Fix Windows UTF-8 encoding errors across entire backend (251 instances) (#782)

* Fix UTF-8 encoding for Priorities 1-2 (Core & Agents - 18 instances)

Add encoding="utf-8" to file operations in:
- Priority 1: Core Infrastructure (8 instances)
  - core/progress.py (6 read operations)
  - core/debug.py (1 append operation)
  - core/workspace/setup.py (1 read operation)

- Priority 2: Agent System (10 instances)
  - agents/utils.py (1 read)
  - agents/tools_pkg/tools/subtask.py (1 read, 1 write)
  - agents/tools_pkg/tools/memory.py (2 read, 1 write, 1 append)
  - agents/tools_pkg/tools/qa.py (1 read, 1 write)
  - agents/tools_pkg/tools/progress.py (1 read)

All changes use double quotes for ruff format compliance.

* Fix UTF-8 encoding for Priorities 3-4 (Spec & Project - 26 instances)

Add encoding="utf-8" to file operations in:
- Priority 3: Spec Pipeline (21 instances)
  - spec/context.py (4: 2 read, 2 write)
  - spec/complexity.py (3: 2 read, 1 write)
  - spec/requirements.py (3: 2 read, 1 write)
  - spec/validator.py (3 write operations)
  - spec/writer.py (2: 1 read, 1 write)
  - spec/discovery.py (1 read)
  - spec/pipeline/orchestrator.py (2 read)
  - spec/phases/requirements_phases.py (1 write)
  - spec/validate_pkg/auto_fix.py (2: 1 read, 1 write)

- Priority 4: Project Analyzer (5 instances)
  - project/analyzer.py (2: 1 read, 1 write)
  - project/config_parser.py (2 read operations)
  - project/stack_detector.py (1 read)

All changes use double quotes for ruff format compliance.

* Fix UTF-8 encoding for Priorities 5-7 (Services, Analysis, Ideation - 43 instances)

Add encoding="utf-8" to file operations in:
- Priority 5: Services (12 instances)
  - services/recovery.py (8: 4 read, 4 write)
  - services/context.py (4 read operations)

- Priority 6: Analysis & QA (6 instances)
  - analysis/analyzers/__init__.py (2 write)
  - analysis/insight_extractor.py (1 read)
  - qa/criteria.py (2: 1 read, 1 write)
  - qa/report.py (1 read)

- Priority 7: Ideation & Roadmap (25 instances)
  - ideation/analyzer.py (3 read)
  - ideation/formatter.py (4 read, 1 write)
  - ideation/phase_executor.py (5: 3 read, 2 write)
  - ideation/runner.py (1 read)
  - runners/roadmap/competitor_analyzer.py (3: 1 read, 2 write)
  - runners/roadmap/graph_integration.py (3 write)
  - runners/roadmap/orchestrator.py (1 read)
  - runners/roadmap/phases.py (2 read)
  - runners/insights_runner.py (3 read)

All changes use double quotes for ruff format compliance.

* Fix UTF-8 encoding for Priorities 8-14 (All remaining - 85+ instances)

Add encoding="utf-8" to file operations across all remaining modules:

Priorities 8-10 (Merge, Memory, Integrations - 26 instances):
- merge/ (4 files)
- memory/ (3 files)
- context/ (3 files)
- integrations/ (4 files)

Priorities 11-14 (GitHub, GitLab, AI, Other - 59 instances):
- runners/github/ (19 files)
- runners/gitlab/ (3 files)
- runners/ai_analyzer/ (1 file)

All changes use double quotes for ruff format compliance.
Applied using Python regex script for efficiency.

* Fix UTF-8 encoding for missed instances (23 instances)

Fix remaining instances missed by batch script:
- cli/batch_commands.py (3 instances)
- cli/followup_commands.py (1 instance)
- core/client.py (1 instance)
- phase_config.py (1 instance)
- planner_lib/context.py (4 instances)
- prediction/main.py (1 instance)
- prediction/memory_loader.py (1 instance)
- prompts_pkg/prompts.py (2 instances)
- review/formatters.py (1 instance)
- review/state.py (2 instances)
- spec/phases/spec_phases.py (1 instance)
- spec/pipeline/models.py (1 instance)
- spec/validate_pkg/validators/context_validator.py (1 instance)
- spec/validate_pkg/validators/implementation_plan_validator.py (1 instance)
- ui/status.py (2 instances)

All encoding parameters use double quotes for ruff format compliance.
Verified: 0 instances without encoding remain in source code.

* Fix missed os.fdopen() calls and duplicate encoding bug

Thorough verification found 3 additional issues:
- runners/github/file_lock.py:462 - os.fdopen missing encoding
- runners/github/trust.py:442 - os.fdopen missing encoding
- runners/insights_runner.py:372 - duplicate encoding parameter

All fixed. Final count: 251 instances with encoding="utf-8"

* Fix missed Path.read_text() and Path.write_text() encoding (99 instances)

Gemini Code Assist review found instances we missed:
- Path.read_text() without encoding: 77 instances → fixed
- Path.write_text() without encoding: 22 instances → fixed

Total UTF-8 encoding fixes: 350 instances across codebase
- open() operations: 251 instances
- Path.read_text(): 98 instances
- Path.write_text(): 30 instances

All text file operations now explicitly use encoding="utf-8".

Addresses feedback from PR #782 review.

* Fix critical syntax errors from CodeRabbit review

- Fix os.getpid() syntax error in core/workspace/models.py (2 instances)
  Changed: os.getpid(, encoding="utf-8") -> str(os.getpid())

- Fix json.dumps invalid encoding parameter (3 instances)
  json.dumps() doesn't accept encoding parameter
  Changed: json.dumps(data, encoding="utf-8") -> json.dumps(data)
  Files: runners/ai_analyzer/cache_manager.py, runners/github/test_file_lock.py

- Fix tempfile.NamedTemporaryFile missing encoding
  Added encoding="utf-8" to spec/requirements.py:22

- Fix subprocess.run text=True to encoding
  Changed: text=True -> encoding="utf-8" in core/workspace/setup.py:375

All critical syntax errors from CodeRabbit review resolved.

* Fix critical syntax errors in test_context_gatherer.py

- Line 78: Move encoding="utf-8" outside of JS string content
  Changed: write_text("...encoding="utf-8"...")
  To: write_text("...", encoding="utf-8")

- Line 102: Move encoding="utf-8" outside of JS string content
  Changed: write_text("...encoding="utf-8"...")
  To: write_text("...", encoding="utf-8")

Fixes syntax errors where encoding parameter was incorrectly placed
inside the JavaScript code string instead of as write_text() parameter.

* Fix CodeRabbit issues: UnicodeDecodeError handling and trailing newlines

- Add UnicodeDecodeError to exception handling in agents/utils.py and spec/validate_pkg/auto_fix.py
- Fix trailing newline preservation in merge/file_merger.py (2 locations)
- Add encoding parameter to atomic_write() in runners/github/file_lock.py

These fixes ensure robust error handling for malformed UTF-8 files
and preserve file formatting during merge operations.

* Fix test fixture to use UTF-8 encoding consistently

Update spec_file fixture in tests/conftest.py to write spec file
with encoding="utf-8" to match how it's read in validators.

This ensures consistency between test fixtures and production code.

* Fix linting errors and security vulnerabilities from merge

- Remove unused tree-sitter methods in semantic_analyzer.py that caused F821 undefined name errors
- Fix regex injection vulnerability in bump-version.js by properly escaping all regex special characters
- Add escapeRegex() function to prevent security issues when version string is used in RegExp constructor

Resolves ruff linting failures and CodeQL security alerts.

* Fix code formatting for ruff compliance

Apply formatting fixes to meet line length requirements:
- context/builder.py: Split long line with array slicing
- planner_lib/context.py: Split long ternary expression
- spec/requirements.py: Split long tempfile.NamedTemporaryFile call

Resolves ruff format check failures.

* Fix missing UTF-8 encoding in init.py gitignore operations

Found by pre-commit hook testing in PR #795:
- Line 96: Path.read_text() without encoding
- Line 122: Path.write_text() without encoding

These handle .gitignore file operations and could fail on Windows
with special characters in gitignore comments or entries.

Total fixes in PR #782: 253 instances (was 251, +2 from init.py)

* Add pre-commit hook for UTF-8 encoding enforcement

1. Encoding Check Script (scripts/check_encoding.py):
   - Validates all file operations have encoding="utf-8"
   - Checks open(), Path.read_text(), Path.write_text()
   - Checks json.load/dump with open()
   - Allows binary mode without encoding
   - Windows-compatible emoji output with UTF-8 reconfiguration

2. Pre-commit Config (.pre-commit-config.yaml):
   - Added check-file-encoding hook for apps/backend/
   - Runs automatically before commits
   - Scoped to backend Python files only

3. Tests (tests/test_check_encoding.py):
   - Comprehensive test coverage (10 tests, all passing)
   - Tests detection of missing encoding
   - Tests allowlist for binary files
   - Tests multiple issues in single file
   - Tests file type filtering

Purpose:
- Prevent regression of 251 UTF-8 encoding fixes from PR #782
- Catch missing encoding in new code during development
- Fast feedback loop for developers

Implementation Notes:
- Hook scoped to apps/backend/ to avoid false positives in test code
- Uses simple regex matching for speed
- Compatible with existing pre-commit infrastructure
- Already caught 6 real issues in apps/backend/core/progress.py

Related: PR #782 - Fix Windows UTF-8 encoding errors

* Address CodeRabbit and Gemini review feedback

Fixes based on automated review comments:

1. Binary Mode Detection (Critical Fix):
   - Replaced brittle regex with robust pattern: r'["'][rwax+]*b[rwax+]*["']'
   - Now correctly detects all binary modes: rb, wb, ab, r+b, w+b, etc.
   - Prevents false positives on text mode 'w' without 'b'
   - Added comprehensive tests for wb, ab, and text w modes

2. Encoding Detection Robustness (Critical Fix):
   - Changed from 'encoding=' string match to word boundary regex: r'\bencoding\s*='
   - Now handles encoding with spaces: encoding = "utf-8"
   - Prevents false matches of substrings containing 'encoding='
   - Applied across all checks (open, read_text, write_text, json.load, json.dump)
   - Added test for spaces around equals sign

3. Test Coverage Improvements:
   - Added json.dump() with encoding test (passing case)
   - Added json.dump() without encoding test (failing case)
   - Fixed test assertions to match actual behavior (== 1 not == 2)
   - Added 6 new tests for improved binary/text mode coverage
   - Total tests increased from 10 to 16, all passing ✅

4. Code Cleanup:
   - Removed unused pytest import (CodeQL warning)
   - Simplified check_files() to remove unused variable tracking

All changes validated with comprehensive test suite (16/16 passing).

Related: PR #795 review feedback from CodeRabbit and Gemini Code Assist

* docs: Add UTF-8 encoding guidelines and Windows development guide

1. CONTRIBUTING.md:
   - Added concise file encoding section after Code Style
   - DO/DON'T examples for common file operations
   - Covers open(), Path methods, json operations
   - References PR #782 and windows-development.md

2. guides/windows-development.md (NEW):
   - Comprehensive Windows development guide
   - File encoding (cp1252 vs UTF-8 issue)
   - Line endings, path separators, shell commands
   - Development environment recommendations
   - Common pitfalls and solutions
   - Testing guidelines

3. .github/PULL_REQUEST_TEMPLATE.md:
   - Added encoding checklist item for Python PRs
   - Helps catch missing encoding during review

4. guides/README.md:
   - Added windows-development.md to guide index
   - Organized with CLI-USAGE and linux guides

Purpose: Educate developers about UTF-8 encoding requirements to prevent
regressions of the 251 encoding issues fixed in PR #782. Automated checking
via pre-commit hooks (PR #795) + developer education ensures long-term
Windows compatibility.

Related:
- PR #782: Fix Windows UTF-8 encoding errors (251 instances)
- PR #795: Add pre-commit hooks for encoding enforcement

* Address review comments from CodeRabbit and Gemini

1. Fix CONTRIBUTING.md markdown linting issues
   - Add blank lines around code blocks (MD031)
   - Add JSON write example with ensure_ascii=False (Gemini suggestion)

2. Fix guides/windows-development.md markdown linting (39 violations)
   - Rename duplicate headings: "The Problem"/"The Solution" → "Problem"/"Solution" (MD024)
   - Add blank lines around all code blocks (MD031)
   - Add language specifiers to code blocks (MD040)
   - Add blank lines before/after headings (MD022)
   - Wrap long lines to <=80 characters (MD013)
   - Add blank line before list (MD032)
   - Use Gemini's idiomatic line ending normalization pattern

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix additional UTF-8 encoding issues and improve encoding check script

- Add encoding="utf-8" to 5 files that were missing it:
  - cli/workspace_commands.py: read_text for worktree config
  - context/pattern_discovery.py: read_text with errors param
  - context/search.py: read_text with errors param
  - core/sentry.py: open for package.json version detection
  - core/workspace/setup.py: open for security profile JSON

- Improve check_encoding.py script to reduce false positives:
  - Use negative lookbehind to exclude os.open(), urlopen(), etc.
  - Handle nested parentheses correctly when checking args
  - Skip self.method.read_text() calls (custom methods, not Path)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix missing UTF-8 encoding in locked_write() function

Add encoding parameter to locked_write() async context manager and
use it in os.fdopen() call. This fixes HIGH priority issue from PR review
where locked_write() was missing UTF-8 encoding support, which could cause
encoding errors on Windows when writing files with non-ASCII content.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Add UnicodeDecodeError handling for file loading resilience

Address CodeRabbit review feedback:
- runner.py: Add UnicodeDecodeError to exception handling when loading batch files
- trust.py: Add exception handling in get_state() and get_all_states() to
  gracefully handle corrupted state files instead of failing completely

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix atomic_write to handle binary mode correctly

The atomic_write function was unconditionally passing encoding to os.fdopen,
which would crash with ValueError if called with binary mode (e.g., 'wb').
Apply the same fix used in locked_write: only pass encoding for text modes.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix run_git() call with invalid parameters in setup.py

Remove capture_output and encoding kwargs from run_git() call - these
parameters are already handled internally by run_git() and passing them
causes TypeError since the function doesn't accept them.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix CodeQL warnings and potential double-newline bug

- Remove unused is_path_call variables in check_encoding.py
- Remove unused failed_count variable in check_encoding.py
- Remove unused escapeRegex function in bump-version.js
- Fix potential double-newline when adding imports in file_merger.py
  (strip trailing newlines from content_after before inserting)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix Ruff formatting: wrap long line in file_merger.py

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Add UnicodeDecodeError handling to all JSON file loading

Comprehensively add UnicodeDecodeError to exception handlers across
the codebase to handle legacy-encoded or corrupted files gracefully:

- 32+ locations now catch UnicodeDecodeError alongside OSError and
  json.JSONDecodeError
- context/builder.py: Regenerate index on decode failure
- planner_lib/context.py: Use empty dicts on decode failure
- check_encoding.py: Handle OSError for unreadable files
- cleanup.py: Handle decode errors in index pruning

This ensures the codebase is robust against non-UTF-8 files that may
exist from previous Windows runs with cp1252 encoding.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Add explanatory comments to empty except clauses

Address CodeQL notices about empty except clauses with just 'pass'
by adding explanatory comments describing the intent.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix review issues from Andy's Auto Claude PR Review

1. [HIGH] Fix double-close bug in trust.py:449
   - Remove try/except around os.fdopen since it takes ownership of fd
   - The with statement handles closing, no need for explicit os.close()

2. [LOW] Fix dead code in file_merger.py:87,159
   - Simplify endswith check to just '\n' since content is already
     normalized to LF at that point

3. [LOW] Fix escaped backslash-n in test_context_gatherer.py:150
   - Change "\n" (literal backslash-n) to "\n" (actual newline)

4. [LOW] Fix coder.md examples missing encoding parameter
   - Add encoding="utf-8" to read_text() and open() calls in examples

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

---------

Co-authored-by: TamerineSky <TamerineSky@users.noreply.github.com>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

.github/PULL_REQUEST_TEMPLATE.md

@@ -39,6 +39,7 @@ Follow conventional commits: `<type>: <subject>`
 - [ ] I've tested my changes locally
 - [ ] I've followed the code principles (SOLID, DRY, KISS)
 - [ ] My PR is small and focused (< 400 lines ideally)
+- [ ] **(Python only)** All file operations specify `encoding="utf-8"` for text files
 
 ## Platform Testing Checklist
 

.pre-commit-config.yaml

@@ -76,6 +76,17 @@ repos:
         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: v0.14.10

CONTRIBUTING.md

@@ -357,6 +357,64 @@ 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

apps/backend/agents/coder.py

@@ -226,7 +226,7 @@ async def run_autonomous_agent(
             print("  PAUSED BY HUMAN")
             print("=" * 70)
 
-            pause_content = pause_file.read_text().strip()
+            pause_content = pause_file.read_text(encoding="utf-8").strip()
             if pause_content:
                 print(f"\nMessage: {pause_content}")
 

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

@@ -171,7 +171,7 @@ def create_memory_tools(spec_dir: Path, project_dir: Path) -> list:
             # 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 = {
@@ -187,7 +187,7 @@ 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)
@@ -246,7 +246,7 @@ 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"
@@ -303,7 +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", {})
@@ -319,7 +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
@@ -333,7 +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

@@ -140,7 +140,7 @@ 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)
 
             qa_session = _apply_qa_update(plan, status, issues, tests_passed)

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

@@ -113,7 +113,7 @@ 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)
 
             subtask_found = _update_subtask_in_plan(plan, subtask_id, status, notes)

apps/backend/agents/utils.py

@@ -48,9 +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
 
 

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/project_analyzer_module.py

@@ -287,6 +287,6 @@ 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/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

@@ -237,7 +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
@@ -280,7 +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.

apps/backend/analysis/test_discovery.py

@@ -302,7 +302,7 @@ class TestDiscovery:
         try:
             with open(package_json, encoding="utf-8") as f:
                 pkg = json.load(f)
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             return
 
         deps = pkg.get("dependencies", {})
@@ -398,7 +398,7 @@ class TestDiscovery:
         # Check pyproject.toml
         pyproject = project_dir / "pyproject.toml"
         if pyproject.exists():
-            content = pyproject.read_text()
+            content = pyproject.read_text(encoding="utf-8")
 
             # Check for pytest
             if "pytest" in content:
@@ -418,7 +418,7 @@ class TestDiscovery:
         # Check requirements.txt
         requirements = project_dir / "requirements.txt"
         if requirements.exists():
-            content = requirements.read_text().lower()
+            content = requirements.read_text(encoding="utf-8").lower()
             if "pytest" in content and not any(
                 f.name == "pytest" for f in result.frameworks
             ):
@@ -496,7 +496,7 @@ class TestDiscovery:
         if not gemfile.exists():
             return
 
-        content = gemfile.read_text().lower()
+        content = gemfile.read_text(encoding="utf-8").lower()
 
         if "rspec" in content or (project_dir / ".rspec").exists():
             result.frameworks.append(

apps/backend/cli/batch_commands.py

@@ -31,7 +31,7 @@ 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")
@@ -81,7 +81,7 @@ 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(
@@ -145,7 +145,7 @@ 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:

apps/backend/cli/build_commands.py

@@ -421,7 +421,7 @@ 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"),

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/workspace_commands.py

@@ -182,7 +182,7 @@ def _detect_worktree_base_branch(
     config_path = worktree_path / ".auto-claude" / "worktree-config.json"
     if config_path.exists():
         try:
-            config = json.loads(config_path.read_text())
+            config = json.loads(config_path.read_text(encoding="utf-8"))
             if config.get("base_branch"):
                 debug(
                     MODULE,

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/client.py

@@ -875,7 +875,7 @@ def create_client(
 
     # Write settings to a file in the project directory
     settings_file = project_dir / ".claude_settings.json"
-    with open(settings_file, "w") as f:
+    with open(settings_file, "w", encoding="utf-8") as f:
         json.dump(security_settings, f, indent=2)
 
     print(f"Security settings: {settings_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

apps/backend/core/progress.py

@@ -43,7 +43,7 @@ def count_subtasks(spec_dir: Path) -> tuple[int, int]:
         return 0, 0
 
     try:
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             plan = json.load(f)
 
         total = 0
@@ -56,7 +56,7 @@ def count_subtasks(spec_dir: Path) -> tuple[int, int]:
                     completed += 1
 
         return completed, total
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return 0, 0
 
 
@@ -81,7 +81,7 @@ def count_subtasks_detailed(spec_dir: Path) -> dict:
         return result
 
     try:
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             plan = json.load(f)
 
         for phase in plan.get("phases", []):
@@ -94,7 +94,7 @@ def count_subtasks_detailed(spec_dir: Path) -> dict:
                     result["pending"] += 1
 
         return result
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return result
 
 
@@ -182,7 +182,7 @@ def print_progress_summary(spec_dir: Path, show_next: bool = True) -> None:
 
         # Phase summary
         try:
-            with open(spec_dir / "implementation_plan.json") as f:
+            with open(spec_dir / "implementation_plan.json", encoding="utf-8") as f:
                 plan = json.load(f)
 
             print("\nPhases:")
@@ -230,8 +230,8 @@ def print_progress_summary(spec_dir: Path, show_next: bool = True) -> None:
                         f"  {icon(Icons.ARROW_RIGHT)} Next: {highlight(next_id)} - {next_desc}"
                     )
 
-        except (OSError, json.JSONDecodeError):
-            pass
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
+            pass  # Ignore corrupted/unreadable progress files
     else:
         print()
         print_status("No implementation subtasks yet - planner needs to run", "pending")
@@ -302,7 +302,7 @@ def get_plan_summary(spec_dir: Path) -> dict:
         }
 
     try:
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             plan = json.load(f)
 
         summary = {
@@ -355,7 +355,7 @@ def get_plan_summary(spec_dir: Path) -> dict:
 
         return summary
 
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return {
             "workflow_type": None,
             "total_phases": 0,
@@ -376,7 +376,7 @@ def get_current_phase(spec_dir: Path) -> dict | None:
         return None
 
     try:
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             plan = json.load(f)
 
         for phase in plan.get("phases", []):
@@ -396,7 +396,7 @@ def get_current_phase(spec_dir: Path) -> dict | None:
 
         return None
 
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return None
 
 
@@ -470,7 +470,7 @@ def get_next_subtask(spec_dir: Path) -> dict | None:
 
         return None
 
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return None
 
 

apps/backend/core/sentry.py

@@ -53,7 +53,7 @@ def _get_version() -> str:
         if package_json.exists():
             import json
 
-            with open(package_json) as f:
+            with open(package_json, encoding="utf-8") as f:
                 data = json.load(f)
                 return data.get("version", "0.0.0")
     except Exception as e:

apps/backend/core/workspace/models.py

@@ -93,7 +93,7 @@ class MergeLock:
                 os.close(fd)
 
                 # Write our PID to the lock file
-                self.lock_file.write_text(str(os.getpid()))
+                self.lock_file.write_text(str(os.getpid()), encoding="utf-8")
                 self.acquired = True
                 return self
 
@@ -101,7 +101,7 @@ class MergeLock:
                 # Lock file exists - check if process is still running
                 if self.lock_file.exists():
                     try:
-                        pid = int(self.lock_file.read_text().strip())
+                        pid = int(self.lock_file.read_text(encoding="utf-8").strip())
                         # Import locally to avoid circular dependency
                         import os as _os
 
@@ -183,7 +183,7 @@ class SpecNumberLock:
                 os.close(fd)
 
                 # Write our PID to the lock file
-                self.lock_file.write_text(str(os.getpid()))
+                self.lock_file.write_text(str(os.getpid()), encoding="utf-8")
                 self.acquired = True
                 return self
 
@@ -191,7 +191,7 @@ class SpecNumberLock:
                 # Lock file exists - check if process is still running
                 if self.lock_file.exists():
                     try:
-                        pid = int(self.lock_file.read_text().strip())
+                        pid = int(self.lock_file.read_text(encoding="utf-8").strip())
                         import os as _os
 
                         try:

apps/backend/core/workspace/setup.py

@@ -412,10 +412,10 @@ def setup_workspace(
         if PROFILE_FILENAME in security_files_copied:
             profile_path = worktree_info.path / PROFILE_FILENAME
             try:
-                with open(profile_path) as f:
+                with open(profile_path, encoding="utf-8") as f:
                     profile_data = json.load(f)
                 profile_data["inherited_from"] = str(project_dir.resolve())
-                with open(profile_path, "w") as f:
+                with open(profile_path, "w", encoding="utf-8") as f:
                     json.dump(profile_data, f, indent=2)
                 debug(
                     MODULE, f"Marked security profile as inherited from {project_dir}"
@@ -474,7 +474,7 @@ def ensure_timeline_hook_installed(project_dir: Path) -> None:
 
         # Handle worktrees (where .git is a file, not directory)
         if git_dir.is_file():
-            content = git_dir.read_text().strip()
+            content = git_dir.read_text(encoding="utf-8").strip()
             if content.startswith("gitdir:"):
                 git_dir = Path(content.split(":", 1)[1].strip())
             else:
@@ -484,7 +484,7 @@ def ensure_timeline_hook_installed(project_dir: Path) -> None:
 
         # Check if hook already installed
         if hook_path.exists():
-            if "FileTimelineTracker" in hook_path.read_text():
+            if "FileTimelineTracker" in hook_path.read_text(encoding="utf-8"):
                 debug(MODULE, "FileTimelineTracker hook already installed")
                 return
 
@@ -522,7 +522,7 @@ def initialize_timeline_tracking(
         if source_spec_dir:
             plan_path = source_spec_dir / "implementation_plan.json"
             if plan_path.exists():
-                with open(plan_path) as f:
+                with open(plan_path, encoding="utf-8") as f:
                     plan = json.load(f)
                 task_title = plan.get("title", spec_name)
                 task_intent = plan.get("description", "")
@@ -533,6 +533,7 @@ def initialize_timeline_tracking(
                         files_to_modify.extend(subtask.get("files", []))
 
         # Get the current branch point commit
+        # Note: run_git() already handles capture_output and encoding internally
         result = run_git(
             ["rev-parse", "HEAD"],
             cwd=project_dir,

apps/backend/ideation/analyzer.py

@@ -51,7 +51,7 @@ class ProjectAnalyzer:
         project_index_path = self.project_dir / ".auto-claude" / "project_index.json"
         if project_index_path.exists():
             try:
-                with open(project_index_path) as f:
+                with open(project_index_path, encoding="utf-8") as f:
                     index = json.load(f)
                     # Extract tech stack from services
                     for service_name, service_info in index.get("services", {}).items():
@@ -70,7 +70,7 @@ class ProjectAnalyzer:
             )
             if roadmap_path.exists():
                 try:
-                    with open(roadmap_path) as f:
+                    with open(roadmap_path, encoding="utf-8") as f:
                         roadmap = json.load(f)
                         # Extract planned features
                         for feature in roadmap.get("features", []):
@@ -87,7 +87,7 @@ class ProjectAnalyzer:
             )
             if discovery_path.exists() and not context["target_audience"]:
                 try:
-                    with open(discovery_path) as f:
+                    with open(discovery_path, encoding="utf-8") as f:
                         discovery = json.load(f)
                         audience = discovery.get("target_audience", {})
                         context["target_audience"] = audience.get("primary_persona")
@@ -109,7 +109,7 @@ class ProjectAnalyzer:
                         spec_file = spec_dir / "spec.md"
                         if spec_file.exists():
                             # Extract title from spec
-                            content = spec_file.read_text()
+                            content = spec_file.read_text(encoding="utf-8")
                             lines = content.split("\n")
                             for line in lines:
                                 if line.startswith("# "):

apps/backend/ideation/formatter.py

@@ -39,7 +39,7 @@ class IdeationFormatter:
         existing_session = None
         if append and ideation_file.exists():
             try:
-                with open(ideation_file) as f:
+                with open(ideation_file, encoding="utf-8") as f:
                     existing_session = json.load(f)
                     existing_ideas = existing_session.get("ideas", [])
                     print_status(
@@ -56,7 +56,7 @@ class IdeationFormatter:
             type_file = self.output_dir / f"{ideation_type}_ideas.json"
             if type_file.exists():
                 try:
-                    with open(type_file) as f:
+                    with open(type_file, encoding="utf-8") as f:
                         data = json.load(f)
                         ideas = data.get(ideation_type, [])
                         new_ideas.extend(ideas)
@@ -123,7 +123,7 @@ class IdeationFormatter:
                 ideation_session["summary"]["by_status"].get(idea_status, 0) + 1
             )
 
-        with open(ideation_file, "w") as f:
+        with open(ideation_file, "w", encoding="utf-8") as f:
             json.dump(ideation_session, f, indent=2)
 
         action = "Updated" if append else "Created"
@@ -139,7 +139,7 @@ class IdeationFormatter:
         context_data = {}
         if context_file.exists():
             try:
-                with open(context_file) as f:
+                with open(context_file, encoding="utf-8") as f:
                     context_data = json.load(f)
             except json.JSONDecodeError:
                 pass

apps/backend/ideation/generator.py

@@ -80,7 +80,7 @@ class IdeationGenerator:
             return False, f"Prompt not found: {prompt_path}"
 
         # Load prompt
-        prompt = prompt_path.read_text()
+        prompt = prompt_path.read_text(encoding="utf-8")
 
         # Add context
         prompt += f"\n\n---\n\n**Output Directory**: {self.output_dir}\n"

apps/backend/ideation/phase_executor.py

@@ -85,7 +85,7 @@ class PhaseExecutor:
 
         if not is_graphiti_enabled():
             print_status("Graphiti not enabled, skipping graph hints", "info")
-            with open(hints_file, "w") as f:
+            with open(hints_file, "w", encoding="utf-8") as f:
                 json.dump(
                     {
                         "enabled": False,
@@ -131,7 +131,7 @@ class PhaseExecutor:
                 total_hints += len(result)
 
         # Save hints
-        with open(hints_file, "w") as f:
+        with open(hints_file, "w", encoding="utf-8") as f:
             json.dump(
                 {
                     "enabled": True,
@@ -178,11 +178,11 @@ class PhaseExecutor:
         graph_hints = {}
         if hints_file.exists():
             try:
-                with open(hints_file) as f:
+                with open(hints_file, encoding="utf-8") as f:
                     hints_data = json.load(f)
                     graph_hints = hints_data.get("hints_by_type", {})
-            except (OSError, json.JSONDecodeError):
-                pass
+            except (OSError, json.JSONDecodeError, UnicodeDecodeError):
+                pass  # Use empty hints if file is corrupted/unreadable
 
         # Write context file
         context_data = {
@@ -200,7 +200,7 @@ class PhaseExecutor:
             "created_at": datetime.now().isoformat(),
         }
 
-        with open(context_file, "w") as f:
+        with open(context_file, "w", encoding="utf-8") as f:
             json.dump(context_data, f, indent=2)
 
         print_status("Created ideation_context.json", "success")
@@ -252,7 +252,7 @@ class PhaseExecutor:
         if output_file.exists() and not self.refresh:
             # Load and validate existing ideas - only skip if we have valid ideas
             try:
-                with open(output_file) as f:
+                with open(output_file, encoding="utf-8") as f:
                     data = json.load(f)
                     count = len(data.get(ideation_type, []))
 

apps/backend/ideation/prioritizer.py

@@ -48,7 +48,7 @@ class IdeaPrioritizer:
             }
 
         try:
-            content = output_file.read_text()
+            content = output_file.read_text(encoding="utf-8")
             data = json.loads(content)
             debug_verbose(
                 "ideation_prioritizer",
@@ -102,7 +102,7 @@ class IdeaPrioritizer:
             return {
                 "success": False,
                 "error": f"Invalid JSON: {e}",
-                "current_content": output_file.read_text()
+                "current_content": output_file.read_text(encoding="utf-8")
                 if output_file.exists()
                 else "",
                 "count": 0,

apps/backend/ideation/runner.py

@@ -232,7 +232,7 @@ class IdeationOrchestrator:
         """Print summary of ideation generation results."""
         ideation_file = self.output_dir / "ideation.json"
         if ideation_file.exists():
-            with open(ideation_file) as f:
+            with open(ideation_file, encoding="utf-8") as f:
                 ideation = json.load(f)
 
             ideas = ideation.get("ideas", [])

apps/backend/init.py

@@ -57,7 +57,7 @@ def ensure_gitignore_entry(project_dir: Path, entry: str = ".auto-claude/") -> b
 
     # Check if .gitignore exists and if entry is already present
     if gitignore_path.exists():
-        content = gitignore_path.read_text()
+        content = gitignore_path.read_text(encoding="utf-8")
         lines = content.splitlines()
 
         if _entry_exists_in_gitignore(lines, entry):
@@ -72,14 +72,14 @@ def ensure_gitignore_entry(project_dir: Path, entry: str = ".auto-claude/") -> b
         content += "\n# Auto Claude data directory\n"
         content += entry + "\n"
 
-        gitignore_path.write_text(content)
+        gitignore_path.write_text(content, encoding="utf-8")
         return True
     else:
         # Create new .gitignore with the entry
         content = "# Auto Claude data directory\n"
         content += entry + "\n"
 
-        gitignore_path.write_text(content)
+        gitignore_path.write_text(content, encoding="utf-8")
         return True
 
 
@@ -177,7 +177,7 @@ def ensure_all_gitignore_entries(
 
     # Read existing content or start fresh
     if gitignore_path.exists():
-        content = gitignore_path.read_text()
+        content = gitignore_path.read_text(encoding="utf-8")
         lines = content.splitlines()
     else:
         content = ""
@@ -203,7 +203,7 @@ def ensure_all_gitignore_entries(
         content += entry + "\n"
         added_entries.append(entry)
 
-    gitignore_path.write_text(content)
+    gitignore_path.write_text(content, encoding="utf-8")
 
     # Auto-commit if requested and entries were added
     if auto_commit and added_entries:

apps/backend/integrations/graphiti/config.py

@@ -507,7 +507,7 @@ class GraphitiState:
     def save(self, spec_dir: Path) -> None:
         """Save state to the spec directory."""
         marker_file = spec_dir / GRAPHITI_STATE_MARKER
-        with open(marker_file, "w") as f:
+        with open(marker_file, "w", encoding="utf-8") as f:
             json.dump(self.to_dict(), f, indent=2)
 
     @classmethod
@@ -518,9 +518,9 @@ class GraphitiState:
             return None
 
         try:
-            with open(marker_file) as f:
+            with open(marker_file, encoding="utf-8") as f:
                 return cls.from_dict(json.load(f))
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             return None
 
     def record_error(self, error_msg: str) -> None:

apps/backend/integrations/linear/config.py

@@ -126,7 +126,7 @@ class LinearProjectState:
     def save(self, spec_dir: Path) -> None:
         """Save state to the spec directory."""
         marker_file = spec_dir / LINEAR_PROJECT_MARKER
-        with open(marker_file, "w") as f:
+        with open(marker_file, "w", encoding="utf-8") as f:
             json.dump(self.to_dict(), f, indent=2)
 
     @classmethod
@@ -137,9 +137,9 @@ class LinearProjectState:
             return None
 
         try:
-            with open(marker_file) as f:
+            with open(marker_file, encoding="utf-8") as f:
                 return cls.from_dict(json.load(f))
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             return None
 
 

apps/backend/integrations/linear/integration.py

@@ -158,9 +158,9 @@ class LinearManager:
             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
 
     def get_subtasks_for_sync(self) -> list[dict]:

apps/backend/integrations/linear/updater.py

@@ -81,7 +81,7 @@ class LinearTaskState:
     def save(self, spec_dir: Path) -> None:
         """Save state to the spec directory."""
         state_file = spec_dir / LINEAR_TASK_FILE
-        with open(state_file, "w") as f:
+        with open(state_file, "w", encoding="utf-8") as f:
             json.dump(self.to_dict(), f, indent=2)
 
     @classmethod
@@ -92,9 +92,9 @@ class LinearTaskState:
             return None
 
         try:
-            with open(state_file) as f:
+            with open(state_file, encoding="utf-8") as f:
                 return cls.from_dict(json.load(f))
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             return None
 
 

apps/backend/memory/codebase_map.py

@@ -38,9 +38,9 @@ def update_codebase_map(spec_dir: Path, discoveries: dict[str, str]) -> None:
     # Load existing map or create new
     if map_file.exists():
         try:
-            with open(map_file) as f:
+            with open(map_file, encoding="utf-8") as f:
                 codebase_map = json.load(f)
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             codebase_map = {}
     else:
         codebase_map = {}
@@ -58,7 +58,7 @@ def update_codebase_map(spec_dir: Path, discoveries: dict[str, str]) -> None:
     )
 
     # Write back
-    with open(map_file, "w") as f:
+    with open(map_file, "w", encoding="utf-8") as f:
         json.dump(codebase_map, f, indent=2, sort_keys=True)
 
     # Also save to Graphiti if enabled
@@ -90,12 +90,12 @@ def load_codebase_map(spec_dir: Path) -> dict[str, str]:
         return {}
 
     try:
-        with open(map_file) as f:
+        with open(map_file, encoding="utf-8") as f:
             codebase_map = json.load(f)
 
         # Remove metadata before returning
         codebase_map.pop("_metadata", None)
         return codebase_map
 
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return {}

apps/backend/memory/patterns.py

@@ -36,7 +36,7 @@ def append_gotcha(spec_dir: Path, gotcha: str) -> None:
     # Load existing gotchas
     existing_gotchas = set()
     if gotchas_file.exists():
-        content = gotchas_file.read_text()
+        content = gotchas_file.read_text(encoding="utf-8")
         # Extract bullet points
         for line in content.split("\n"):
             line = line.strip()
@@ -47,7 +47,7 @@ def append_gotcha(spec_dir: Path, gotcha: str) -> None:
     gotcha_stripped = gotcha.strip()
     if gotcha_stripped and gotcha_stripped not in existing_gotchas:
         # Append to file
-        with open(gotchas_file, "a") as f:
+        with open(gotchas_file, "a", encoding="utf-8") as f:
             if gotchas_file.stat().st_size == 0:
                 # First entry - add header
                 f.write("# Gotchas and Pitfalls\n\n")
@@ -80,7 +80,7 @@ def load_gotchas(spec_dir: Path) -> list[str]:
     if not gotchas_file.exists():
         return []
 
-    content = gotchas_file.read_text()
+    content = gotchas_file.read_text(encoding="utf-8")
     gotchas = []
 
     for line in content.split("\n"):
@@ -112,7 +112,7 @@ def append_pattern(spec_dir: Path, pattern: str) -> None:
     # Load existing patterns
     existing_patterns = set()
     if patterns_file.exists():
-        content = patterns_file.read_text()
+        content = patterns_file.read_text(encoding="utf-8")
         # Extract bullet points
         for line in content.split("\n"):
             line = line.strip()
@@ -123,7 +123,7 @@ def append_pattern(spec_dir: Path, pattern: str) -> None:
     pattern_stripped = pattern.strip()
     if pattern_stripped and pattern_stripped not in existing_patterns:
         # Append to file
-        with open(patterns_file, "a") as f:
+        with open(patterns_file, "a", encoding="utf-8") as f:
             if patterns_file.stat().st_size == 0:
                 # First entry - add header
                 f.write("# Code Patterns\n\n")
@@ -156,7 +156,7 @@ def load_patterns(spec_dir: Path) -> list[str]:
     if not patterns_file.exists():
         return []
 
-    content = patterns_file.read_text()
+    content = patterns_file.read_text(encoding="utf-8")
     patterns = []
 
     for line in content.split("\n"):

apps/backend/memory/sessions.py

@@ -76,7 +76,7 @@ def save_session_insights(
     }
 
     # Write to file (always use file-based storage)
-    with open(session_file, "w") as f:
+    with open(session_file, "w", encoding="utf-8") as f:
         json.dump(session_data, f, indent=2)
 
     # Also save to Graphiti if enabled (non-blocking, errors logged but not raised)
@@ -110,9 +110,9 @@ def load_all_insights(spec_dir: Path) -> list[dict[str, Any]]:
     insights = []
     for session_file in session_files:
         try:
-            with open(session_file) as f:
+            with open(session_file, encoding="utf-8") as f:
                 insights.append(json.load(f))
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             # Skip corrupted files
             continue
 

apps/backend/merge/file_evolution/storage.py

@@ -61,7 +61,7 @@ class EvolutionStorage:
             return {}
 
         try:
-            with open(self.evolution_file) as f:
+            with open(self.evolution_file, encoding="utf-8") as f:
                 data = json.load(f)
 
             evolutions = {}
@@ -88,7 +88,7 @@ class EvolutionStorage:
                 for file_path, evolution in evolutions.items()
             }
 
-            with open(self.evolution_file, "w") as f:
+            with open(self.evolution_file, "w", encoding="utf-8") as f:
                 json.dump(data, f, indent=2)
 
             logger.debug(f"Saved evolution data for {len(evolutions)} files")

apps/backend/merge/file_merger.py

@@ -83,10 +83,16 @@ def apply_single_task_changes(
             # Addition - need to determine where to add
             if change.change_type == ChangeType.ADD_IMPORT:
                 # Add import at top
+                # Content is already normalized to LF, so only check for \n
+                has_trailing_newline = content.endswith("\n")
                 lines = content.splitlines()
                 import_end = find_import_end(lines, file_path)
-                lines.insert(import_end, change.content_after)
+                # Strip trailing newline from content_after to prevent double newlines
+                # (content_after may include newline from diff generation)
+                lines.insert(import_end, change.content_after.rstrip("\n\r"))
                 content = line_ending.join(lines)
+                if has_trailing_newline:
+                    content += line_ending
             elif change.change_type == ChangeType.ADD_FUNCTION:
                 # Add function at end (before exports)
                 content += f"{line_ending}{line_ending}{change.content_after}"
@@ -149,13 +155,21 @@ def combine_non_conflicting_changes(
 
     # Add imports
     if imports:
+        # Content is already normalized to LF, so only check for \n
+        has_trailing_newline = content.endswith("\n")
         lines = content.splitlines()
         import_end = find_import_end(lines, file_path)
         for imp in imports:
-            if imp.content_after and imp.content_after not in content:
-                lines.insert(import_end, imp.content_after)
+            # Strip trailing newline from content_after to prevent double newlines
+            import_content = (
+                imp.content_after.rstrip("\n\r") if imp.content_after else ""
+            )
+            if import_content and import_content not in content:
+                lines.insert(import_end, import_content)
                 import_end += 1
         content = line_ending.join(lines)
+        if has_trailing_newline:
+            content += line_ending
 
     # Apply modifications
     for mod in modifications:

apps/backend/merge/install_hook.py

@@ -75,7 +75,7 @@ def install_hook(project_path: Path) -> bool:
     # Handle worktrees (where .git is a file, not directory)
     if git_dir.is_file():
         # Read the gitdir from the file
-        content = git_dir.read_text().strip()
+        content = git_dir.read_text(encoding="utf-8").strip()
         if content.startswith("gitdir:"):
             git_dir = Path(content.split(":", 1)[1].strip())
         else:
@@ -93,7 +93,7 @@ def install_hook(project_path: Path) -> bool:
 
     # Check if hook already exists
     if hook_path.exists():
-        existing = hook_path.read_text()
+        existing = hook_path.read_text(encoding="utf-8")
         if "FileTimelineTracker" in existing:
             print(f"Hook already installed at {hook_path}")
             return True
@@ -104,13 +104,13 @@ def install_hook(project_path: Path) -> bool:
         print(f"Backed up existing hook to {backup_path}")
 
         # Append our hook to existing
-        with open(hook_path, "a") as f:
+        with open(hook_path, "a", encoding="utf-8") as f:
             f.write("\n\n# FileTimelineTracker integration\n")
             f.write(HOOK_SCRIPT.split("#!/bin/bash", 1)[1])  # Skip shebang
         print(f"Appended FileTimelineTracker hook to {hook_path}")
     else:
         # Write new hook
-        hook_path.write_text(HOOK_SCRIPT)
+        hook_path.write_text(HOOK_SCRIPT, encoding="utf-8")
         print(f"Created new hook at {hook_path}")
 
     # Make executable
@@ -127,7 +127,7 @@ def uninstall_hook(project_path: Path) -> bool:
     git_dir = project_path / ".git"
 
     if git_dir.is_file():
-        content = git_dir.read_text().strip()
+        content = git_dir.read_text(encoding="utf-8").strip()
         if content.startswith("gitdir:"):
             git_dir = Path(content.split(":", 1)[1].strip())
 
@@ -137,7 +137,7 @@ def uninstall_hook(project_path: Path) -> bool:
         print("No hook to uninstall")
         return True
 
-    content = hook_path.read_text()
+    content = hook_path.read_text(encoding="utf-8")
     if "FileTimelineTracker" not in content:
         print("Hook does not contain FileTimelineTracker integration")
         return True

apps/backend/merge/models.py

@@ -108,5 +108,5 @@ class MergeReport:
 
     def save(self, path: Path) -> None:
         """Save report to JSON file."""
-        with open(path, "w") as f:
+        with open(path, "w", encoding="utf-8") as f:
             json.dump(self.to_dict(), f, indent=2)

apps/backend/merge/timeline_persistence.py

@@ -71,13 +71,13 @@ class TimelinePersistence:
             return timelines
 
         try:
-            with open(index_path) as f:
+            with open(index_path, encoding="utf-8") as f:
                 index = json.load(f)
 
             for file_path in index.get("files", []):
                 timeline_file = self._get_timeline_file_path(file_path)
                 if timeline_file.exists():
-                    with open(timeline_file) as f:
+                    with open(timeline_file, encoding="utf-8") as f:
                         data = json.load(f)
                     timelines[file_path] = FileTimeline.from_dict(data)
 
@@ -101,7 +101,7 @@ class TimelinePersistence:
             timeline_file = self._get_timeline_file_path(file_path)
             timeline_file.parent.mkdir(parents=True, exist_ok=True)
 
-            with open(timeline_file, "w") as f:
+            with open(timeline_file, "w", encoding="utf-8") as f:
                 json.dump(timeline.to_dict(), f, indent=2)
 
         except Exception as e:
@@ -119,7 +119,7 @@ class TimelinePersistence:
             "files": file_paths,
             "last_updated": datetime.now().isoformat(),
         }
-        with open(index_path, "w") as f:
+        with open(index_path, "w", encoding="utf-8") as f:
             json.dump(index, f, indent=2)
 
     def _get_timeline_file_path(self, file_path: str) -> Path:

apps/backend/phase_config.py

@@ -164,7 +164,7 @@ def load_task_metadata(spec_dir: Path) -> TaskMetadataConfig | None:
         return None
 
     try:
-        with open(metadata_path) as f:
+        with open(metadata_path, encoding="utf-8") as f:
             return json.load(f)
     except (json.JSONDecodeError, OSError):
         return None

apps/backend/planner_lib/context.py

@@ -41,21 +41,29 @@ class ContextLoader:
         """Load all context files from spec directory."""
         # Read spec.md
         spec_file = self.spec_dir / "spec.md"
-        spec_content = spec_file.read_text() if spec_file.exists() else ""
+        spec_content = (
+            spec_file.read_text(encoding="utf-8") if spec_file.exists() else ""
+        )
 
         # Read project_index.json
         index_file = self.spec_dir / "project_index.json"
         project_index = {}
         if index_file.exists():
-            with open(index_file) as f:
-                project_index = json.load(f)
+            try:
+                with open(index_file, encoding="utf-8") as f:
+                    project_index = json.load(f)
+            except (OSError, json.JSONDecodeError, UnicodeDecodeError):
+                pass  # Use empty dict on error
 
         # Read context.json
         context_file = self.spec_dir / "context.json"
         task_context = {}
         if context_file.exists():
-            with open(context_file) as f:
-                task_context = json.load(f)
+            try:
+                with open(context_file, encoding="utf-8") as f:
+                    task_context = json.load(f)
+            except (OSError, json.JSONDecodeError, UnicodeDecodeError):
+                pass  # Use empty dict on error
 
         # Determine services involved
         services = task_context.get("scoped_services", [])
@@ -89,7 +97,7 @@ class ContextLoader:
         requirements_file = self.spec_dir / "requirements.json"
         if requirements_file.exists():
             try:
-                with open(requirements_file) as f:
+                with open(requirements_file, encoding="utf-8") as f:
                     requirements = json.load(f)
                 declared_type = _normalize_workflow_type(
                     requirements.get("workflow_type", "")
@@ -103,7 +111,7 @@ class ContextLoader:
         assessment_file = self.spec_dir / "complexity_assessment.json"
         if assessment_file.exists():
             try:
-                with open(assessment_file) as f:
+                with open(assessment_file, encoding="utf-8") as f:
                     assessment = json.load(f)
                 declared_type = _normalize_workflow_type(
                     assessment.get("workflow_type", "")

apps/backend/prediction/main.py

@@ -52,7 +52,7 @@ def main():
             print(f"Error: No implementation_plan.json found in {spec_dir}")
             sys.exit(1)
 
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             plan = json.load(f)
 
         # Find first pending subtask

apps/backend/prediction/memory_loader.py

@@ -33,7 +33,7 @@ class MemoryLoader:
             return []
 
         gotchas = []
-        content = self.gotchas_file.read_text()
+        content = self.gotchas_file.read_text(encoding="utf-8")
 
         # Parse markdown list items
         for line in content.split("\n"):
@@ -56,7 +56,7 @@ class MemoryLoader:
             return []
 
         patterns = []
-        content = self.patterns_file.read_text()
+        content = self.patterns_file.read_text(encoding="utf-8")
 
         # Parse markdown sections
         current_pattern = None
@@ -89,8 +89,8 @@ class MemoryLoader:
             return []
 
         try:
-            with open(self.history_file) as f:
+            with open(self.history_file, encoding="utf-8") as f:
                 history = json.load(f)
                 return history.get("attempts", [])
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             return []

apps/backend/project/analyzer.py

@@ -69,7 +69,7 @@ class ProjectAnalyzer:
             return None
 
         try:
-            with open(profile_path) as f:
+            with open(profile_path, encoding="utf-8") as f:
                 data = json.load(f)
             return SecurityProfile.from_dict(data)
         except (OSError, json.JSONDecodeError, KeyError):
@@ -80,7 +80,7 @@ class ProjectAnalyzer:
         profile_path = self.get_profile_path()
         profile_path.parent.mkdir(parents=True, exist_ok=True)
 
-        with open(profile_path, "w") as f:
+        with open(profile_path, "w", encoding="utf-8") as f:
             json.dump(profile.to_dict(), f, indent=2)
 
     def compute_project_hash(self) -> str:

apps/backend/project/config_parser.py

@@ -38,7 +38,7 @@ class ConfigParser:
     def read_json(self, filename: str) -> dict | None:
         """Read a JSON file from project root."""
         try:
-            with open(self.project_dir / filename) as f:
+            with open(self.project_dir / filename, encoding="utf-8") as f:
                 return json.load(f)
         except (FileNotFoundError, json.JSONDecodeError):
             return None
@@ -59,7 +59,7 @@ class ConfigParser:
     def read_text(self, filename: str) -> str | None:
         """Read a text file from project root."""
         try:
-            with open(self.project_dir / filename) as f:
+            with open(self.project_dir / filename, encoding="utf-8") as f:
                 return f.read()
         except (OSError, FileNotFoundError):
             return None

apps/backend/project/stack_detector.py

@@ -248,7 +248,7 @@ class StackDetector:
                 "**/*.yaml"
             ) + self.parser.glob_files("**/*.yml"):
                 try:
-                    with open(yaml_file) as f:
+                    with open(yaml_file, encoding="utf-8") as f:
                         content = f.read()
                         if "apiVersion:" in content and "kind:" in content:
                             self.stack.infrastructure.append("kubernetes")

apps/backend/prompts/coder.md

@@ -942,13 +942,13 @@ if insights["discoveries"]["patterns_found"]:
     # Load existing patterns
     existing_patterns = set()
     if patterns_file.exists():
-        content = patterns_file.read_text()
+        content = patterns_file.read_text(encoding="utf-8")
         for line in content.split("\n"):
             if line.strip().startswith("- "):
                 existing_patterns.add(line.strip()[2:])
 
     # Add new patterns
-    with open(patterns_file, "a") as f:
+    with open(patterns_file, "a", encoding="utf-8") as f:
         if patterns_file.stat().st_size == 0:
             f.write("# Code Patterns\n\n")
             f.write("Established patterns to follow in this codebase:\n\n")
@@ -965,13 +965,13 @@ if insights["discoveries"]["gotchas_encountered"]:
     # Load existing gotchas
     existing_gotchas = set()
     if gotchas_file.exists():
-        content = gotchas_file.read_text()
+        content = gotchas_file.read_text(encoding="utf-8")
         for line in content.split("\n"):
             if line.strip().startswith("- "):
                 existing_gotchas.add(line.strip()[2:])
 
     # Add new gotchas
-    with open(gotchas_file, "a") as f:
+    with open(gotchas_file, "a", encoding="utf-8") as f:
         if gotchas_file.stat().st_size == 0:
             f.write("# Gotchas and Pitfalls\n\n")
             f.write("Things to watch out for in this codebase:\n\n")

apps/backend/prompts_pkg/prompt_generator.py

@@ -336,7 +336,7 @@ def load_subtask_context(
         full_path = project_dir / pattern_path
         if full_path.exists():
             try:
-                lines = full_path.read_text().split("\n")
+                lines = full_path.read_text(encoding="utf-8").split("\n")
                 if len(lines) > max_file_lines:
                     content = "\n".join(lines[:max_file_lines])
                     content += (
@@ -353,7 +353,7 @@ def load_subtask_context(
         full_path = project_dir / file_path
         if full_path.exists():
             try:
-                lines = full_path.read_text().split("\n")
+                lines = full_path.read_text(encoding="utf-8").split("\n")
                 if len(lines) > max_file_lines:
                     content = "\n".join(lines[:max_file_lines])
                     content += (

apps/backend/prompts_pkg/prompts.py

@@ -173,7 +173,7 @@ def get_planner_prompt(spec_dir: Path) -> str:
             "Make sure the auto-claude/prompts/planner.md file exists."
         )
 
-    prompt = prompt_file.read_text()
+    prompt = prompt_file.read_text(encoding="utf-8")
 
     # Inject spec directory information at the beginning
     spec_context = f"""## SPEC LOCATION
@@ -216,7 +216,7 @@ def get_coding_prompt(spec_dir: Path) -> str:
             "Make sure the auto-claude/prompts/coder.md file exists."
         )
 
-    prompt = prompt_file.read_text()
+    prompt = prompt_file.read_text(encoding="utf-8")
 
     spec_context = f"""## SPEC LOCATION
 
@@ -240,7 +240,7 @@ The project root is the parent of auto-claude/. All code goes in the project roo
     # Check for human input file
     human_input_file = spec_dir / "HUMAN_INPUT.md"
     if human_input_file.exists():
-        human_input = human_input_file.read_text().strip()
+        human_input = human_input_file.read_text(encoding="utf-8").strip()
         if human_input:
             spec_context += f"""## HUMAN INPUT (READ THIS FIRST!)
 
@@ -275,7 +275,7 @@ def _get_recovery_context(spec_dir: Path) -> str:
         return ""
 
     try:
-        with open(attempt_history_file) as f:
+        with open(attempt_history_file, encoding="utf-8") as f:
             history = json.load(f)
 
         # Check for stuck subtasks
@@ -321,7 +321,7 @@ Subtasks with previous attempts:
 
         return ""
 
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return ""
 
 
@@ -344,7 +344,7 @@ def get_followup_planner_prompt(spec_dir: Path) -> str:
             "Make sure the auto-claude/prompts/followup_planner.md file exists."
         )
 
-    prompt = prompt_file.read_text()
+    prompt = prompt_file.read_text(encoding="utf-8")
 
     # Inject spec directory information at the beginning
     spec_context = f"""## SPEC LOCATION (FOLLOW-UP MODE)
@@ -405,7 +405,7 @@ def is_first_run(spec_dir: Path) -> bool:
         # Check if any phase has subtasks
         total_subtasks = sum(len(phase.get("subtasks", [])) for phase in phases)
         return total_subtasks == 0
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         # If we can't read the file, treat as first run
         return True
 
@@ -426,7 +426,7 @@ def _load_prompt_file(filename: str) -> str:
     prompt_file = PROMPTS_DIR / filename
     if not prompt_file.exists():
         raise FileNotFoundError(f"Prompt file not found: {prompt_file}")
-    return prompt_file.read_text()
+    return prompt_file.read_text(encoding="utf-8")
 
 
 def get_qa_reviewer_prompt(spec_dir: Path, project_dir: Path) -> str:

apps/backend/qa/criteria.py

@@ -21,9 +21,9 @@ 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
 
 
@@ -31,7 +31,7 @@ def save_implementation_plan(spec_dir: Path, plan: dict) -> bool:
     """Save the implementation plan JSON."""
     plan_file = spec_dir / "implementation_plan.json"
     try:
-        with open(plan_file, "w") as f:
+        with open(plan_file, "w", encoding="utf-8") as f:
             json.dump(plan, f, indent=2)
         return True
     except OSError:

apps/backend/qa/fixer.py

@@ -38,7 +38,7 @@ def load_qa_fixer_prompt() -> str:
     prompt_file = QA_PROMPTS_DIR / "qa_fixer.md"
     if not prompt_file.exists():
         raise FileNotFoundError(f"QA fixer prompt not found: {prompt_file}")
-    return prompt_file.read_text()
+    return prompt_file.read_text(encoding="utf-8")
 
 
 # =============================================================================

apps/backend/qa/report.py

@@ -324,7 +324,7 @@ These issues have appeared {RECURRING_ISSUE_THRESHOLD}+ times without being reso
 - `implementation_plan.json` - Full iteration history
 """
 
-    escalation_file.write_text(content)
+    escalation_file.write_text(content, encoding="utf-8")
     print(f"\n📝 Escalation file created: {escalation_file}")
 
 
@@ -345,7 +345,7 @@ def create_manual_test_plan(spec_dir: Path, spec_name: str) -> Path:
     spec_file = spec_dir / "spec.md"
     spec_content = ""
     if spec_file.exists():
-        spec_content = spec_file.read_text()
+        spec_content = spec_file.read_text(encoding="utf-8")
 
     # Extract acceptance criteria from spec if present
     acceptance_criteria = []
@@ -439,7 +439,7 @@ _Add any observations or issues found during testing_
 
 """
 
-    manual_plan_file.write_text(content)
+    manual_plan_file.write_text(content, encoding="utf-8")
     return manual_plan_file
 
 
@@ -460,9 +460,9 @@ def check_test_discovery(spec_dir: Path) -> dict[str, Any] | None:
         return None
 
     try:
-        with open(discovery_file) as f:
+        with open(discovery_file, encoding="utf-8") as f:
             return json.load(f)
-    except (OSError, json.JSONDecodeError):
+    except (OSError, json.JSONDecodeError, UnicodeDecodeError):
         return None
 
 

apps/backend/review/formatters.py

@@ -159,7 +159,7 @@ def display_plan_summary(spec_dir: Path) -> None:
         return
 
     try:
-        with open(plan_file) as f:
+        with open(plan_file, encoding="utf-8") as f:
             plan = json.load(f)
     except (OSError, json.JSONDecodeError) as e:
         print_status(f"Could not read implementation_plan.json: {e}", "error")

apps/backend/review/state.py

@@ -85,7 +85,7 @@ class ReviewState:
     def save(self, spec_dir: Path) -> None:
         """Save state to the spec directory."""
         state_file = Path(spec_dir) / REVIEW_STATE_FILE
-        with open(state_file, "w") as f:
+        with open(state_file, "w", encoding="utf-8") as f:
             json.dump(self.to_dict(), f, indent=2)
 
     @classmethod
@@ -100,9 +100,9 @@ class ReviewState:
             return cls()
 
         try:
-            with open(state_file) as f:
+            with open(state_file, encoding="utf-8") as f:
                 return cls.from_dict(json.load(f))
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             return cls()
 
     def is_approved(self) -> bool:

apps/backend/runners/ai_analyzer/cache_manager.py

@@ -48,7 +48,7 @@ class CacheManager:
             return None
 
         print(f"✓ Using cached AI insights ({hours_old:.1f} hours old)")
-        return json.loads(self.cache_file.read_text())
+        return json.loads(self.cache_file.read_text(encoding="utf-8"))
 
     def save_result(self, result: dict[str, Any]) -> None:
         """
@@ -57,5 +57,5 @@ class CacheManager:
         Args:
             result: Analysis result to cache
         """
-        self.cache_file.write_text(json.dumps(result, indent=2))
+        self.cache_file.write_text(json.dumps(result, indent=2), encoding="utf-8")
         print(f"\n✓ AI insights cached to: {self.cache_file}")

apps/backend/runners/ai_analyzer/claude_client.py

@@ -87,7 +87,7 @@ class ClaudeAnalysisClient:
         }
 
         settings_file = self.project_dir / ".claude_ai_analyzer_settings.json"
-        with open(settings_file, "w") as f:
+        with open(settings_file, "w", encoding="utf-8") as f:
             json.dump(settings, f, indent=2)
 
         return settings_file

apps/backend/runners/ai_analyzer_runner.py

@@ -56,7 +56,7 @@ def main() -> int:
         print(f"Run: python analyzer.py --project-dir {args.project_dir} --index")
         return 1
 
-    project_index = json.loads(index_path.read_text())
+    project_index = json.loads(index_path.read_text(encoding="utf-8"))
 
     # Import here to avoid import errors if dependencies are missing
     try:

apps/backend/runners/github/audit.py

@@ -369,7 +369,7 @@ class AuditLogger:
 
         try:
             log_file = self._get_log_file_path()
-            with open(log_file, "a") as f:
+            with open(log_file, "a", encoding="utf-8") as f:
                 f.write(entry.to_json() + "\n")
         except Exception as e:
             logger.error(f"Failed to write audit log: {e}")
@@ -585,7 +585,7 @@ class AuditLogger:
 
         for log_file in sorted(self.log_dir.glob("audit_*.jsonl"), reverse=True):
             try:
-                with open(log_file) as f:
+                with open(log_file, encoding="utf-8") as f:
                     for line in f:
                         if not line.strip():
                             continue

apps/backend/runners/github/batch_issues.py

@@ -368,7 +368,7 @@ class IssueBatch:
         if not batch_file.exists():
             return None
 
-        with open(batch_file) as f:
+        with open(batch_file, encoding="utf-8") as f:
             data = json.load(f)
         return cls.from_dict(data)
 
@@ -448,7 +448,7 @@ class IssueBatcher:
         """Load batch index from disk."""
         index_file = self.github_dir / "batches" / "index.json"
         if index_file.exists():
-            with open(index_file) as f:
+            with open(index_file, encoding="utf-8") as f:
                 data = json.load(f)
             self._batch_index = {
                 int(k): v for k, v in data.get("issue_to_batch", {}).items()
@@ -460,7 +460,7 @@ class IssueBatcher:
         batches_dir.mkdir(parents=True, exist_ok=True)
 
         index_file = batches_dir / "index.json"
-        with open(index_file, "w") as f:
+        with open(index_file, "w", encoding="utf-8") as f:
             json.dump(
                 {
                     "issue_to_batch": self._batch_index,
@@ -1107,7 +1107,7 @@ class IssueBatcher:
         batches = []
         for batch_file in batches_dir.glob("batch_*.json"):
             try:
-                with open(batch_file) as f:
+                with open(batch_file, encoding="utf-8") as f:
                     data = json.load(f)
                 batches.append(IssueBatch.from_dict(data))
             except Exception as e:

apps/backend/runners/github/batch_validator.py

@@ -230,7 +230,7 @@ class BatchValidator:
             }
 
             settings_file = self.project_dir / ".batch_validator_settings.json"
-            with open(settings_file, "w") as f:
+            with open(settings_file, "w", encoding="utf-8") as f:
                 json.dump(settings, f)
 
             try:

apps/backend/runners/github/bot_detection.py

@@ -85,7 +85,7 @@ class BotDetectionState:
         if not state_file.exists():
             return cls()
 
-        with open(state_file) as f:
+        with open(state_file, encoding="utf-8") as f:
             return cls.from_dict(json.load(f))
 
 

apps/backend/runners/github/cleanup.py

@@ -248,9 +248,9 @@ class DataCleaner:
     ) -> bool:
         """Process a single file for cleanup."""
         try:
-            with open(file_path) as f:
+            with open(file_path, encoding="utf-8") as f:
                 data = json.load(f)
-        except (OSError, json.JSONDecodeError):
+        except (OSError, json.JSONDecodeError, UnicodeDecodeError):
             # Corrupted file, mark for deletion
             if not dry_run:
                 file_size = file_path.stat().st_size
@@ -327,7 +327,7 @@ class DataCleaner:
         data["_archived_at"] = datetime.now(timezone.utc).isoformat()
         data["_original_path"] = str(file_path)
 
-        with open(archive_path, "w") as f:
+        with open(archive_path, "w", encoding="utf-8") as f:
             json.dump(data, f, indent=2)
 
         # Remove original
@@ -350,7 +350,7 @@ class DataCleaner:
                 continue
 
             try:
-                with open(index_path) as f:
+                with open(index_path, encoding="utf-8") as f:
                     index_data = json.load(f)
 
                 if not isinstance(index_data, dict):
@@ -375,12 +375,12 @@ class DataCleaner:
                     for key in to_remove:
                         del items[key]
 
-                    with open(index_path, "w") as f:
+                    with open(index_path, "w", encoding="utf-8") as f:
                         json.dump(index_data, f, indent=2)
 
                 result.pruned_index_entries += pruned
 
-            except (OSError, json.JSONDecodeError, KeyError):
+            except (OSError, json.JSONDecodeError, UnicodeDecodeError, KeyError):
                 result.errors.append(f"Error pruning index: {index_path}")
 
     async def _clean_audit_logs(

apps/backend/runners/github/context_gatherer.py

@@ -782,7 +782,7 @@ class PRContextGatherer:
         # Check for package.json (Node.js)
         if (self.project_dir / "package.json").exists():
             try:
-                with open(self.project_dir / "package.json") as f:
+                with open(self.project_dir / "package.json", encoding="utf-8") as f:
                     pkg_data = json.load(f)
                     if "workspaces" in pkg_data:
                         structure_info.append(

apps/backend/runners/github/duplicates.py

@@ -347,7 +347,7 @@ class DuplicateDetector:
         if not cache_file.exists():
             return {}
 
-        with open(cache_file) as f:
+        with open(cache_file, encoding="utf-8") as f:
             data = json.load(f)
 
         cache = {}
@@ -365,7 +365,7 @@ class DuplicateDetector:
             "embeddings": [e.to_dict() for e in cache.values()],
             "last_updated": datetime.now(timezone.utc).isoformat(),
         }
-        with open(cache_file, "w") as f:
+        with open(cache_file, "w", encoding="utf-8") as f:
             json.dump(data, f)
 
     async def get_embedding(

apps/backend/runners/github/file_lock.py

@@ -212,7 +212,7 @@ class FileLock:
 
 
 @contextmanager
-def atomic_write(filepath: str | Path, mode: str = "w"):
+def atomic_write(filepath: str | Path, mode: str = "w", encoding: str = "utf-8"):
     """
     Atomic file write using temp file and rename.
 
@@ -222,6 +222,7 @@ def atomic_write(filepath: str | Path, mode: str = "w"):
     Args:
         filepath: Target file path
         mode: File open mode (default: "w")
+        encoding: Text encoding (default: "utf-8")
 
     Example:
         with atomic_write("/path/to/file.json") as f:
@@ -236,8 +237,9 @@ def atomic_write(filepath: str | Path, mode: str = "w"):
     )
 
     try:
-        # Open temp file with requested mode
-        with os.fdopen(fd, mode) as f:
+        # Open temp file with requested mode and encoding
+        # Only use encoding for text modes (not binary modes)
+        with os.fdopen(fd, mode, encoding=encoding if "b" not in mode else None) as f:
             yield f
 
         # Atomic replace - succeeds or fails completely
@@ -254,7 +256,10 @@ def atomic_write(filepath: str | Path, mode: str = "w"):
 
 @asynccontextmanager
 async def locked_write(
-    filepath: str | Path, timeout: float = 5.0, mode: str = "w"
+    filepath: str | Path,
+    timeout: float = 5.0,
+    mode: str = "w",
+    encoding: str = "utf-8",
 ) -> Any:
     """
     Async context manager combining file locking and atomic writes.
@@ -266,6 +271,7 @@ async def locked_write(
         filepath: Target file path
         timeout: Lock timeout in seconds (default: 5.0)
         mode: File open mode (default: "w")
+        encoding: Text encoding (default: "utf-8")
 
     Example:
         async with locked_write("/path/to/file.json", timeout=5.0) as f:
@@ -291,7 +297,8 @@ async def locked_write(
 
         try:
             # Open temp file and yield to caller
-            f = os.fdopen(fd, mode)
+            # Only use encoding for text modes (not binary modes)
+            f = os.fdopen(fd, mode, encoding=encoding if "b" not in mode else None)
             try:
                 yield f
             finally:
@@ -348,7 +355,7 @@ async def locked_read(filepath: str | Path, timeout: float = 5.0) -> Any:
 
     try:
         # Open file for reading
-        with open(filepath) as f:
+        with open(filepath, encoding="utf-8") as f:
             yield f
     finally:
         # Release lock
@@ -441,7 +448,7 @@ async def locked_json_update(
         # Read current data
         def _read_json():
             if filepath.exists():
-                with open(filepath) as f:
+                with open(filepath, encoding="utf-8") as f:
                     return json.load(f)
             return None
 
@@ -459,7 +466,7 @@ async def locked_json_update(
         )
 
         try:
-            with os.fdopen(fd, "w") as f:
+            with os.fdopen(fd, "w", encoding="utf-8") as f:
                 json.dump(updated_data, f, indent=indent)
 
             await asyncio.get_running_loop().run_in_executor(

apps/backend/runners/github/learning.py

@@ -299,7 +299,7 @@ class LearningTracker:
         """Load all outcomes from disk."""
         for file in self.learning_dir.glob("*_outcomes.json"):
             try:
-                with open(file) as f:
+                with open(file, encoding="utf-8") as f:
                     data = json.load(f)
                     for item in data.get("outcomes", []):
                         outcome = ReviewOutcome.from_dict(item)

apps/backend/runners/github/lifecycle.py

@@ -409,7 +409,7 @@ class LifecycleManager:
         if not file.exists():
             return None
 
-        with open(file) as f:
+        with open(file, encoding="utf-8") as f:
             data = json.load(f)
         return IssueLifecycle.from_dict(data)
 
@@ -426,7 +426,7 @@ class LifecycleManager:
     def save(self, lifecycle: IssueLifecycle) -> None:
         """Save lifecycle state."""
         file = self._get_file(lifecycle.repo, lifecycle.issue_number)
-        with open(file, "w") as f:
+        with open(file, "w", encoding="utf-8") as f:
             json.dump(lifecycle.to_dict(), f, indent=2)
 
     def transition(
@@ -509,7 +509,7 @@ class LifecycleManager:
         safe_repo = repo.replace("/", "_")
 
         for file in self.lifecycle_dir.glob(f"{safe_repo}_*.json"):
-            with open(file) as f:
+            with open(file, encoding="utf-8") as f:
                 data = json.load(f)
                 lifecycle = IssueLifecycle.from_dict(data)
                 if lifecycle.current_state == state:
@@ -523,7 +523,7 @@ class LifecycleManager:
         safe_repo = repo.replace("/", "_")
 
         for file in self.lifecycle_dir.glob(f"{safe_repo}_*.json"):
-            with open(file) as f:
+            with open(file, encoding="utf-8") as f:
                 data = json.load(f)
                 state = data.get("current_state", "new")
                 counts[state] = counts.get(state, 0) + 1

apps/backend/runners/github/memory_integration.py

@@ -193,7 +193,7 @@ class GitHubMemoryIntegration:
         insights_file = self.memory_dir / f"{self.repo.replace('/', '_')}_insights.json"
         if insights_file.exists():
             try:
-                with open(insights_file) as f:
+                with open(insights_file, encoding="utf-8") as f:
                     self._local_insights = json.load(f).get("insights", [])
             except (json.JSONDecodeError, KeyError):
                 self._local_insights = []
@@ -201,7 +201,7 @@ class GitHubMemoryIntegration:
     def _save_local_insights(self) -> None:
         """Save insights locally."""
         insights_file = self.memory_dir / f"{self.repo.replace('/', '_')}_insights.json"
-        with open(insights_file, "w") as f:
+        with open(insights_file, "w", encoding="utf-8") as f:
             json.dump(
                 {
                     "repo": self.repo,

apps/backend/runners/github/models.py

@@ -550,7 +550,7 @@ class PRReviewResult:
         if not review_file.exists():
             return None
 
-        with open(review_file) as f:
+        with open(review_file, encoding="utf-8") as f:
             return cls.from_dict(json.load(f))
 
 
@@ -663,7 +663,7 @@ class TriageResult:
         if not triage_file.exists():
             return None
 
-        with open(triage_file) as f:
+        with open(triage_file, encoding="utf-8") as f:
             return cls.from_dict(json.load(f))
 
 
@@ -797,7 +797,7 @@ class AutoFixState:
         if not autofix_file.exists():
             return None
 
-        with open(autofix_file) as f:
+        with open(autofix_file, encoding="utf-8") as f:
             return cls.from_dict(json.load(f))
 
 
@@ -879,7 +879,7 @@ class GitHubRunnerConfig:
         settings.pop("token", None)
         settings.pop("bot_token", None)
 
-        with open(config_file, "w") as f:
+        with open(config_file, "w", encoding="utf-8") as f:
             json.dump(settings, f, indent=2)
 
     @classmethod
@@ -890,7 +890,7 @@ class GitHubRunnerConfig:
         config_file = github_dir / "config.json"
 
         if config_file.exists():
-            with open(config_file) as f:
+            with open(config_file, encoding="utf-8") as f:
                 settings = json.load(f)
         else:
             settings = {}

apps/backend/runners/github/multi_repo.py

@@ -340,7 +340,7 @@ class MultiRepoConfig:
             "repos": [c.to_dict() for c in self.repos.values()],
             "last_updated": datetime.now(timezone.utc).isoformat(),
         }
-        with open(file_path, "w") as f:
+        with open(file_path, "w", encoding="utf-8") as f:
             json.dump(data, f, indent=2)
 
     @classmethod
@@ -349,7 +349,7 @@ class MultiRepoConfig:
         if not config_file.exists():
             return cls()
 
-        with open(config_file) as f:
+        with open(config_file, encoding="utf-8") as f:
             data = json.load(f)
 
         repos = [RepoConfig.from_dict(r) for r in data.get("repos", [])]

apps/backend/runners/github/onboarding.py

@@ -301,7 +301,7 @@ class OnboardingManager:
 
         if self.state_file.exists():
             try:
-                with open(self.state_file) as f:
+                with open(self.state_file, encoding="utf-8") as f:
                     data = json.load(f)
                     self._state = OnboardingState.from_dict(data)
             except (json.JSONDecodeError, KeyError):
@@ -315,7 +315,7 @@ class OnboardingManager:
         """Save onboarding state."""
         state = self.get_state()
         self.state_file.parent.mkdir(parents=True, exist_ok=True)
-        with open(self.state_file, "w") as f:
+        with open(self.state_file, "w", encoding="utf-8") as f:
             json.dump(state.to_dict(), f, indent=2)
 
     async def run_setup(

apps/backend/runners/github/override.py

@@ -300,7 +300,7 @@ class OverrideManager:
         if not grace_file.exists():
             return None
 
-        with open(grace_file) as f:
+        with open(grace_file, encoding="utf-8") as f:
             data = json.load(f)
 
         entry_data = data.get("entries", {}).get(str(issue_number))
@@ -778,7 +778,7 @@ class OverrideManager:
         if not history_file.exists():
             return []
 
-        with open(history_file) as f:
+        with open(history_file, encoding="utf-8") as f:
             data = json.load(f)
 
         records = []
@@ -809,7 +809,7 @@ class OverrideManager:
         if not history_file.exists():
             return {"total": 0, "by_type": {}, "by_actor": {}}
 
-        with open(history_file) as f:
+        with open(history_file, encoding="utf-8") as f:
             data = json.load(f)
 
         stats = {

apps/backend/runners/github/purge_strategy.py

@@ -224,7 +224,7 @@ class PurgeStrategy:
             result: PurgeResult to update
         """
         try:
-            with open(file_path) as f:
+            with open(file_path, encoding="utf-8") as f:
                 data = json.load(f)
 
             # Verify key matches value

apps/backend/runners/github/runner.py

@@ -613,9 +613,9 @@ async def cmd_approve_batches(args) -> int:
 
     # Load approved batches from file
     try:
-        with open(args.batch_file) as f:
+        with open(args.batch_file, encoding="utf-8") as f:
             approved_batches = json.load(f)
-    except (json.JSONDecodeError, FileNotFoundError) as e:
+    except (json.JSONDecodeError, FileNotFoundError, UnicodeDecodeError) as e:
         safe_print(f"Error loading batch file: {e}")
         return 1
 

apps/backend/runners/github/test_context_gatherer.py

@@ -75,11 +75,11 @@ def test_find_test_files(tmp_path):
 
     # Create source file
     source_file = src_dir / "utils.ts"
-    source_file.write_text("export const add = (a, b) => a + b;")
+    source_file.write_text("export const add = (a, b) => a + b;", encoding="utf-8")
 
     # Create test file
     test_file = src_dir / "utils.test.ts"
-    test_file.write_text("import { add } from './utils';")
+    test_file.write_text("import { add } from './utils';", encoding="utf-8")
 
     gatherer = PRContextGatherer(project_dir, 1)
 
@@ -99,11 +99,11 @@ def test_resolve_import_path(tmp_path):
 
     # Create imported file
     utils_file = src_dir / "utils.ts"
-    utils_file.write_text("export const helper = () => {};")
+    utils_file.write_text("export const helper = () => {};", encoding="utf-8")
 
     # Create importing file
     app_file = src_dir / "app.ts"
-    app_file.write_text("import { helper } from './utils';")
+    app_file.write_text("import { helper } from './utils';", encoding="utf-8")
 
     gatherer = PRContextGatherer(project_dir, 1)
 
@@ -128,7 +128,7 @@ def test_detect_repo_structure_monorepo(tmp_path):
 
     # Create package.json with workspaces
     package_json = project_dir / "package.json"
-    package_json.write_text('{"workspaces": ["apps/*"]}')
+    package_json.write_text('{"workspaces": ["apps/*"]}', encoding="utf-8")
 
     gatherer = PRContextGatherer(project_dir, 1)
 
@@ -147,7 +147,7 @@ def test_detect_repo_structure_python(tmp_path):
 
     # Create pyproject.toml
     pyproject = project_dir / "pyproject.toml"
-    pyproject.write_text("[tool.poetry]\\nname = 'test'")
+    pyproject.write_text("[tool.poetry]\nname = 'test'", encoding="utf-8")
 
     gatherer = PRContextGatherer(project_dir, 1)
 
@@ -163,8 +163,8 @@ def test_find_config_files(tmp_path):
     src_dir.mkdir(parents=True)
 
     # Create config files
-    (src_dir / "tsconfig.json").write_text("{}")
-    (src_dir / "package.json").write_text("{}")
+    (src_dir / "tsconfig.json").write_text("{}", encoding="utf-8")
+    (src_dir / "package.json").write_text("{}", encoding="utf-8")
 
     gatherer = PRContextGatherer(project_dir, 1)
 

apps/backend/runners/github/test_file_lock.py

@@ -28,7 +28,7 @@ async def test_basic_file_lock():
 
     with tempfile.TemporaryDirectory() as tmpdir:
         test_file = Path(tmpdir) / "test.txt"
-        test_file.write_text("initial content")
+        test_file.write_text("initial content", encoding="utf-8")
 
         # Acquire lock and hold it
         async with FileLock(test_file, timeout=5.0):
@@ -55,7 +55,7 @@ async def test_locked_write():
         print(f"✓ Written to {test_file.name}")
 
         # Verify data was written correctly
-        with open(test_file) as f:
+        with open(test_file, encoding="utf-8") as f:
             loaded = json.load(f)
             assert loaded == data
             print(f"✓ Data verified: {loaded}")
@@ -113,12 +113,12 @@ async def test_concurrent_updates_without_lock():
         test_file = Path(tmpdir) / "unsafe.json"
 
         # Initialize counter
-        test_file.write_text(json.dumps({"count": 0}))
+        test_file.write_text(json.dumps({"count": 0}), encoding="utf-8")
 
         async def unsafe_increment():
             """Increment without locking - RACE CONDITION!"""
             # Read
-            with open(test_file) as f:
+            with open(test_file, encoding="utf-8") as f:
                 data = json.load(f)
 
             # Simulate some processing
@@ -126,14 +126,14 @@ async def test_concurrent_updates_without_lock():
 
             # Write
             data["count"] += 1
-            with open(test_file, "w") as f:
+            with open(test_file, "w", encoding="utf-8") as f:
                 json.dump(data, f)
 
         # Run 10 concurrent increments
         await asyncio.gather(*[unsafe_increment() for _ in range(10)])
 
         # Check final count
-        with open(test_file) as f:
+        with open(test_file, encoding="utf-8") as f:
             final = json.load(f)
 
         print("✗ Expected count: 10")
@@ -182,7 +182,7 @@ async def test_lock_timeout():
 
     with tempfile.TemporaryDirectory() as tmpdir:
         test_file = Path(tmpdir) / "timeout.json"
-        test_file.write_text(json.dumps({"data": "test"}))
+        test_file.write_text(json.dumps({"data": "test"}), encoding="utf-8")
 
         # Acquire lock and hold it
         lock1 = FileLock(test_file, timeout=1.0)

apps/backend/runners/github/trust.py

@@ -420,9 +420,13 @@ class TrustManager:
 
         state_file = self._get_state_file(repo)
         if state_file.exists():
-            with open(state_file) as f:
-                data = json.load(f)
-                state = TrustState.from_dict(data)
+            try:
+                with open(state_file, encoding="utf-8") as f:
+                    data = json.load(f)
+                    state = TrustState.from_dict(data)
+            except (json.JSONDecodeError, UnicodeDecodeError):
+                # Return default state if file is corrupted
+                state = TrustState(repo=repo)
         else:
             state = TrustState(repo=repo)
 
@@ -438,12 +442,9 @@ class TrustManager:
 
         # Write with restrictive permissions (0o600 = owner read/write only)
         fd = os.open(str(state_file), os.O_WRONLY | os.O_CREAT | os.O_TRUNC, 0o600)
-        try:
-            with os.fdopen(fd, "w") as f:
-                json.dump(state.to_dict(), f, indent=2)
-        except Exception:
-            os.close(fd)
-            raise
+        # os.fdopen takes ownership of fd and will close it when the with block exits
+        with os.fdopen(fd, "w", encoding="utf-8") as f:
+            json.dump(state.to_dict(), f, indent=2)
 
     def get_trust_level(self, repo: str) -> TrustLevel:
         """Get current trust level for a repository."""
@@ -514,9 +515,13 @@ class TrustManager:
         """Get trust states for all repos."""
         states = []
         for file in self.trust_dir.glob("*.json"):
-            with open(file) as f:
-                data = json.load(f)
-                states.append(TrustState.from_dict(data))
+            try:
+                with open(file, encoding="utf-8") as f:
+                    data = json.load(f)
+                    states.append(TrustState.from_dict(data))
+            except (json.JSONDecodeError, UnicodeDecodeError):
+                # Skip corrupted state files
+                continue
         return states
 
     def get_summary(self) -> dict[str, Any]:

apps/backend/runners/gitlab/glab_client.py

@@ -253,7 +253,7 @@ def load_gitlab_config(project_dir: Path) -> GitLabConfig | None:
         return None
 
     try:
-        with open(config_path) as f:
+        with open(config_path, encoding="utf-8") as f:
             data = json.load(f)
 
         token = data.get("token")

apps/backend/runners/gitlab/models.py

@@ -184,7 +184,7 @@ class MRReviewResult:
         mr_dir.mkdir(parents=True, exist_ok=True)
 
         review_file = mr_dir / f"review_{self.mr_iid}.json"
-        with open(review_file, "w") as f:
+        with open(review_file, "w", encoding="utf-8") as f:
             json.dump(self.to_dict(), f, indent=2)
 
     @classmethod
@@ -194,7 +194,7 @@ class MRReviewResult:
         if not review_file.exists():
             return None
 
-        with open(review_file) as f:
+        with open(review_file, encoding="utf-8") as f:
             return cls.from_dict(json.load(f))
 
 

apps/backend/runners/gitlab/runner.py

@@ -91,7 +91,7 @@ def get_config(args) -> GitLabRunnerConfig:
         config_path = Path(args.project_dir) / ".auto-claude" / "gitlab" / "config.json"
         if config_path.exists():
             try:
-                with open(config_path) as f:
+                with open(config_path, encoding="utf-8") as f:
                     data = json.load(f)
                     project = data.get("project", "")
                     instance_url = data.get("instance_url", instance_url)

apps/backend/runners/insights_runner.py

@@ -58,7 +58,7 @@ def load_project_context(project_dir: str) -> str:
     index_path = Path(project_dir) / ".auto-claude" / "project_index.json"
     if index_path.exists():
         try:
-            with open(index_path) as f:
+            with open(index_path, encoding="utf-8") as f:
                 index = json.load(f)
             # Summarize the index for context
             summary = {
@@ -77,7 +77,7 @@ def load_project_context(project_dir: str) -> str:
     roadmap_path = Path(project_dir) / ".auto-claude" / "roadmap" / "roadmap.json"
     if roadmap_path.exists():
         try:
-            with open(roadmap_path) as f:
+            with open(roadmap_path, encoding="utf-8") as f:
                 roadmap = json.load(f)
             # Summarize roadmap
             features = roadmap.get("features", [])

apps/backend/runners/roadmap/competitor_analyzer.py

@@ -123,7 +123,7 @@ Output your findings to competitor_analysis.json.
         Returns RoadmapPhaseResult if validation succeeds, None otherwise.
         """
         try:
-            with open(self.analysis_file) as f:
+            with open(self.analysis_file, encoding="utf-8") as f:
                 data = json.load(f)
 
             if "competitors" in data:
@@ -146,7 +146,7 @@ Output your findings to competitor_analysis.json.
 
     def _create_disabled_analysis_file(self):
         """Create an analysis file indicating the feature is disabled."""
-        with open(self.analysis_file, "w") as f:
+        with open(self.analysis_file, "w", encoding="utf-8") as f:
             json.dump(
                 {
                     "enabled": False,
@@ -181,5 +181,5 @@ Output your findings to competitor_analysis.json.
         if errors:
             data["errors"] = errors
 
-        with open(self.analysis_file, "w") as f:
+        with open(self.analysis_file, "w", encoding="utf-8") as f:
             json.dump(data, f, indent=2)

apps/backend/runners/roadmap/executor.py

@@ -102,7 +102,7 @@ class AgentExecutor:
             return False, f"Prompt not found: {prompt_path}"
 
         # Load prompt
-        prompt = prompt_path.read_text()
+        prompt = prompt_path.read_text(encoding="utf-8")
         debug_detailed(
             "roadmap_executor", "Loaded prompt file", prompt_length=len(prompt)
         )

apps/backend/runners/roadmap/graph_integration.py

@@ -81,7 +81,7 @@ class GraphHintsProvider:
 
     def _create_disabled_hints_file(self):
         """Create a hints file indicating Graphiti is disabled."""
-        with open(self.hints_file, "w") as f:
+        with open(self.hints_file, "w", encoding="utf-8") as f:
             json.dump(
                 {
                     "enabled": False,
@@ -95,7 +95,7 @@ class GraphHintsProvider:
 
     def _save_hints(self, hints: list):
         """Save retrieved hints to file."""
-        with open(self.hints_file, "w") as f:
+        with open(self.hints_file, "w", encoding="utf-8") as f:
             json.dump(
                 {
                     "enabled": True,
@@ -109,7 +109,7 @@ class GraphHintsProvider:
 
     def _save_error_hints(self, error: str):
         """Save error information to hints file."""
-        with open(self.hints_file, "w") as f:
+        with open(self.hints_file, "w", encoding="utf-8") as f:
             json.dump(
                 {
                     "enabled": True,