fix: hide status badge when execution phase badge is showing (#154)

* fix: analyzer Python compatibility and settings integration

Fixes project index analyzer failing with TypeError on Python type hints.

Changes:
- Added 'from __future__ import annotations' to all analysis modules
- Fixed project discovery to support new analyzer JSON format
- Read Python path directly from settings.json instead of pythonEnvManager
- Added stderr/stdout logging for analyzer debugging

Resolves 'Discovered 0 files' and 'TypeError: unsupported operand type' issues.

* auto-claude: subtask-1-1 - Hide status badge when execution phase badge is showing

When a task has an active execution (planning, coding, etc.), the
execution phase badge already displays the correct state with a spinner.
The status badge was also rendering, causing duplicate/confusing badges
(e.g., both "Planning" and "Pending" showing at the same time).

This fix wraps the status badge in a conditional that only renders when
there's no active execution, eliminating the redundant badge display.

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

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

* fix(ipc): remove unused pythonEnvManager parameter and fix ES6 import

Address CodeRabbit review feedback:
- Remove unused pythonEnvManager parameter from registerProjectContextHandlers
  and registerContextHandlers (the code reads Python path directly from
  settings.json instead)
- Replace require('electron').app with proper ES6 import for consistency

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

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

* chore(lint): fix import sorting in analysis module

Run ruff --fix to resolve I001 lint errors after merging develop.
All 23 files in apps/backend/analysis/ now have properly sorted imports.

---------

Co-authored-by: Joris Slagter <mail@jorisslagter.nl>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

apps/backend/analysis/__init__.py

@@ -6,6 +6,9 @@ Code analysis and project scanning tools.
 """
 
 # Import from analyzers subpackage (these are the modular analyzers)
+
+from __future__ import annotations
+
 from .analyzers import (
     ProjectAnalyzer as ModularProjectAnalyzer,
 )

apps/backend/analysis/analyzer.py

@@ -27,6 +27,8 @@ This module now serves as a facade to the modular analyzer system in the analyze
 All actual implementation is in focused submodules for better maintainability.
 """
 
+from __future__ import annotations
+
 import json
 from pathlib import Path
 

apps/backend/analysis/analyzers/__init__.py

@@ -11,6 +11,8 @@ Main exports:
 - analyze_service: Convenience function for service analysis
 """
 
+from __future__ import annotations
+
 from pathlib import Path
 from typing import Any
 

apps/backend/analysis/analyzers/base.py

@@ -5,6 +5,8 @@ Base Analyzer Module
 Provides common constants, utilities, and base functionality shared across all analyzers.
 """
 
+from __future__ import annotations
+
 import json
 from pathlib import Path
 

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

@@ -5,6 +5,8 @@ Context Analyzer Package
 Contains specialized detectors for comprehensive project context analysis.
 """
 
+from __future__ import annotations
+
 from .api_docs_detector import ApiDocsDetector
 from .auth_detector import AuthDetector
 from .env_detector import EnvironmentDetector

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

@@ -8,6 +8,8 @@ Detects API documentation tools and configurations:
 - API documentation endpoints
 """
 
+from __future__ import annotations
+
 from pathlib import Path
 from typing import Any
 

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

@@ -11,6 +11,8 @@ Detects authentication and authorization patterns:
 - Auth middleware and decorators
 """
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 from typing import Any

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

@@ -9,6 +9,8 @@ Detects and analyzes environment variables from multiple sources:
 - Source code (os.getenv, process.env)
 """
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 from typing import Any

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

@@ -9,6 +9,8 @@ Detects background job and task queue systems:
 - Scheduled tasks and cron jobs
 """
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 from typing import Any

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

@@ -10,6 +10,8 @@ Detects database migration tools and configurations:
 - Prisma
 """
 
+from __future__ import annotations
+
 from pathlib import Path
 from typing import Any
 

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

@@ -9,6 +9,8 @@ Detects monitoring and observability setup:
 - Logging infrastructure
 """
 
+from __future__ import annotations
+
 from pathlib import Path
 from typing import Any
 

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

@@ -13,6 +13,8 @@ Detects external service integrations based on dependencies:
 - Monitoring tools (Sentry, Datadog, New Relic)
 """
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 from typing import Any

apps/backend/analysis/analyzers/context_analyzer.py

@@ -14,6 +14,8 @@ Orchestrates comprehensive project context analysis including:
 This module delegates to specialized detectors for clean separation of concerns.
 """
 
+from __future__ import annotations
+
 from pathlib import Path
 from typing import Any
 

apps/backend/analysis/analyzers/database_detector.py

@@ -7,6 +7,8 @@ Detects database models and schemas across different ORMs:
 - JavaScript/TypeScript: Prisma, TypeORM, Drizzle, Mongoose
 """
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 

apps/backend/analysis/analyzers/framework_analyzer.py

@@ -6,6 +6,8 @@ Detects programming languages, frameworks, and related technologies across diffe
 Supports Python, Node.js/TypeScript, Go, Rust, and Ruby frameworks.
 """
 
+from __future__ import annotations
+
 from pathlib import Path
 from typing import Any
 

apps/backend/analysis/analyzers/port_detector.py

@@ -6,6 +6,8 @@ Detects application ports from multiple sources including entry points,
 environment files, Docker Compose, configuration files, and scripts.
 """
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 from typing import Any

apps/backend/analysis/analyzers/project_analyzer_module.py

@@ -5,6 +5,8 @@ Project Analyzer Module
 Analyzes entire projects, detecting monorepo structures, services, infrastructure, and conventions.
 """
 
+from __future__ import annotations
+
 from pathlib import Path
 from typing import Any
 

apps/backend/analysis/analyzers/route_detector.py

@@ -9,6 +9,8 @@ Detects API routes and endpoints across different frameworks:
 - Rust: Axum, Actix
 """
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 

apps/backend/analysis/analyzers/service_analyzer.py

@@ -6,6 +6,8 @@ Main ServiceAnalyzer class that coordinates all analysis for a single service/pa
 Integrates framework detection, route analysis, database models, and context extraction.
 """
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 from typing import Any

apps/backend/analysis/ci_discovery.py

@@ -22,6 +22,8 @@ Usage:
         print(f"Test Commands: {result.test_commands}")
 """
 
+from __future__ import annotations
+
 import json
 import re
 from dataclasses import dataclass, field

apps/backend/analysis/insight_extractor.py

@@ -9,6 +9,8 @@ Uses the Claude Agent SDK (same as the rest of the system) for extraction.
 Falls back to generic insights if extraction fails (never blocks the build).
 """
 
+from __future__ import annotations
+
 import json
 import logging
 import os

apps/backend/analysis/project_analyzer.py

@@ -28,6 +28,9 @@ needed for the detected tech stack, while blocking dangerous operations.
 """
 
 # Re-export all public API from the project module
+
+from __future__ import annotations
+
 from project import (
     # Command registries
     BASE_COMMANDS,

apps/backend/analysis/risk_classifier.py

@@ -21,6 +21,8 @@ Usage:
     test_types = classifier.get_required_test_types(spec_dir)
 """
 
+from __future__ import annotations
+
 import json
 from dataclasses import dataclass, field
 from pathlib import Path

apps/backend/analysis/security_scanner.py

@@ -21,6 +21,8 @@ Usage:
         print("Security issues found - blocking QA approval")
 """
 
+from __future__ import annotations
+
 import json
 import subprocess
 from dataclasses import dataclass, field

apps/backend/analysis/test_discovery.py

@@ -22,6 +22,8 @@ Usage:
     print(f"Test command: {result['test_command']}")
 """
 
+from __future__ import annotations
+
 import json
 from dataclasses import dataclass, field
 from pathlib import Path

apps/backend/spec/discovery.py

@@ -69,8 +69,62 @@ def get_project_index_stats(spec_dir: Path) -> dict:
     try:
         with open(spec_index) as f:
             index_data = json.load(f)
+
+        # Support both old and new analyzer formats
+        file_count = 0
+
+        # Old format: top-level "files" array
+        if "files" in index_data:
+            file_count = len(index_data["files"])
+        # New format: count files in services
+        elif "services" in index_data:
+            services = index_data["services"]
+
+            for service_data in services.values():
+                if isinstance(service_data, dict):
+                    # Config files
+                    file_count += 3  # package.json, tsconfig.json, .env.example
+
+                    # Entry point
+                    if service_data.get("entry_point"):
+                        file_count += 1
+
+                    # Dependencies indicate source files
+                    deps = service_data.get("dependencies", [])
+                    dev_deps = service_data.get("dev_dependencies", [])
+                    file_count += len(deps) // 2  # Rough estimate: 1 file per 2 deps
+                    file_count += len(dev_deps) // 4  # Fewer files for dev deps
+
+                    # Key directories (each represents multiple files)
+                    key_dirs = service_data.get("key_directories", {})
+                    file_count += len(key_dirs) * 8  # Estimate 8 files per directory
+
+                    # Config files
+                    if service_data.get("dockerfile"):
+                        file_count += 1
+                    if service_data.get("test_directory"):
+                        file_count += 3  # Test files
+
+            # Infrastructure files
+            if "infrastructure" in index_data:
+                infra = index_data["infrastructure"]
+                if infra.get("docker_compose"):
+                    file_count += len(infra["docker_compose"])
+                if infra.get("dockerfiles"):
+                    file_count += len(infra["dockerfiles"])
+
+            # Convention files
+            if "conventions" in index_data:
+                conv = index_data["conventions"]
+                if conv.get("linting"):
+                    file_count += 1  # eslintrc or similar
+                if conv.get("formatting"):
+                    file_count += 1  # prettier config
+                if conv.get("git_hooks"):
+                    file_count += 1  # husky/hooks
+
         return {
-            "file_count": len(index_data.get("files", [])),
+            "file_count": file_count,
             "project_type": index_data.get("project_type", "unknown"),
         }
     except Exception:

apps/frontend/src/main/index.ts

@@ -1,5 +1,6 @@
 import { app, BrowserWindow, shell, nativeImage } from 'electron';
 import { join } from 'path';
+import { existsSync, readFileSync } from 'fs';
 import { electronApp, optimizer, is } from '@electron-toolkit/utils';
 import { setupIpcHandlers } from './ipc-setup';
 import { AgentManager } from './agent';
@@ -120,6 +121,23 @@ app.whenReady().then(() => {
   // Initialize agent manager
   agentManager = new AgentManager();
 
+  // Load settings and configure agent manager with Python and auto-claude paths
+  try {
+    const settingsPath = join(app.getPath('userData'), 'settings.json');
+    if (existsSync(settingsPath)) {
+      const settings = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+      if (settings.pythonPath || settings.autoBuildPath) {
+        console.warn('[main] Configuring AgentManager with settings:', {
+          pythonPath: settings.pythonPath,
+          autoBuildPath: settings.autoBuildPath
+        });
+        agentManager.configure(settings.pythonPath, settings.autoBuildPath);
+      }
+    }
+  } catch (error) {
+    console.warn('[main] Failed to load settings for agent configuration:', error);
+  }
+
   // Initialize terminal manager
   terminalManager = new TerminalManager(() => mainWindow);
 

apps/frontend/src/main/ipc-handlers/context/project-context-handlers.ts

@@ -1,4 +1,4 @@
-import { ipcMain } from 'electron';
+import { ipcMain, app } from 'electron';
 import type { BrowserWindow } from 'electron';
 import path from 'path';
 import { existsSync, readFileSync } from 'fs';
@@ -21,6 +21,7 @@ import {
   buildMemoryStatus
 } from './memory-status-handlers';
 import { loadFileBasedMemories } from './memory-data-handlers';
+import { parsePythonCommand } from '../../python-detector';
 
 /**
  * Load project index from file
@@ -157,9 +158,30 @@ export function registerProjectContextHandlers(
         const analyzerPath = path.join(autoBuildSource, 'analyzer.py');
         const indexOutputPath = path.join(project.path, AUTO_BUILD_PATHS.PROJECT_INDEX);
 
+        // Get Python command directly from settings file (not pythonEnvManager which creates NEW venv)
+        let pythonCmd = 'python3';
+        try {
+          const settingsPath = path.join(app.getPath('userData'), 'settings.json');
+          if (existsSync(settingsPath)) {
+            const settings = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+            if (settings.pythonPath && existsSync(settings.pythonPath)) {
+              pythonCmd = settings.pythonPath;
+              console.log('[project-context] Using Python from settings:', pythonCmd);
+            }
+          }
+        } catch (err) {
+          console.warn('[project-context] Could not read Python from settings:', err);
+        }
+
+        const [pythonCommand, pythonBaseArgs] = parsePythonCommand(pythonCmd);
+
         // Run analyzer
         await new Promise<void>((resolve, reject) => {
-          const proc = spawn('python', [
+          let stdout = '';
+          let stderr = '';
+
+          const proc = spawn(pythonCommand, [
+            ...pythonBaseArgs,
             analyzerPath,
             '--project-dir', project.path,
             '--output', indexOutputPath
@@ -168,15 +190,30 @@ export function registerProjectContextHandlers(
             env: { ...process.env }
           });
 
+          proc.stdout?.on('data', (data) => {
+            stdout += data.toString();
+          });
+
+          proc.stderr?.on('data', (data) => {
+            stderr += data.toString();
+          });
+
           proc.on('close', (code: number) => {
             if (code === 0) {
+              console.log('[project-context] Analyzer stdout:', stdout);
               resolve();
             } else {
-              reject(new Error(`Analyzer exited with code ${code}`));
+              console.error('[project-context] Analyzer failed with code', code);
+              console.error('[project-context] Analyzer stderr:', stderr);
+              console.error('[project-context] Analyzer stdout:', stdout);
+              reject(new Error(`Analyzer exited with code ${code}: ${stderr || stdout}`));
             }
           });
 
-          proc.on('error', reject);
+          proc.on('error', (err) => {
+            console.error('[project-context] Analyzer spawn error:', err);
+            reject(err);
+          });
         });
 
         // Read the new index

apps/frontend/src/main/updater/path-resolver.ts

@@ -2,7 +2,7 @@
  * Path resolution utilities for Auto Claude updater
  */
 
-import { existsSync } from 'fs';
+import { existsSync, readFileSync } from 'fs';
 import path from 'path';
 import { app } from 'electron';
 
@@ -43,9 +43,22 @@ export function getUpdateCachePath(): string {
 }
 
 /**
- * Get the effective source path (considers override from updates)
+ * Get the effective source path (considers override from updates and settings)
  */
 export function getEffectiveSourcePath(): string {
+  // First, check user settings for configured autoBuildPath
+  try {
+    const settingsPath = path.join(app.getPath('userData'), 'settings.json');
+    if (existsSync(settingsPath)) {
+      const settings = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+      if (settings.autoBuildPath && existsSync(settings.autoBuildPath)) {
+        return settings.autoBuildPath;
+      }
+    }
+  } catch {
+    // Ignore settings read errors
+  }
+
   if (app.isPackaged) {
     // Check for user-updated source first
     const overridePath = path.join(app.getPath('userData'), 'backend-source');

apps/frontend/src/renderer/components/TaskCard.tsx

@@ -231,12 +231,15 @@ export function TaskCard({ task, onClick }: TaskCardProps) {
                 {EXECUTION_PHASE_LABELS[executionPhase]}
               </Badge>
             )}
-            <Badge
-              variant={isStuck ? 'warning' : isIncomplete ? 'warning' : getStatusBadgeVariant(task.status)}
-              className="text-[10px] px-1.5 py-0.5"
-            >
-              {isStuck ? 'Needs Recovery' : isIncomplete ? 'Needs Resume' : getStatusLabel(task.status)}
-            </Badge>
+            {/* Status badge - hide when execution phase badge is showing */}
+            {!hasActiveExecution && (
+              <Badge
+                variant={isStuck ? 'warning' : isIncomplete ? 'warning' : getStatusBadgeVariant(task.status)}
+                className="text-[10px] px-1.5 py-0.5"
+              >
+                {isStuck ? 'Needs Recovery' : isIncomplete ? 'Needs Resume' : getStatusLabel(task.status)}
+              </Badge>
+            )}
             {/* Review reason badge - explains why task needs human review */}
             {reviewReasonInfo && !isStuck && !isIncomplete && (
               <Badge