pushed": raw_result.get("pushed", False),
+        "remote": raw_result.get("remote", ""),
+        "branch": raw_result.get("branch", ""),
+    }
+
+    if result.get("success"):
+        pr_url = result.get("pr_url")
+        already_exists = result.get("already_exists", False)
+
+        if already_exists:
+            print(f"\n{icon(Icons.SUCCESS)} PR already exists!")
+        else:
+            print(f"\n{icon(Icons.SUCCESS)} PR created successfully!")
+
+        if pr_url:
+            print(f"\n{icon(Icons.LINK)} {pr_url}")
+        else:
+            print(f"\n{icon(Icons.INFO)} Check GitHub for the PR URL")
+
+        print("\nNext steps:")
+        print("  1. Review the PR on GitHub")
+        print("  2. Request reviews from your team")
+        print("  3. Merge when approved")
+
+        # Output JSON for frontend parsing
+        print(json.dumps(result))
+        return result
+    else:
+        error = result.get("error", "Unknown error")
+        print(f"\n{icon(Icons.ERROR)} Failed to create PR: {error}")
+        # Output JSON for frontend parsing
+        print(json.dumps(result))
+        return result
+
+
+def cleanup_old_worktrees_command(
+    project_dir: Path, days: int = 30, dry_run: bool = False
+) -> dict:
+    """
+    Clean up old worktrees that haven't been modified in the specified number of days.
+
+    Args:
+        project_dir: Project root directory
+        days: Number of days threshold (default: 30)
+        dry_run: If True, only show what would be removed (default: False)
+
+    Returns:
+        Dictionary with cleanup results
+    """
+    try:
+        manager = WorktreeManager(project_dir)
+
+        removed, failed = manager.cleanup_old_worktrees(
+            days_threshold=days, dry_run=dry_run
+        )
+
+        return {
+            "success": True,
+            "removed": removed,
+            "failed": failed,
+            "dry_run": dry_run,
+            "days_threshold": days,
+        }
+
+    except Exception as e:
+        return {
+            "success": False,
+            "error": str(e),
+            "removed": [],
+            "failed": [],
+        }
+
+
+def worktree_summary_command(project_dir: Path) -> dict:
+    """
+    Get a summary of all worktrees with age information.
+
+    Args:
+        project_dir: Project root directory
+
+    Returns:
+        Dictionary with worktree summary data
+    """
+    try:
+        manager = WorktreeManager(project_dir)
+
+        # Print to console for CLI usage
+        manager.print_worktree_summary()
+
+        # Also return data for programmatic access
+        worktrees = manager.list_all_worktrees()
+        warning = manager.get_worktree_count_warning()
+
+        # Categorize by age
+        recent = []
+        week_old = []
+        month_old = []
+        very_old = []
+        unknown_age = []
+
+        for info in worktrees:
+            data = {
+                "spec_name": info.spec_name,
+                "days_since_last_commit": info.days_since_last_commit,
+                "commit_count": info.commit_count,
+            }
+
+            if info.days_since_last_commit is None:
+                unknown_age.append(data)
+            elif info.days_since_last_commit < 7:
+                recent.append(data)
+            elif info.days_since_last_commit < 30:
+                week_old.append(data)
+            elif info.days_since_last_commit < 90:
+                month_old.append(data)
+            else:
+                very_old.append(data)
+
+        return {
+            "success": True,
+            "total_worktrees": len(worktrees),
+            "categories": {
+                "recent": recent,
+                "week_old": week_old,
+                "month_old": month_old,
+                "very_old": very_old,
+                "unknown_age": unknown_age,
+            },
+            "warning": warning,
+        }
+
+    except Exception as e:
+        return {
+            "success": False,
+            "error": str(e),
+            "total_worktrees": 0,
+            "categories": {},
+            "warning": None,
+        }

apps/backend/commit_message.py

@@ -186,9 +186,15 @@ Fixes #N (if applicable)"""
     return prompt
 
 
-async def _call_claude_haiku(prompt: str) -> str:
-    """Call Claude Haiku with low thinking for fast commit message generation."""
+async def _call_claude(prompt: str) -> str:
+    """Call Claude for commit message generation.
+
+    Reads model/thinking settings from environment variables:
+    - UTILITY_MODEL_ID: Full model ID (e.g., "claude-haiku-4-5-20251001")
+    - UTILITY_THINKING_BUDGET: Thinking budget tokens (e.g., "1024")
+    """
     from core.auth import ensure_claude_code_oauth_token, get_auth_token
+    from core.model_config import get_utility_model_config
 
     if not get_auth_token():
         logger.warning("No authentication token found")
@@ -197,19 +203,23 @@ async def _call_claude_haiku(prompt: str) -> str:
     ensure_claude_code_oauth_token()
 
     try:
-        from claude_agent_sdk import ClaudeAgentOptions, ClaudeSDKClient
+        from core.simple_client import create_simple_client
     except ImportError:
-        logger.warning("claude_agent_sdk not installed")
+        logger.warning("core.simple_client not available")
         return ""
 
-    client = ClaudeSDKClient(
-        options=ClaudeAgentOptions(
-            model="claude-haiku-4-5-20251001",
-            system_prompt=SYSTEM_PROMPT,
-            allowed_tools=[],
-            max_turns=1,
-            max_thinking_tokens=1024,  # Low thinking for speed
-        )
+    # Get model settings from environment (passed from frontend)
+    model, thinking_budget = get_utility_model_config()
+
+    logger.info(
+        f"Commit message using model={model}, thinking_budget={thinking_budget}"
+    )
+
+    client = create_simple_client(
+        agent_type="commit_message",
+        model=model,
+        system_prompt=SYSTEM_PROMPT,
+        max_thinking_tokens=thinking_budget,
     )
 
     try:
@@ -221,7 +231,9 @@ async def _call_claude_haiku(prompt: str) -> str:
                 msg_type = type(msg).__name__
                 if msg_type == "AssistantMessage" and hasattr(msg, "content"):
                     for block in msg.content:
-                        if hasattr(block, "text"):
+                        # Must check block type - only TextBlock has .text attribute
+                        block_type = type(block).__name__
+                        if block_type == "TextBlock" and hasattr(block, "text"):
                             response_text += block.text
 
             logger.info(f"Generated commit message: {len(response_text)} chars")
@@ -287,11 +299,9 @@ def generate_commit_message_sync(
             import concurrent.futures
 
             with concurrent.futures.ThreadPoolExecutor() as pool:
-                result = pool.submit(
-                    lambda: asyncio.run(_call_claude_haiku(prompt))
-                ).result()
+                result = pool.submit(lambda: asyncio.run(_call_claude(prompt))).result()
         else:
-            result = asyncio.run(_call_claude_haiku(prompt))
+            result = asyncio.run(_call_claude(prompt))
 
         if result:
             return result
@@ -353,7 +363,7 @@ async def generate_commit_message(
 
     # Call Claude
     try:
-        result = await _call_claude_haiku(prompt)
+        result = await _call_claude(prompt)
         if result:
             return result
     except Exception as e:

apps/backend/context/builder.py

@@ -37,8 +37,12 @@ class ContextBuilder:
         """Load project index from file or create new one (.auto-claude is the installed instance)."""
         index_file = self.project_dir / ".auto-claude" / "project_index.json"
         if index_file.exists():
-            with open(index_file) as f:
-                return json.load(f)
+            try:
+                with open(index_file, encoding="utf-8") as f:
+                    return json.load(f)
+            except (OSError, json.JSONDecodeError, UnicodeDecodeError):
+                # Corrupted or legacy-encoded file, regenerate
+                pass
 
         # Try to create one
         from analyzer import analyze_project
@@ -230,7 +234,9 @@ class ContextBuilder:
         if context_file.exists():
             return {
                 "source": "SERVICE_CONTEXT.md",
-                "content": context_file.read_text()[:2000],  # First 2000 chars
+                "content": context_file.read_text(encoding="utf-8")[
+                    :2000
+                ],  # First 2000 chars
             }
 
         # Generate basic context from service info

apps/backend/context/main.py

@@ -72,7 +72,7 @@ def build_task_context(
 
     if output_file:
         output_file.parent.mkdir(parents=True, exist_ok=True)
-        with open(output_file, "w") as f:
+        with open(output_file, "w", encoding="utf-8") as f:
             json.dump(result, f, indent=2)
         print(f"Task context saved to: {output_file}")
 

apps/backend/context/pattern_discovery.py

@@ -38,7 +38,7 @@ class PatternDiscoverer:
         for match in reference_files[:max_files]:
             try:
                 file_path = self.project_dir / match.path
-                content = file_path.read_text(errors="ignore")
+                content = file_path.read_text(encoding="utf-8", errors="ignore")
 
                 # Look for common patterns
                 for keyword in keywords:

apps/backend/context/search.py

@@ -41,7 +41,7 @@ class CodeSearcher:
 
         for file_path in self._iter_code_files(service_path):
             try:
-                content = file_path.read_text(errors="ignore")
+                content = file_path.read_text(encoding="utf-8", errors="ignore")
                 content_lower = content.lower()
 
                 # Score this file

apps/backend/context/serialization.py

@@ -41,7 +41,7 @@ def save_context(context: TaskContext, output_file: Path) -> None:
         output_file: Path to output JSON file
     """
     output_file.parent.mkdir(parents=True, exist_ok=True)
-    with open(output_file, "w") as f:
+    with open(output_file, "w", encoding="utf-8") as f:
         json.dump(serialize_context(context), f, indent=2)
 
 
@@ -55,5 +55,5 @@ def load_context(input_file: Path) -> dict:
     Returns:
         Context dictionary
     """
-    with open(input_file) as f:
+    with open(input_file, encoding="utf-8") as f:
         return json.load(f)

apps/backend/core/agent.py

@@ -39,7 +39,7 @@ from agents import (
     run_followup_planner,
     save_session_memory,
     save_session_to_graphiti,
-    sync_plan_to_source,
+    sync_spec_to_source,
 )
 
 # Ensure all exports are available at module level
@@ -57,7 +57,7 @@ __all__ = [
     "load_implementation_plan",
     "find_subtask_in_plan",
     "find_phase_for_subtask",
-    "sync_plan_to_source",
+    "sync_spec_to_source",
     "AUTO_CONTINUE_DELAY_SECONDS",
     "HUMAN_INTERVENTION_FILE",
 ]

apps/backend/core/debug.py

@@ -110,7 +110,7 @@ def _write_log(message: str, to_file: bool = True) -> None:
                 import re
 
                 clean_message = re.sub(r"\033\[[0-9;]*m", "", message)
-                with open(log_file, "a") as f:
+                with open(log_file, "a", encoding="utf-8") as f:
                     f.write(clean_message + "\n")
             except Exception:
                 pass  # Silently fail file logging
@@ -235,10 +235,10 @@ def debug_section(module: str, title: str) -> None:
         return
 
     timestamp = datetime.now().strftime("%H:%M:%S.%f")[:-3]
-    separator = "─" * 60
-    log_line = f"\n{Colors.TIMESTAMP}[{timestamp}]{Colors.RESET} {Colors.DEBUG}{Colors.BOLD}┌{separator}┐{Colors.RESET}"
-    log_line += f"\n{Colors.TIMESTAMP}         {Colors.RESET} {Colors.DEBUG}{Colors.BOLD}│ {module}: {title}{' ' * (58 - len(module) - len(title) - 2)}│{Colors.RESET}"
-    log_line += f"\n{Colors.TIMESTAMP}         {Colors.RESET} {Colors.DEBUG}{Colors.BOLD}└{separator}┘{Colors.RESET}"
+    separator = "-" * 60
+    log_line = f"\n{Colors.TIMESTAMP}[{timestamp}]{Colors.RESET} {Colors.DEBUG}{Colors.BOLD}+{separator}+{Colors.RESET}"
+    log_line += f"\n{Colors.TIMESTAMP}         {Colors.RESET} {Colors.DEBUG}{Colors.BOLD}| {module}: {title}{' ' * (58 - len(module) - len(title) - 2)}|{Colors.RESET}"
+    log_line += f"\n{Colors.TIMESTAMP}         {Colors.RESET} {Colors.DEBUG}{Colors.BOLD}+{separator}+{Colors.RESET}"
 
     _write_log(log_line)
 

apps/backend/core/dependency_validator.py

@@ -0,0 +1,134 @@
+"""
+Dependency Validator
+====================
+
+Validates platform-specific dependencies are installed before running agents.
+"""
+
+import sys
+from pathlib import Path
+
+from core.platform import is_linux, is_windows
+
+
+def validate_platform_dependencies() -> None:
+    """
+    Validate that platform-specific dependencies are installed.
+
+    Raises:
+        SystemExit: If required platform-specific dependencies are missing,
+                   with helpful installation instructions.
+    """
+    # Check Windows-specific dependencies (all Python versions per ACS-306)
+    # pywin32 is required on all Python versions on Windows - MCP library unconditionally imports win32api
+    if is_windows():
+        try:
+            import pywintypes  # noqa: F401
+        except ImportError:
+            _exit_with_pywin32_error()
+
+    # Check Linux-specific dependencies (ACS-310)
+    # Note: secretstorage is optional for app functionality (falls back to .env),
+    # but we validate it to ensure proper OAuth token storage via keyring
+    if is_linux():
+        try:
+            import secretstorage  # noqa: F401
+        except ImportError:
+            _warn_missing_secretstorage()
+
+
+def _exit_with_pywin32_error() -> None:
+    """Exit with helpful error message for missing pywin32."""
+    # Use sys.prefix to detect the virtual environment path
+    # This works for venv and poetry environments
+    # Check for common Windows activation scripts (activate, activate.bat, Activate.ps1)
+    scripts_dir = Path(sys.prefix) / "Scripts"
+    activation_candidates = [
+        scripts_dir / "activate",
+        scripts_dir / "activate.bat",
+        scripts_dir / "Activate.ps1",
+    ]
+    venv_activate = next((p for p in activation_candidates if p.exists()), None)
+
+    # Build activation step only if activate script exists
+    activation_step = ""
+    if venv_activate:
+        activation_step = (
+            "To fix this:\n"
+            "1. Activate your virtual environment:\n"
+            f"   {venv_activate}\n"
+            "\n"
+            "2. Install pywin32:\n"
+            "   pip install pywin32>=306\n"
+            "\n"
+            "   Or reinstall all dependencies:\n"
+            "   pip install -r requirements.txt\n"
+        )
+    else:
+        # For system Python or environments without activate script
+        activation_step = (
+            "To fix this:\n"
+            "Install pywin32:\n"
+            "   pip install pywin32>=306\n"
+            "\n"
+            "   Or reinstall all dependencies:\n"
+            "   pip install -r requirements.txt\n"
+        )
+
+    sys.exit(
+        "Error: Required Windows dependency 'pywin32' is not installed.\n"
+        "\n"
+        "Auto Claude requires pywin32 on Windows for:\n"
+        "  - MCP library (win32api, win32con, win32job modules)\n"
+        "  - LadybugDB/Graphiti memory integration\n"
+        "\n"
+        f"{activation_step}"
+        "\n"
+        f"Current Python: {sys.executable}\n"
+    )
+
+
+def _warn_missing_secretstorage() -> None:
+    """Emit warning message for missing secretstorage.
+
+    Note: This is a warning, not a hard error - the app will fall back to .env
+    file storage for OAuth tokens. We warn users to ensure they understand the
+    security implications.
+    """
+    # Use sys.prefix to detect the virtual environment path
+    venv_activate = Path(sys.prefix) / "bin" / "activate"
+    # Only include activation instruction if venv script actually exists
+    activation_prefix = (
+        f"1. Activate your virtual environment:\n   source {venv_activate}\n\n"
+        if venv_activate.exists()
+        else ""
+    )
+    # Adjust step number based on whether activation step is included
+    install_step = (
+        "2. Install secretstorage:\n"
+        if activation_prefix
+        else "Install secretstorage:\n"
+    )
+
+    sys.stderr.write(
+        "Warning: Linux dependency 'secretstorage' is not installed.\n"
+        "\n"
+        "Auto Claude can use secretstorage for secure OAuth token storage via\n"
+        "the system keyring (gnome-keyring, kwallet, etc.). Without it, tokens\n"
+        "will be stored in plaintext in your .env file.\n"
+        "\n"
+        "To enable keyring integration:\n"
+        f"{activation_prefix}"
+        f"{install_step}"
+        "   pip install 'secretstorage>=3.3.3'\n"
+        "\n"
+        "   Or reinstall all dependencies:\n"
+        "   pip install -r requirements.txt\n"
+        "\n"
+        "Note: The app will continue to work, but OAuth tokens will be stored\n"
+        "in your .env file instead of the system keyring.\n"
+        "\n"
+        f"Current Python: {sys.executable}\n"
+    )
+    sys.stderr.flush()
+    # Continue execution - this is a warning, not a blocking error

apps/backend/core/error_utils.py

@@ -0,0 +1,120 @@
+"""
+Shared Error Utilities
+======================
+
+Common error detection and classification functions used across
+agent sessions, QA, and other modules.
+"""
+
+import re
+
+
+def is_tool_concurrency_error(error: Exception) -> bool:
+    """
+    Check if an error is a 400 tool concurrency error from Claude API.
+
+    Tool concurrency errors occur when too many tools are used simultaneously
+    in a single API request, hitting Claude's concurrent tool use limit.
+
+    Args:
+        error: The exception to check
+
+    Returns:
+        True if this is a tool concurrency error, False otherwise
+    """
+    error_str = str(error).lower()
+    # Check for 400 status AND tool concurrency keywords
+    return "400" in error_str and (
+        ("tool" in error_str and "concurrency" in error_str)
+        or "too many tools" in error_str
+        or "concurrent tool" in error_str
+    )
+
+
+def is_rate_limit_error(error: Exception) -> bool:
+    """
+    Check if an error is a rate limit error (429 or similar).
+
+    Rate limit errors occur when the API usage quota is exceeded,
+    either for session limits or weekly limits.
+
+    Args:
+        error: The exception to check
+
+    Returns:
+        True if this is a rate limit error, False otherwise
+    """
+    error_str = str(error).lower()
+
+    # Check for HTTP 429 with word boundaries to avoid false positives
+    if re.search(r"\b429\b", error_str):
+        return True
+
+    # Check for other rate limit indicators
+    return any(
+        p in error_str
+        for p in [
+            "limit reached",
+            "rate limit",
+            "too many requests",
+            "usage limit",
+            "quota exceeded",
+        ]
+    )
+
+
+def is_authentication_error(error: Exception) -> bool:
+    """
+    Check if an error is an authentication error (401, token expired, etc.).
+
+    Authentication errors occur when OAuth tokens are invalid, expired,
+    or have been revoked (e.g., after token refresh on another process).
+
+    Validation approach:
+    - HTTP 401 status code is checked with word boundaries to minimize false positives
+    - Additional string patterns are validated against lowercase error messages
+    - Patterns are designed to match known Claude API and OAuth error formats
+
+    Known false positive risks:
+    - Generic error messages containing "unauthorized" or "access denied" may match
+      even if not related to authentication (e.g., file permission errors)
+    - Error messages containing these keywords in user-provided content could match
+    - Mitigation: HTTP 401 check provides strong signal; string patterns are secondary
+
+    Real-world validation:
+    - Pattern matching has been tested against actual Claude API error responses
+    - False positive rate is acceptable given the recovery mechanism (prompt user to re-auth)
+    - If false positive occurs, user can simply resume without re-authenticating
+
+    Args:
+        error: The exception to check
+
+    Returns:
+        True if this is an authentication error, False otherwise
+    """
+    error_str = str(error).lower()
+
+    # Check for HTTP 401 with word boundaries to avoid false positives
+    if re.search(r"\b401\b", error_str):
+        return True
+
+    # Check for other authentication indicators
+    # NOTE: "authentication failed" and "authentication error" are more specific patterns
+    # to reduce false positives from generic "authentication" mentions
+    return any(
+        p in error_str
+        for p in [
+            "authentication failed",
+            "authentication error",
+            "unauthorized",
+            "invalid token",
+            "token expired",
+            "authentication_error",
+            "invalid_token",
+            "token_expired",
+            "not authenticated",
+            "http 401",
+            "does not have access to claude",
+            "please login again",
+        ]
+    )

apps/backend/core/fast_mode.py

@@ -0,0 +1,76 @@
+"""
+Fast Mode Settings Helper
+=========================
+
+Manages the fastMode flag in ~/.claude/settings.json for temporary
+per-task fast mode overrides. Shared by both client.py and simple_client.py.
+"""
+
+import json
+import logging
+from pathlib import Path
+
+from core.file_utils import write_json_atomic
+
+logger = logging.getLogger(__name__)
+
+_fast_mode_atexit_registered = False
+
+
+def _write_fast_mode_setting(enabled: bool) -> None:
+    """Write fastMode value to ~/.claude/settings.json (atomic read-modify-write).
+
+    Uses write_json_atomic from core.file_utils to prevent corruption when
+    multiple concurrent task processes modify the file simultaneously.
+    """
+    settings_file = Path.home() / ".claude" / "settings.json"
+    try:
+        settings: dict = {}
+        if settings_file.exists():
+            settings = json.loads(settings_file.read_text(encoding="utf-8"))
+
+        if settings.get("fastMode") != enabled:
+            settings["fastMode"] = enabled
+            settings_file.parent.mkdir(parents=True, exist_ok=True)
+            # Atomic write using shared utility
+            write_json_atomic(settings_file, settings)
+            state = "true" if enabled else "false"
+            logger.info(
+                f"[Fast Mode] Wrote fastMode={state} to ~/.claude/settings.json"
+            )
+    except Exception as e:
+        logger.warning(f"[Fast Mode] Could not update ~/.claude/settings.json: {e}")
+
+
+def _disable_fast_mode_on_exit() -> None:
+    """atexit handler: restore fastMode=false so interactive CLI sessions stay standard."""
+    _write_fast_mode_setting(False)
+
+
+def ensure_fast_mode_in_user_settings() -> None:
+    """
+    Enable fastMode in ~/.claude/settings.json and register cleanup.
+
+    The CLI reads fastMode from user settings (loaded via --setting-sources user).
+    This function:
+    1. Writes fastMode=true before spawning the CLI subprocess
+    2. Registers an atexit handler to restore fastMode=false when the process exits
+
+    This ensures fast mode is a temporary override per task process, not a permanent
+    setting change. The CLI subprocess reads settings at startup, so restoring false
+    after exit doesn't affect running tasks — only prevents fast mode from leaking
+    into subsequent interactive CLI sessions or non-fast-mode tasks.
+    """
+    global _fast_mode_atexit_registered
+
+    _write_fast_mode_setting(True)
+
+    # Register cleanup once per process — idempotent on repeated calls
+    if not _fast_mode_atexit_registered:
+        import atexit
+
+        atexit.register(_disable_fast_mode_on_exit)
+        _fast_mode_atexit_registered = True
+        logger.info(
+            "[Fast Mode] Registered atexit cleanup (will restore fastMode=false)"
+        )

apps/backend/core/file_utils.py

@@ -0,0 +1,121 @@
+#!/usr/bin/env python3
+"""
+Atomic File Write Utilities
+============================
+
+Synchronous utilities for atomic file writes to prevent corruption.
+
+Uses temp file + os.replace() pattern which is atomic on POSIX systems
+and atomic on Windows when source and destination are on the same volume.
+
+Usage:
+    from core.file_utils import write_json_atomic
+
+    write_json_atomic("/path/to/file.json", {"key": "value"})
+"""
+
+import json
+import logging
+import os
+import tempfile
+from collections.abc import Iterator
+from contextlib import contextmanager
+from pathlib import Path
+from typing import IO, Any, Literal
+
+
+@contextmanager
+def atomic_write(
+    filepath: str | Path,
+    mode: Literal["w", "wb", "wt"] = "w",
+    encoding: str | None = "utf-8",
+) -> Iterator[IO]:
+    """
+    Atomic file write using temp file and rename.
+
+    Writes to .tmp file first, then atomically replaces target file
+    using os.replace() which is atomic on POSIX systems and same-volume Windows.
+
+    Note: This function supports both text and binary modes. For binary modes
+    (mode containing 'b'), encoding must be None.
+
+    Args:
+        filepath: Target file path
+        mode: File open mode (default: "w", text mode only)
+        encoding: File encoding for text modes, None for binary (default: "utf-8")
+
+    Example:
+        with atomic_write("/path/to/file.json") as f:
+            json.dump(data, f)
+
+    Yields:
+        File handle to temp file
+    """
+    filepath = Path(filepath)
+    filepath.parent.mkdir(parents=True, exist_ok=True)
+
+    # Binary modes require encoding=None
+    actual_encoding = None if "b" in mode else encoding
+
+    # Create temp file in same directory for atomic rename
+    fd, tmp_path = tempfile.mkstemp(
+        dir=filepath.parent, prefix=f".{filepath.name}.tmp.", suffix=""
+    )
+
+    # Open temp file with requested mode
+    # If fdopen fails, close fd and clean up temp file
+    try:
+        f = os.fdopen(fd, mode, encoding=actual_encoding)
+    except Exception:
+        os.close(fd)
+        os.unlink(tmp_path)
+        raise
+
+    try:
+        with f:
+            yield f
+    except Exception:
+        # Clean up temp file on error (replace didn't happen yet)
+        try:
+            os.unlink(tmp_path)
+        except Exception as cleanup_err:
+            # Best-effort cleanup, ignore errors to not mask original exception
+            # Log cleanup failure for debugging (orphaned temp files may accumulate)
+            logging.warning(
+                f"Failed to cleanup temp file {tmp_path}: {cleanup_err}",
+                exc_info=True,
+            )
+        raise
+    else:
+        # Atomic replace - only runs if no exception was raised
+        # If os.replace itself fails, do NOT clean up (may be partially renamed)
+        os.replace(tmp_path, filepath)
+
+
+def write_json_atomic(
+    filepath: str | Path,
+    data: Any,
+    indent: int = 2,
+    ensure_ascii: bool = False,
+    encoding: str = "utf-8",
+) -> None:
+    """
+    Write JSON data to file atomically.
+
+    This function prevents file corruption by:
+    1. Writing to a temporary file first
+    2. Only replacing the target file if the write succeeds
+    3. Using os.replace() for atomicity
+
+    Args:
+        filepath: Target file path
+        data: Data to serialize as JSON
+        indent: JSON indentation (default: 2)
+        ensure_ascii: Whether to escape non-ASCII characters (default: False)
+        encoding: File encoding (default: "utf-8")
+
+    Example:
+        write_json_atomic("/path/to/file.json", {"key": "value"})
+    """
+    with atomic_write(filepath, "w", encoding=encoding) as f:
+        json.dump(data, f, indent=indent, ensure_ascii=ensure_ascii)

apps/backend/core/gh_executable.py

@@ -0,0 +1,192 @@
+#!/usr/bin/env python3
+"""
+GitHub CLI Executable Finder
+============================
+
+Utility to find the gh (GitHub CLI) executable, with platform-specific fallbacks.
+"""
+
+import os
+import shutil
+import subprocess
+
+from core.platform import get_where_exe_path
+
+_cached_gh_path: str | None = None
+
+
+def invalidate_gh_cache() -> None:
+    """Invalidate the cached gh executable path.
+
+    Useful when gh may have been uninstalled, updated, or when
+    GITHUB_CLI_PATH environment variable has changed.
+    """
+    global _cached_gh_path
+    _cached_gh_path = None
+
+
+def _verify_gh_executable(path: str) -> bool:
+    """Verify that a path is a valid gh executable by checking version.
+
+    Args:
+        path: Path to the potential gh executable
+
+    Returns:
+        True if the path points to a valid gh executable, False otherwise
+    """
+    try:
+        result = subprocess.run(
+            [path, "--version"],
+            capture_output=True,
+            text=True,
+            encoding="utf-8",
+            timeout=5,
+        )
+        return result.returncode == 0
+    except (subprocess.TimeoutExpired, OSError):
+        return False
+
+
+def _run_where_command() -> str | None:
+    """Run Windows 'where gh' command to find gh executable.
+
+    Returns:
+        First path found, or None if command failed
+    """
+    try:
+        result = subprocess.run(
+            [get_where_exe_path(), "gh"],
+            capture_output=True,
+            text=True,
+            encoding="utf-8",
+            timeout=5,
+        )
+        if result.returncode == 0 and result.stdout.strip():
+            found_path = result.stdout.strip().split("\n")[0].strip()
+            if (
+                found_path
+                and os.path.isfile(found_path)
+                and _verify_gh_executable(found_path)
+            ):
+                return found_path
+    except (subprocess.TimeoutExpired, OSError):
+        # 'where' command failed or timed out - fall through to return None
+        pass
+    return None
+
+
+def get_gh_executable() -> str | None:
+    """Find the gh executable, with platform-specific fallbacks.
+
+    Returns the path to gh executable, or None if not found.
+
+    Priority order:
+    1. GITHUB_CLI_PATH env var (user-configured path from frontend)
+    2. shutil.which (if gh is in PATH)
+    3. Homebrew paths on macOS
+    4. Windows Program Files paths
+    5. Windows 'where' command
+
+    Caches the result after first successful find. Use invalidate_gh_cache()
+    to force re-detection (e.g., after gh installation/uninstallation).
+    """
+    global _cached_gh_path
+
+    # Return cached result if available AND still exists
+    if _cached_gh_path is not None and os.path.isfile(_cached_gh_path):
+        return _cached_gh_path
+
+    _cached_gh_path = _find_gh_executable()
+    return _cached_gh_path
+
+
+def _find_gh_executable() -> str | None:
+    """Internal function to find gh executable."""
+    # 1. Check GITHUB_CLI_PATH env var (set by Electron frontend)
+    env_path = os.environ.get("GITHUB_CLI_PATH")
+    if env_path and os.path.isfile(env_path) and _verify_gh_executable(env_path):
+        return env_path
+
+    # 2. Try shutil.which (works if gh is in PATH)
+    gh_path = shutil.which("gh")
+    if gh_path and _verify_gh_executable(gh_path):
+        return gh_path
+
+    # 3. macOS-specific: check Homebrew paths
+    if os.name != "nt":  # Unix-like systems (macOS, Linux)
+        homebrew_paths = [
+            "/opt/homebrew/bin/gh",  # Apple Silicon
+            "/usr/local/bin/gh",  # Intel Mac
+            "/home/linuxbrew/.linuxbrew/bin/gh",  # Linux Homebrew
+        ]
+        for path in homebrew_paths:
+            if os.path.isfile(path) and _verify_gh_executable(path):
+                return path
+
+    # 4. Windows-specific: check Program Files paths
+    if os.name == "nt":
+        windows_paths = [
+            os.path.expandvars(r"%PROGRAMFILES%\GitHub CLI\gh.exe"),
+            os.path.expandvars(r"%PROGRAMFILES(X86)%\GitHub CLI\gh.exe"),
+            os.path.expandvars(r"%LOCALAPPDATA%\Programs\GitHub CLI\gh.exe"),
+        ]
+        for path in windows_paths:
+            if os.path.isfile(path) and _verify_gh_executable(path):
+                return path
+
+        # 5. Try 'where' command with full path (works even when System32 isn't in PATH)
+        return _run_where_command()
+
+    return None
+
+
+def run_gh(
+    args: list[str],
+    cwd: str | None = None,
+    timeout: int = 60,
+    input_data: str | None = None,
+) -> subprocess.CompletedProcess:
+    """Run a gh command with proper executable finding.
+
+    Args:
+        args: gh command arguments (without 'gh' prefix)
+        cwd: Working directory for the command
+        timeout: Command timeout in seconds (default: 60)
+        input_data: Optional string data to pass to stdin
+
+    Returns:
+        CompletedProcess with command results.
+    """
+    gh = get_gh_executable()
+    if not gh:
+        return subprocess.CompletedProcess(
+            args=["gh"] + args,
+            returncode=-1,
+            stdout="",
+            stderr="GitHub CLI (gh) not found. Install from https://cli.github.com/",
+        )
+    try:
+        return subprocess.run(
+            [gh] + args,
+            cwd=cwd,
+            input=input_data,
+            capture_output=True,
+            text=True,
+            encoding="utf-8",
+            errors="replace",
+            timeout=timeout,
+        )
+    except subprocess.TimeoutExpired:
+        return subprocess.CompletedProcess(
+            args=[gh] + args,
+            returncode=-1,
+            stdout="",
+            stderr=f"Command timed out after {timeout} seconds",
+        )
+    except FileNotFoundError:
+        return subprocess.CompletedProcess(
+            args=[gh] + args,
+            returncode=-1,
+            stdout="",
+            stderr="GitHub CLI (gh) executable not found. Install from https://cli.github.com/",
+        )

apps/backend/core/git_executable.py

@@ -0,0 +1,199 @@
+#!/usr/bin/env python3
+"""
+Git Executable Finder and Isolation
+====================================
+
+Utility to find the git executable, with Windows-specific fallbacks.
+Also provides environment isolation to prevent pre-commit hooks and
+other git configurations from affecting worktree operations.
+
+Separated into its own module to avoid circular imports.
+"""
+
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+from core.platform import get_where_exe_path
+
+# Git environment variables that can interfere with worktree operations
+# when set by pre-commit hooks or other git configurations.
+# These must be cleared to prevent cross-worktree contamination.
+GIT_ENV_VARS_TO_CLEAR = [
+    "GIT_DIR",
+    "GIT_WORK_TREE",
+    "GIT_INDEX_FILE",
+    "GIT_OBJECT_DIRECTORY",
+    "GIT_ALTERNATE_OBJECT_DIRECTORIES",
+    # Identity variables that could be set by hooks
+    "GIT_AUTHOR_NAME",
+    "GIT_AUTHOR_EMAIL",
+    "GIT_AUTHOR_DATE",
+    "GIT_COMMITTER_NAME",
+    "GIT_COMMITTER_EMAIL",
+    "GIT_COMMITTER_DATE",
+]
+
+_cached_git_path: str | None = None
+
+
+def get_isolated_git_env(base_env: dict | None = None) -> dict:
+    """
+    Create an isolated environment for git operations.
+
+    Clears git environment variables that may be set by pre-commit hooks
+    or other git configurations, preventing cross-worktree contamination
+    and ensuring git operations target the intended repository.
+
+    Args:
+        base_env: Base environment dict to copy from. If None, uses os.environ.
+
+    Returns:
+        Environment dict safe for git subprocess operations.
+    """
+    env = dict(base_env) if base_env is not None else os.environ.copy()
+
+    for key in GIT_ENV_VARS_TO_CLEAR:
+        env.pop(key, None)
+
+    # Disable user's pre-commit hooks during Auto-Claude managed git operations
+    # to prevent double-hook execution and potential conflicts
+    env["HUSKY"] = "0"
+
+    return env
+
+
+def get_git_executable() -> str:
+    """Find the git executable, with Windows-specific fallbacks.
+
+    Returns the path to git executable. On Windows, checks multiple sources:
+    1. CLAUDE_CODE_GIT_BASH_PATH env var (set by Electron frontend)
+    2. shutil.which (if git is in PATH)
+    3. Common installation locations
+    4. Windows 'where' command
+
+    Caches the result after first successful find.
+    """
+    global _cached_git_path
+
+    # Return cached result if available
+    if _cached_git_path is not None:
+        return _cached_git_path
+
+    git_path = _find_git_executable()
+    _cached_git_path = git_path
+    return git_path
+
+
+def _find_git_executable() -> str:
+    """Internal function to find git executable."""
+    # 1. Check CLAUDE_CODE_GIT_BASH_PATH (set by Electron frontend)
+    # This env var points to bash.exe, we can derive git.exe from it
+    bash_path = os.environ.get("CLAUDE_CODE_GIT_BASH_PATH")
+    if bash_path:
+        try:
+            bash_path_obj = Path(bash_path)
+            if bash_path_obj.exists():
+                git_dir = bash_path_obj.parent.parent
+                # Try cmd/git.exe first (preferred), then bin/git.exe
+                for git_subpath in ["cmd/git.exe", "bin/git.exe"]:
+                    git_path = git_dir / git_subpath
+                    if git_path.is_file():
+                        return str(git_path)
+        except (OSError, ValueError):
+            pass  # Invalid path or permission error - try next method
+
+    # 2. Try shutil.which (works if git is in PATH)
+    git_path = shutil.which("git")
+    if git_path:
+        return git_path
+
+    # 3. Windows-specific: check common installation locations
+    if os.name == "nt":
+        common_paths = [
+            os.path.expandvars(r"%PROGRAMFILES%\Git\cmd\git.exe"),
+            os.path.expandvars(r"%PROGRAMFILES%\Git\bin\git.exe"),
+            os.path.expandvars(r"%PROGRAMFILES(X86)%\Git\cmd\git.exe"),
+            os.path.expandvars(r"%LOCALAPPDATA%\Programs\Git\cmd\git.exe"),
+            r"C:\Program Files\Git\cmd\git.exe",
+            r"C:\Program Files (x86)\Git\cmd\git.exe",
+        ]
+        for path in common_paths:
+            try:
+                if os.path.isfile(path):
+                    return path
+            except OSError:
+                continue
+
+        # 4. Try 'where' command with full path (works even when System32 isn't in PATH)
+        try:
+            result = subprocess.run(
+                [get_where_exe_path(), "git"],
+                capture_output=True,
+                text=True,
+                timeout=5,
+            )
+            if result.returncode == 0 and result.stdout.strip():
+                found_path = result.stdout.strip().split("\n")[0].strip()
+                if found_path and os.path.isfile(found_path):
+                    return found_path
+        except (subprocess.TimeoutExpired, OSError):
+            pass  # 'where' command failed - fall through to default
+
+    # Default fallback - let subprocess handle it (may fail)
+    return "git"
+
+
+def run_git(
+    args: list[str],
+    cwd: Path | str | None = None,
+    timeout: int = 60,
+    input_data: str | None = None,
+    env: dict | None = None,
+    isolate_env: bool = True,
+) -> subprocess.CompletedProcess:
+    """Run a git command with proper executable finding and environment isolation.
+
+    Args:
+        args: Git command arguments (without 'git' prefix)
+        cwd: Working directory for the command
+        timeout: Command timeout in seconds (default: 60)
+        input_data: Optional string data to pass to stdin
+        env: Custom environment dict. If None and isolate_env=True, uses isolated env.
+        isolate_env: If True (default), clears git env vars to prevent hook interference.
+
+    Returns:
+        CompletedProcess with command results.
+    """
+    git = get_git_executable()
+
+    if env is None and isolate_env:
+        env = get_isolated_git_env()
+
+    try:
+        return subprocess.run(
+            [git] + args,
+            cwd=cwd,
+            input=input_data,
+            capture_output=True,
+            text=True,
+            encoding="utf-8",
+            errors="replace",
+            timeout=timeout,
+            env=env,
+        )
+    except subprocess.TimeoutExpired:
+        return subprocess.CompletedProcess(
+            args=[git] + args,
+            returncode=-1,
+            stdout="",
+            stderr=f"Command timed out after {timeout} seconds",
+        )
+    except FileNotFoundError:
+        return subprocess.CompletedProcess(
+            args=[git] + args,
+            returncode=-1,
+            stdout="",
+            stderr="Git executable not found. Please ensure git is installed and in PATH.",
+        )