feat: unify Claude API key and profile system with flexible key sourcing

- Add ApiKeySource type ('inline' | 'env' | 'credentials') to ClaudeApiProfile
- Allow profiles to source API keys from credentials.json or environment variables
- Add provider templates: OpenRouter, MiniMax, MiniMax (China)
- Auto-migrate existing users with Anthropic key to "Direct Anthropic" profile
- Update all API call sites to pass credentials for key resolution
- Add API key source selector to profile creation UI
- Increment settings version to 5 for migration support

This allows users to:
- Share a single API key across multiple profile configurations
- Use environment variables for CI/CD deployments
- Easily switch between providers without re-entering keys

.github/actions/setup-project/action.yml

@@ -41,7 +41,8 @@ runs:
       # Use npm install instead of npm ci to correctly resolve platform-specific
       # optional dependencies (e.g., @tailwindcss/oxide, lightningcss binaries)
       # Skip scripts to avoid electron-builder install-app-deps which uses too much memory
-      run: npm install --ignore-scripts
+      # Use --force to allow platform-specific dev dependencies like dmg-license on non-darwin platforms
+      run: npm install --ignore-scripts --force
 
     - name: Install Linux native bindings
       shell: bash

.github/workflows/format-check.yml

@@ -25,7 +25,7 @@ jobs:
           cache-dependency-path: package-lock.json
 
       - name: Install dependencies
-        run: npm install --ignore-scripts
+        run: npm install --ignore-scripts --force
 
       - name: Check formatting
         run: npm run format:check

.github/workflows/release.yml

@@ -35,6 +35,11 @@ jobs:
         with:
           check-lockfile: 'true'
 
+      - name: Install RPM build tools (Linux)
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash
+        run: sudo apt-get update && sudo apt-get install -y rpm
+
       - name: Build Electron app (macOS)
         if: matrix.os == 'macos-latest'
         shell: bash
@@ -73,7 +78,7 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: linux-builds
-          path: apps/ui/release/*.{AppImage,deb}
+          path: apps/ui/release/*.{AppImage,deb,rpm}
           retention-days: 30
 
   upload:
@@ -104,8 +109,8 @@ jobs:
         uses: softprops/action-gh-release@v2
         with:
           files: |
-            artifacts/macos-builds/*
-            artifacts/windows-builds/*
-            artifacts/linux-builds/*
+            artifacts/macos-builds/*.{dmg,zip,blockmap}
+            artifacts/windows-builds/*.{exe,blockmap}
+            artifacts/linux-builds/*.{AppImage,deb,rpm,blockmap}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

CLAUDE.md

@@ -166,7 +166,11 @@ Use `resolveModelString()` from `@automaker/model-resolver` to convert model ali
 ## Environment Variables
 
 - `ANTHROPIC_API_KEY` - Anthropic API key (or use Claude Code CLI auth)
+- `HOST` - Host to bind server to (default: 0.0.0.0)
+- `HOSTNAME` - Hostname for user-facing URLs (default: localhost)
 - `PORT` - Server port (default: 3008)
 - `DATA_DIR` - Data storage directory (default: ./data)
 - `ALLOWED_ROOT_DIRECTORY` - Restrict file operations to specific directory
 - `AUTOMAKER_MOCK_AGENT=true` - Enable mock agent mode for CI testing
+- `AUTOMAKER_AUTO_LOGIN=true` - Skip login prompt in development (disabled when NODE_ENV=production)
+- `VITE_HOSTNAME` - Hostname for frontend API URLs (default: localhost)

README.md

@@ -28,6 +28,7 @@
   - [Quick Start](#quick-start)
 - [How to Run](#how-to-run)
   - [Development Mode](#development-mode)
+  - [Interactive TUI Launcher](#interactive-tui-launcher-recommended-for-new-users)
   - [Building for Production](#building-for-production)
   - [Testing](#testing)
   - [Linting](#linting)
@@ -101,11 +102,9 @@ In the Discord, you can:
 
 ### Prerequisites
 
-- **Node.js 18+** (tested with Node.js 22)
+- **Node.js 22+** (required: >=22.0.0 <23.0.0)
 - **npm** (comes with Node.js)
-- **Authentication** (choose one):
-  - **[Claude Code CLI](https://code.claude.com/docs/en/overview)** (recommended) - Install and authenticate, credentials used automatically
-  - **Anthropic API Key** - Direct API key for Claude Agent SDK ([get one here](https://console.anthropic.com/))
+- **[Claude Code CLI](https://code.claude.com/docs/en/overview)** - Install and authenticate with your Anthropic subscription. Automaker integrates with your authenticated Claude Code CLI to access Claude models.
 
 ### Quick Start
 
@@ -117,30 +116,14 @@ cd automaker
 # 2. Install dependencies
 npm install
 
-# 3. Build shared packages (can be skipped - npm run dev does it automatically)
-npm run build:packages
-
-# 4. Start Automaker
+# 3. Start Automaker
 npm run dev
 # Choose between:
 #   1. Web Application (browser at localhost:3007)
 #   2. Desktop Application (Electron - recommended)
 ```
 
-**Authentication Setup:** On first run, Automaker will automatically show a setup wizard where you can configure authentication. You can choose to:
-
-- Use **Claude Code CLI** (recommended) - Automaker will detect your CLI credentials automatically
-- Enter an **API key** directly in the wizard
-
-If you prefer to set up authentication before running (e.g., for headless deployments or CI/CD), you can set it manually:
-
-```bash
-# Option A: Environment variable
-export ANTHROPIC_API_KEY="sk-ant-..."
-
-# Option B: Create .env file in project root
-echo "ANTHROPIC_API_KEY=sk-ant-..." > .env
-```
+**Authentication:** Automaker integrates with your authenticated Claude Code CLI. Make sure you have [installed and authenticated](https://code.claude.com/docs/en/quickstart) the Claude Code CLI before running Automaker. Your CLI credentials will be detected automatically.
 
 **For Development:** `npm run dev` starts the development server with Vite live reload and hot module replacement for fast refresh and instant updates as you make changes.
 
@@ -179,6 +162,40 @@ npm run dev:electron:wsl:gpu
 npm run dev:web
 ```
 
+### Interactive TUI Launcher (Recommended for New Users)
+
+For a user-friendly interactive menu, use the built-in TUI launcher script:
+
+```bash
+# Show interactive menu with all launch options
+./start-automaker.sh
+
+# Or launch directly without menu
+./start-automaker.sh web          # Web browser
+./start-automaker.sh electron     # Desktop app
+./start-automaker.sh electron-debug  # Desktop + DevTools
+
+# Additional options
+./start-automaker.sh --help       # Show all available options
+./start-automaker.sh --version    # Show version information
+./start-automaker.sh --check-deps # Verify project dependencies
+./start-automaker.sh --no-colors  # Disable colored output
+./start-automaker.sh --no-history # Don't remember last choice
+```
+
+**Features:**
+
+- 🎨 Beautiful terminal UI with gradient colors and ASCII art
+- ⌨️ Interactive menu (press 1-3 to select, Q to exit)
+- 💾 Remembers your last choice
+- ✅ Pre-flight checks (validates Node.js, npm, dependencies)
+- 📏 Responsive layout (adapts to terminal size)
+- ⏱️ 30-second timeout for hands-free selection
+- 🌐 Cross-shell compatible (bash/zsh)
+
+**History File:**
+Your last selected mode is saved in `~/.automaker_launcher_history` for quick re-runs.
+
 ### Building for Production
 
 #### Web Application
@@ -197,11 +214,30 @@ npm run build:electron
 # Platform-specific builds
 npm run build:electron:mac     # macOS (DMG + ZIP, x64 + arm64)
 npm run build:electron:win     # Windows (NSIS installer, x64)
-npm run build:electron:linux   # Linux (AppImage + DEB, x64)
+npm run build:electron:linux   # Linux (AppImage + DEB + RPM, x64)
 
 # Output directory: apps/ui/release/
 ```
 
+**Linux Distribution Packages:**
+
+- **AppImage**: Universal format, works on any Linux distribution
+- **DEB**: Ubuntu, Debian, Linux Mint, Pop!\_OS
+- **RPM**: Fedora, RHEL, Rocky Linux, AlmaLinux, openSUSE
+
+**Installing on Fedora/RHEL:**
+
+```bash
+# Download the RPM package
+wget https://github.com/AutoMaker-Org/automaker/releases/latest/download/Automaker-<version>-x86_64.rpm
+
+# Install with dnf (Fedora)
+sudo dnf install ./Automaker-<version>-x86_64.rpm
+
+# Or with yum (RHEL/CentOS)
+sudo yum localinstall ./Automaker-<version>-x86_64.rpm
+```
+
 #### Docker Deployment
 
 Docker provides the most secure way to run Automaker by isolating it from your host filesystem.
@@ -220,16 +256,9 @@ docker-compose logs -f
 docker-compose down
 ```
 
-##### Configuration
+##### Authentication
 
-Create a `.env` file in the project root if using API key authentication:
-
-```bash
-# Optional: Anthropic API key (not needed if using Claude CLI authentication)
-ANTHROPIC_API_KEY=sk-ant-...
-```
-
-**Note:** Most users authenticate via Claude CLI instead of API keys. See [Claude CLI Authentication](#claude-cli-authentication-optional) below.
+Automaker integrates with your authenticated Claude Code CLI. To use CLI authentication in Docker, mount your Claude CLI config directory (see [Claude CLI Authentication](#claude-cli-authentication) below).
 
 ##### Working with Projects (Host Directory Access)
 
@@ -243,9 +272,9 @@ services:
       - /path/to/your/project:/projects/your-project
 ```
 
-##### Claude CLI Authentication (Optional)
+##### Claude CLI Authentication
 
-To use Claude Code CLI authentication instead of an API key, mount your Claude CLI config directory:
+Mount your Claude CLI config directory to use your authenticated CLI credentials:
 
 ```yaml
 services:
@@ -343,10 +372,6 @@ npm run lint
 
 ### Environment Configuration
 
-#### Authentication (if not using Claude Code CLI)
-
-- `ANTHROPIC_API_KEY` - Your Anthropic API key for Claude Agent SDK (not needed if using Claude Code CLI)
-
 #### Optional - Server
 
 - `PORT` - Server port (default: 3008)
@@ -357,49 +382,23 @@ npm run lint
 
 - `AUTOMAKER_API_KEY` - Optional API authentication for the server
 - `ALLOWED_ROOT_DIRECTORY` - Restrict file operations to specific directory
-- `CORS_ORIGIN` - CORS policy (default: \*)
+- `CORS_ORIGIN` - CORS allowed origins (comma-separated list; defaults to localhost only)
 
 #### Optional - Development
 
 - `VITE_SKIP_ELECTRON` - Skip Electron in dev mode
 - `OPEN_DEVTOOLS` - Auto-open DevTools in Electron
+- `AUTOMAKER_SKIP_SANDBOX_WARNING` - Skip sandbox warning dialog (useful for dev/CI)
+- `AUTOMAKER_AUTO_LOGIN=true` - Skip login prompt in development (ignored when NODE_ENV=production)
 
 ### Authentication Setup
 
-#### Option 1: Claude Code CLI (Recommended)
+Automaker integrates with your authenticated Claude Code CLI and uses your Anthropic subscription.
 
 Install and authenticate the Claude Code CLI following the [official quickstart guide](https://code.claude.com/docs/en/quickstart).
 
 Once authenticated, Automaker will automatically detect and use your CLI credentials. No additional configuration needed!
 
-#### Option 2: Direct API Key
-
-If you prefer not to use the CLI, you can provide an Anthropic API key directly using one of these methods:
-
-##### 2a. Shell Configuration
-
-Add to your `~/.bashrc` or `~/.zshrc`:
-
-```bash
-export ANTHROPIC_API_KEY="sk-ant-..."
-```
-
-Then restart your terminal or run `source ~/.bashrc` (or `source ~/.zshrc`).
-
-##### 2b. .env File
-
-Create a `.env` file in the project root (gitignored):
-
-```bash
-ANTHROPIC_API_KEY=sk-ant-...
-PORT=3008
-DATA_DIR=./data
-```
-
-##### 2c. In-App Storage
-
-The application can store your API key securely in the settings UI. The key is persisted in the `DATA_DIR` directory.
-
 ## Features
 
 ### Core Workflow
@@ -508,20 +507,24 @@ Automaker provides several specialized views accessible via the sidebar or keybo
 | **Agent**          | `A`      | Interactive chat sessions with AI agents for exploratory work and questions                      |
 | **Spec**           | `D`      | Project specification editor with AI-powered generation and feature suggestions                  |
 | **Context**        | `C`      | Manage context files (markdown, images) that AI agents automatically reference                   |
-| **Profiles**       | `M`      | Create and manage AI agent profiles with custom prompts and configurations                       |
 | **Settings**       | `S`      | Configure themes, shortcuts, defaults, authentication, and more                                  |
 | **Terminal**       | `T`      | Integrated terminal with tabs, splits, and persistent sessions                                   |
-| **GitHub Issues**  | -        | Import and validate GitHub issues, convert to tasks                                              |
+| **Graph**          | `H`      | Visualize feature dependencies with interactive graph visualization                              |
+| **Ideation**       | `I`      | Brainstorm and generate ideas with AI assistance                                                 |
+| **Memory**         | `Y`      | View and manage agent memory and conversation history                                            |
+| **GitHub Issues**  | `G`      | Import and validate GitHub issues, convert to tasks                                              |
+| **GitHub PRs**     | `R`      | View and manage GitHub pull requests                                                             |
 | **Running Agents** | -        | View all active agents across projects with status and progress                                  |
 
 ### Keyboard Navigation
 
 All shortcuts are customizable in Settings. Default shortcuts:
 
-- **Navigation:** `K` (Board), `A` (Agent), `D` (Spec), `C` (Context), `S` (Settings), `M` (Profiles), `T` (Terminal)
+- **Navigation:** `K` (Board), `A` (Agent), `D` (Spec), `C` (Context), `S` (Settings), `T` (Terminal), `H` (Graph), `I` (Ideation), `Y` (Memory), `G` (GitHub Issues), `R` (GitHub PRs)
 - **UI:** `` ` `` (Toggle sidebar)
-- **Actions:** `N` (New item in current view), `G` (Start next features), `O` (Open project), `P` (Project picker)
+- **Actions:** `N` (New item in current view), `O` (Open project), `P` (Project picker)
 - **Projects:** `Q`/`E` (Cycle previous/next project)
+- **Terminal:** `Alt+D` (Split right), `Alt+S` (Split down), `Alt+W` (Close), `Alt+T` (New tab)
 
 ## Architecture
 
@@ -586,10 +589,16 @@ Stored in `{projectPath}/.automaker/`:
 │       ├── agent-output.md # AI agent output log
 │       └── images/        # Attached images
 ├── context/               # Context files for AI agents
+├── worktrees/             # Git worktree metadata
+├── validations/           # GitHub issue validation results
+├── ideation/              # Brainstorming and analysis data
+│   └── analysis.json      # Project structure analysis
+├── board/                 # Board-related data
+├── images/                # Project-level images
 ├── settings.json          # Project-specific settings
-├── spec.md               # Project specification
-├── analysis.json         # Project structure analysis
-└── feature-suggestions.json # AI-generated suggestions
+├── app_spec.txt           # Project specification (XML format)
+├── active-branches.json   # Active git branches tracking
+└── execution-state.json   # Auto-mode execution state
 ```
 
 #### Global Data
@@ -627,7 +636,6 @@ data/
 
 - [Contributing Guide](./CONTRIBUTING.md) - How to contribute to Automaker
 - [Project Documentation](./docs/) - Architecture guides, patterns, and developer docs
-- [Docker Isolation Guide](./docs/docker-isolation.md) - Security-focused Docker deployment
 - [Shared Packages Guide](./docs/llm-shared-packages.md) - Using monorepo packages
 
 ### Community

apps/server/.env.example

@@ -44,6 +44,11 @@ CORS_ORIGIN=http://localhost:3007
 # OPTIONAL - Server
 # ============================================
 
+# Host to bind the server to (default: 0.0.0.0)
+# Use 0.0.0.0 to listen on all interfaces (recommended for Docker/remote access)
+# Use 127.0.0.1 or localhost to restrict to local connections only
+HOST=0.0.0.0
+
 # Port to run the server on
 PORT=3008
 
@@ -63,6 +68,14 @@ TERMINAL_PASSWORD=
 
 ENABLE_REQUEST_LOGGING=false
 
+# ============================================
+# OPTIONAL - UI Behavior
+# ============================================
+
+# Skip the sandbox warning dialog on startup (default: false)
+# Set to "true" to disable the warning entirely (useful for dev/CI environments)
+AUTOMAKER_SKIP_SANDBOX_WARNING=false
+
 # ============================================
 # OPTIONAL - Debugging
 # ============================================

apps/server/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@automaker/server",
-  "version": "0.11.0",
+  "version": "0.12.0",
   "description": "Backend server for Automaker - provides API for both web and Electron modes",
   "author": "AutoMaker Team",
   "license": "SEE LICENSE IN LICENSE",

apps/server/src/index.ts

@@ -17,9 +17,19 @@ import dotenv from 'dotenv';
 
 import { createEventEmitter, type EventEmitter } from './lib/events.js';
 import { initAllowedPaths } from '@automaker/platform';
-import { createLogger } from '@automaker/utils';
+import { createLogger, setLogLevel, LogLevel } from '@automaker/utils';
 
 const logger = createLogger('Server');
+
+/**
+ * Map server log level string to LogLevel enum
+ */
+const LOG_LEVEL_MAP: Record<string, LogLevel> = {
+  error: LogLevel.ERROR,
+  warn: LogLevel.WARN,
+  info: LogLevel.INFO,
+  debug: LogLevel.DEBUG,
+};
 import { authMiddleware, validateWsConnectionToken, checkRawAuthentication } from './lib/auth.js';
 import { requireJsonContentType } from './middleware/require-json-content-type.js';
 import { createAuthRoutes } from './routes/auth/index.js';
@@ -68,32 +78,72 @@ import { pipelineService } from './services/pipeline-service.js';
 import { createIdeationRoutes } from './routes/ideation/index.js';
 import { IdeationService } from './services/ideation-service.js';
 import { getDevServerService } from './services/dev-server-service.js';
+import { eventHookService } from './services/event-hook-service.js';
+import { createNotificationsRoutes } from './routes/notifications/index.js';
+import { getNotificationService } from './services/notification-service.js';
+import { createEventHistoryRoutes } from './routes/event-history/index.js';
+import { getEventHistoryService } from './services/event-history-service.js';
 
 // Load environment variables
 dotenv.config();
 
 const PORT = parseInt(process.env.PORT || '3008', 10);
+const HOST = process.env.HOST || '0.0.0.0';
+const HOSTNAME = process.env.HOSTNAME || 'localhost';
 const DATA_DIR = process.env.DATA_DIR || './data';
-const ENABLE_REQUEST_LOGGING = process.env.ENABLE_REQUEST_LOGGING !== 'false'; // Default to true
+logger.info('[SERVER_STARTUP] process.env.DATA_DIR:', process.env.DATA_DIR);
+logger.info('[SERVER_STARTUP] Resolved DATA_DIR:', DATA_DIR);
+logger.info('[SERVER_STARTUP] process.cwd():', process.cwd());
+const ENABLE_REQUEST_LOGGING_DEFAULT = process.env.ENABLE_REQUEST_LOGGING !== 'false'; // Default to true
+
+// Runtime-configurable request logging flag (can be changed via settings)
+let requestLoggingEnabled = ENABLE_REQUEST_LOGGING_DEFAULT;
+
+/**
+ * Enable or disable HTTP request logging at runtime
+ */
+export function setRequestLoggingEnabled(enabled: boolean): void {
+  requestLoggingEnabled = enabled;
+}
+
+/**
+ * Get current request logging state
+ */
+export function isRequestLoggingEnabled(): boolean {
+  return requestLoggingEnabled;
+}
+
+// Width for log box content (excluding borders)
+const BOX_CONTENT_WIDTH = 67;
 
 // Check for required environment variables
 const hasAnthropicKey = !!process.env.ANTHROPIC_API_KEY;
 
 if (!hasAnthropicKey) {
+  const wHeader = '⚠️  WARNING: No Claude authentication configured'.padEnd(BOX_CONTENT_WIDTH);
+  const w1 = 'The Claude Agent SDK requires authentication to function.'.padEnd(BOX_CONTENT_WIDTH);
+  const w2 = 'Set your Anthropic API key:'.padEnd(BOX_CONTENT_WIDTH);
+  const w3 = '  export ANTHROPIC_API_KEY="sk-ant-..."'.padEnd(BOX_CONTENT_WIDTH);
+  const w4 = 'Or use the setup wizard in Settings to configure authentication.'.padEnd(
+    BOX_CONTENT_WIDTH
+  );
+
   logger.warn(`
-╔═══════════════════════════════════════════════════════════════════════╗
-║  ⚠️  WARNING: No Claude authentication configured                      ║
-║                                                                       ║
-║  The Claude Agent SDK requires authentication to function.            ║
-║                                                                       ║
-║  Set your Anthropic API key:                                          ║
-║    export ANTHROPIC_API_KEY="sk-ant-..."                              ║
-║                                                                       ║
-║  Or use the setup wizard in Settings to configure authentication.     ║
-╚═══════════════════════════════════════════════════════════════════════╝
+╔═════════════════════════════════════════════════════════════════════╗
+║  ${wHeader}║
+╠═════════════════════════════════════════════════════════════════════╣
+║                                                                     ║
+║  ${w1}║
+║                                                                     ║
+║  ${w2}║
+║  ${w3}║
+║                                                                     ║
+║  ${w4}║
+║                                                                     ║
+╚═════════════════════════════════════════════════════════════════════╝
 `);
 } else {
-  logger.info('✓ ANTHROPIC_API_KEY detected (API key auth)');
+  logger.info('✓ ANTHROPIC_API_KEY detected');
 }
 
 // Initialize security
@@ -103,22 +153,21 @@ initAllowedPaths();
 const app = express();
 
 // Middleware
-// Custom colored logger showing only endpoint and status code (configurable via ENABLE_REQUEST_LOGGING env var)
-if (ENABLE_REQUEST_LOGGING) {
-  morgan.token('status-colored', (_req, res) => {
-    const status = res.statusCode;
-    if (status >= 500) return `\x1b[31m${status}\x1b[0m`; // Red for server errors
-    if (status >= 400) return `\x1b[33m${status}\x1b[0m`; // Yellow for client errors
-    if (status >= 300) return `\x1b[36m${status}\x1b[0m`; // Cyan for redirects
-    return `\x1b[32m${status}\x1b[0m`; // Green for success
-  });
+// Custom colored logger showing only endpoint and status code (dynamically configurable)
+morgan.token('status-colored', (_req, res) => {
+  const status = res.statusCode;
+  if (status >= 500) return `\x1b[31m${status}\x1b[0m`; // Red for server errors
+  if (status >= 400) return `\x1b[33m${status}\x1b[0m`; // Yellow for client errors
+  if (status >= 300) return `\x1b[36m${status}\x1b[0m`; // Cyan for redirects
+  return `\x1b[32m${status}\x1b[0m`; // Green for success
+});
 
-  app.use(
-    morgan(':method :url :status-colored', {
-      skip: (req) => req.url === '/api/health', // Skip health check logs
-    })
-  );
-}
+app.use(
+  morgan(':method :url :status-colored', {
+    // Skip when request logging is disabled or for health check endpoints
+    skip: (req) => !requestLoggingEnabled || req.url === '/api/health',
+  })
+);
 // CORS configuration
 // When using credentials (cookies), origin cannot be '*'
 // We dynamically allow the requesting origin for local development
@@ -142,14 +191,25 @@ app.use(
         return;
       }
 
-      // For local development, allow localhost origins
-      if (
-        origin.startsWith('http://localhost:') ||
-        origin.startsWith('http://127.0.0.1:') ||
-        origin.startsWith('http://[::1]:')
-      ) {
-        callback(null, origin);
-        return;
+      // For local development, allow all localhost/loopback origins (any port)
+      try {
+        const url = new URL(origin);
+        const hostname = url.hostname;
+
+        if (
+          hostname === 'localhost' ||
+          hostname === '127.0.0.1' ||
+          hostname === '::1' ||
+          hostname === '0.0.0.0' ||
+          hostname.startsWith('192.168.') ||
+          hostname.startsWith('10.') ||
+          hostname.startsWith('172.')
+        ) {
+          callback(null, origin);
+          return;
+        }
+      } catch (err) {
+        // Ignore URL parsing errors
       }
 
       // Reject other origins by default for security
@@ -181,8 +241,50 @@ const ideationService = new IdeationService(events, settingsService, featureLoad
 const devServerService = getDevServerService();
 devServerService.setEventEmitter(events);
 
+// Initialize Notification Service with event emitter for real-time updates
+const notificationService = getNotificationService();
+notificationService.setEventEmitter(events);
+
+// Initialize Event History Service
+const eventHistoryService = getEventHistoryService();
+
+// Initialize Event Hook Service for custom event triggers (with history storage)
+eventHookService.initialize(events, settingsService, eventHistoryService);
+
 // Initialize services
 (async () => {
+  // Migrate settings from legacy Electron userData location if needed
+  // This handles users upgrading from versions that stored settings in ~/.config/Automaker (Linux),
+  // ~/Library/Application Support/Automaker (macOS), or %APPDATA%\Automaker (Windows)
+  // to the new shared ./data directory
+  try {
+    const migrationResult = await settingsService.migrateFromLegacyElectronPath();
+    if (migrationResult.migrated) {
+      logger.info(`Settings migrated from legacy location: ${migrationResult.legacyPath}`);
+      logger.info(`Migrated files: ${migrationResult.migratedFiles.join(', ')}`);
+    }
+    if (migrationResult.errors.length > 0) {
+      logger.warn('Migration errors:', migrationResult.errors);
+    }
+  } catch (err) {
+    logger.warn('Failed to check for legacy settings migration:', err);
+  }
+
+  // Apply logging settings from saved settings
+  try {
+    const settings = await settingsService.getGlobalSettings();
+    if (settings.serverLogLevel && LOG_LEVEL_MAP[settings.serverLogLevel] !== undefined) {
+      setLogLevel(LOG_LEVEL_MAP[settings.serverLogLevel]);
+      logger.info(`Server log level set to: ${settings.serverLogLevel}`);
+    }
+    // Apply request logging setting (default true if not set)
+    const enableRequestLog = settings.enableRequestLogging ?? true;
+    setRequestLoggingEnabled(enableRequestLog);
+    logger.info(`HTTP request logging: ${enableRequestLog ? 'enabled' : 'disabled'}`);
+  } catch (err) {
+    logger.warn('Failed to load logging settings, using defaults');
+  }
+
   await agentService.initialize();
   logger.info('Agent service initialized');
 
@@ -219,7 +321,7 @@ app.get('/api/health/detailed', createDetailedHandler());
 app.use('/api/fs', createFsRoutes(events));
 app.use('/api/agent', createAgentRoutes(agentService, events));
 app.use('/api/sessions', createSessionsRoutes(agentService));
-app.use('/api/features', createFeaturesRoutes(featureLoader));
+app.use('/api/features', createFeaturesRoutes(featureLoader, settingsService, events));
 app.use('/api/auto-mode', createAutoModeRoutes(autoModeService));
 app.use('/api/enhance-prompt', createEnhancePromptRoutes(settingsService));
 app.use('/api/worktree', createWorktreeRoutes(events, settingsService));
@@ -240,6 +342,8 @@ app.use('/api/backlog-plan', createBacklogPlanRoutes(events, settingsService));
 app.use('/api/mcp', createMCPRoutes(mcpTestService));
 app.use('/api/pipeline', createPipelineRoutes(pipelineService));
 app.use('/api/ideation', createIdeationRoutes(events, ideationService, featureLoader));
+app.use('/api/notifications', createNotificationsRoutes(notificationService));
+app.use('/api/event-history', createEventHistoryRoutes(eventHistoryService, settingsService));
 
 // Create HTTP server
 const server = createServer(app);
@@ -551,46 +655,81 @@ terminalWss.on('connection', (ws: WebSocket, req: import('http').IncomingMessage
 });
 
 // Start server with error handling for port conflicts
-const startServer = (port: number) => {
-  server.listen(port, () => {
+const startServer = (port: number, host: string) => {
+  server.listen(port, host, () => {
     const terminalStatus = isTerminalEnabled()
       ? isTerminalPasswordRequired()
         ? 'enabled (password protected)'
         : 'enabled'
       : 'disabled';
-    const portStr = port.toString().padEnd(4);
+
+    // Build URLs for display
+    const listenAddr = `${host}:${port}`;
+    const httpUrl = `http://${HOSTNAME}:${port}`;
+    const wsEventsUrl = `ws://${HOSTNAME}:${port}/api/events`;
+    const wsTerminalUrl = `ws://${HOSTNAME}:${port}/api/terminal/ws`;
+    const healthUrl = `http://${HOSTNAME}:${port}/api/health`;
+
+    const sHeader = '🚀 Automaker Backend Server'.padEnd(BOX_CONTENT_WIDTH);
+    const s1 = `Listening:    ${listenAddr}`.padEnd(BOX_CONTENT_WIDTH);
+    const s2 = `HTTP API:     ${httpUrl}`.padEnd(BOX_CONTENT_WIDTH);
+    const s3 = `WebSocket:    ${wsEventsUrl}`.padEnd(BOX_CONTENT_WIDTH);
+    const s4 = `Terminal WS:  ${wsTerminalUrl}`.padEnd(BOX_CONTENT_WIDTH);
+    const s5 = `Health:       ${healthUrl}`.padEnd(BOX_CONTENT_WIDTH);
+    const s6 = `Terminal:     ${terminalStatus}`.padEnd(BOX_CONTENT_WIDTH);
+
     logger.info(`
-╔═══════════════════════════════════════════════════════╗
-║           Automaker Backend Server                    ║
-╠═══════════════════════════════════════════════════════╣
-║  HTTP API:    http://localhost:${portStr}                 ║
-║  WebSocket:   ws://localhost:${portStr}/api/events        ║
-║  Terminal:    ws://localhost:${portStr}/api/terminal/ws   ║
-║  Health:      http://localhost:${portStr}/api/health      ║
-║  Terminal:    ${terminalStatus.padEnd(37)}║
-╚═══════════════════════════════════════════════════════╝
+╔═════════════════════════════════════════════════════════════════════╗
+║  ${sHeader}║
+╠═════════════════════════════════════════════════════════════════════╣
+║                                                                     ║
+║  ${s1}║
+║  ${s2}║
+║  ${s3}║
+║  ${s4}║
+║  ${s5}║
+║  ${s6}║
+║                                                                     ║
+╚═════════════════════════════════════════════════════════════════════╝
 `);
   });
 
   server.on('error', (error: NodeJS.ErrnoException) => {
     if (error.code === 'EADDRINUSE') {
+      const portStr = port.toString();
+      const nextPortStr = (port + 1).toString();
+      const killCmd = `lsof -ti:${portStr} | xargs kill -9`;
+      const altCmd = `PORT=${nextPortStr} npm run dev:server`;
+
+      const eHeader = `❌ ERROR: Port ${portStr} is already in use`.padEnd(BOX_CONTENT_WIDTH);
+      const e1 = 'Another process is using this port.'.padEnd(BOX_CONTENT_WIDTH);
+      const e2 = 'To fix this, try one of:'.padEnd(BOX_CONTENT_WIDTH);
+      const e3 = '1. Kill the process using the port:'.padEnd(BOX_CONTENT_WIDTH);
+      const e4 = `   ${killCmd}`.padEnd(BOX_CONTENT_WIDTH);
+      const e5 = '2. Use a different port:'.padEnd(BOX_CONTENT_WIDTH);
+      const e6 = `   ${altCmd}`.padEnd(BOX_CONTENT_WIDTH);
+      const e7 = '3. Use the init.sh script which handles this:'.padEnd(BOX_CONTENT_WIDTH);
+      const e8 = '   ./init.sh'.padEnd(BOX_CONTENT_WIDTH);
+
       logger.error(`
-╔═══════════════════════════════════════════════════════╗
-║  ❌ ERROR: Port ${port} is already in use              ║
-╠═══════════════════════════════════════════════════════╣
-║  Another process is using this port.                  ║
-║                                                       ║
-║  To fix this, try one of:                             ║
-║                                                       ║
-║  1. Kill the process using the port:                  ║
-║     lsof -ti:${port} | xargs kill -9                   ║
-║                                                       ║
-║  2. Use a different port:                             ║
-║     PORT=${port + 1} npm run dev:server                ║
-║                                                       ║
-║  3. Use the init.sh script which handles this:        ║
-║     ./init.sh                                         ║
-╚═══════════════════════════════════════════════════════╝
+╔═════════════════════════════════════════════════════════════════════╗
+║  ${eHeader}║
+╠═════════════════════════════════════════════════════════════════════╣
+║                                                                     ║
+║  ${e1}║
+║                                                                     ║
+║  ${e2}║
+║                                                                     ║
+║  ${e3}║
+║  ${e4}║
+║                                                                     ║
+║  ${e5}║
+║  ${e6}║
+║                                                                     ║
+║  ${e7}║
+║  ${e8}║
+║                                                                     ║
+╚═════════════════════════════════════════════════════════════════════╝
 `);
       process.exit(1);
     } else {
@@ -600,7 +739,7 @@ const startServer = (port: number) => {
   });
 };
 
-startServer(PORT);
+startServer(PORT, HOST);
 
 // Global error handlers to prevent crashes from uncaught errors
 process.on('unhandledRejection', (reason: unknown, _promise: Promise<unknown>) => {

apps/server/src/lib/app-spec-format.ts

@@ -11,8 +11,12 @@ export { specOutputSchema } from '@automaker/types';
 
 /**
  * Escape special XML characters
+ * Handles undefined/null values by converting them to empty strings
  */
-function escapeXml(str: string): string {
+export function escapeXml(str: string | undefined | null): string {
+  if (str == null) {
+    return '';
+  }
   return str
     .replace(/&/g, '&')
     .replace(/</g, '&lt;')

apps/server/src/lib/auth.ts

@@ -130,19 +130,47 @@ function ensureApiKey(): string {
 // API key - always generated/loaded on startup for CSRF protection
 const API_KEY = ensureApiKey();
 
+// Width for log box content (excluding borders)
+const BOX_CONTENT_WIDTH = 67;
+
 // Print API key to console for web mode users (unless suppressed for production logging)
 if (process.env.AUTOMAKER_HIDE_API_KEY !== 'true') {
+  const autoLoginEnabled = process.env.AUTOMAKER_AUTO_LOGIN === 'true';
+  const autoLoginStatus = autoLoginEnabled ? 'enabled (auto-login active)' : 'disabled';
+
+  // Build box lines with exact padding
+  const header = '🔐 API Key for Web Mode Authentication'.padEnd(BOX_CONTENT_WIDTH);
+  const line1 = "When accessing via browser, you'll be prompted to enter this key:".padEnd(
+    BOX_CONTENT_WIDTH
+  );
+  const line2 = API_KEY.padEnd(BOX_CONTENT_WIDTH);
+  const line3 = 'In Electron mode, authentication is handled automatically.'.padEnd(
+    BOX_CONTENT_WIDTH
+  );
+  const line4 = `Auto-login (AUTOMAKER_AUTO_LOGIN): ${autoLoginStatus}`.padEnd(BOX_CONTENT_WIDTH);
+  const tipHeader = '💡 Tips'.padEnd(BOX_CONTENT_WIDTH);
+  const line5 = 'Set AUTOMAKER_API_KEY env var to use a fixed key'.padEnd(BOX_CONTENT_WIDTH);
+  const line6 = 'Set AUTOMAKER_AUTO_LOGIN=true to skip the login prompt'.padEnd(BOX_CONTENT_WIDTH);
+
   logger.info(`
-╔═══════════════════════════════════════════════════════════════════════╗
-║  🔐 API Key for Web Mode Authentication                               ║
-╠═══════════════════════════════════════════════════════════════════════╣
-║                                                                       ║
-║  When accessing via browser, you'll be prompted to enter this key:    ║
-║                                                                       ║
-║    ${API_KEY}
-║                                                                       ║
-║  In Electron mode, authentication is handled automatically.          ║
-╚═══════════════════════════════════════════════════════════════════════╝
+╔═════════════════════════════════════════════════════════════════════╗
+║  ${header}║
+╠═════════════════════════════════════════════════════════════════════╣
+║                                                                     ║
+║  ${line1}║
+║                                                                     ║
+║  ${line2}║
+║                                                                     ║
+║  ${line3}║
+║                                                                     ║
+║  ${line4}║
+║                                                                     ║
+╠═════════════════════════════════════════════════════════════════════╣
+║  ${tipHeader}║
+╠═════════════════════════════════════════════════════════════════════╣
+║  ${line5}║
+║  ${line6}║
+╚═════════════════════════════════════════════════════════════════════╝
 `);
 } else {
   logger.info('API key banner hidden (AUTOMAKER_HIDE_API_KEY=true)');
@@ -318,6 +346,15 @@ function checkAuthentication(
     return { authenticated: false, errorType: 'invalid_api_key' };
   }
 
+  // Check for session token in query parameter (web mode - needed for image loads)
+  const queryToken = query.token;
+  if (queryToken) {
+    if (validateSession(queryToken)) {
+      return { authenticated: true };
+    }
+    return { authenticated: false, errorType: 'invalid_session' };
+  }
+
   // Check for session cookie (web mode)
   const sessionToken = cookies[SESSION_COOKIE_NAME];
   if (sessionToken && validateSession(sessionToken)) {
@@ -333,8 +370,9 @@ function checkAuthentication(
  * Accepts either:
  * 1. X-API-Key header (for Electron mode)
  * 2. X-Session-Token header (for web mode with explicit token)
- * 3. apiKey query parameter (fallback for cases where headers can't be set)
- * 4. Session cookie (for web mode)
+ * 3. apiKey query parameter (fallback for Electron, cases where headers can't be set)
+ * 4. token query parameter (fallback for web mode, needed for image loads via CSS/img tags)
+ * 5. Session cookie (for web mode)
  */
 export function authMiddleware(req: Request, res: Response, next: NextFunction): void {
   const result = checkAuthentication(

apps/server/src/lib/settings-helpers.ts

@@ -5,12 +5,25 @@
 import type { SettingsService } from '../services/settings-service.js';
 import type { ContextFilesResult, ContextFileInfo } from '@automaker/utils';
 import { createLogger } from '@automaker/utils';
-import type { MCPServerConfig, McpServerConfig, PromptCustomization } from '@automaker/types';
+import type {
+  MCPServerConfig,
+  McpServerConfig,
+  PromptCustomization,
+  ClaudeApiProfile,
+} from '@automaker/types';
 import {
   mergeAutoModePrompts,
   mergeAgentPrompts,
   mergeBacklogPlanPrompts,
   mergeEnhancementPrompts,
+  mergeCommitMessagePrompts,
+  mergeTitleGenerationPrompts,
+  mergeIssueValidationPrompts,
+  mergeIdeationPrompts,
+  mergeAppSpecPrompts,
+  mergeContextDescriptionPrompts,
+  mergeSuggestionsPrompts,
+  mergeTaskExecutionPrompts,
 } from '@automaker/prompts';
 
 const logger = createLogger('SettingsHelper');
@@ -218,6 +231,14 @@ export async function getPromptCustomization(
   agent: ReturnType<typeof mergeAgentPrompts>;
   backlogPlan: ReturnType<typeof mergeBacklogPlanPrompts>;
   enhancement: ReturnType<typeof mergeEnhancementPrompts>;
+  commitMessage: ReturnType<typeof mergeCommitMessagePrompts>;
+  titleGeneration: ReturnType<typeof mergeTitleGenerationPrompts>;
+  issueValidation: ReturnType<typeof mergeIssueValidationPrompts>;
+  ideation: ReturnType<typeof mergeIdeationPrompts>;
+  appSpec: ReturnType<typeof mergeAppSpecPrompts>;
+  contextDescription: ReturnType<typeof mergeContextDescriptionPrompts>;
+  suggestions: ReturnType<typeof mergeSuggestionsPrompts>;
+  taskExecution: ReturnType<typeof mergeTaskExecutionPrompts>;
 }> {
   let customization: PromptCustomization = {};
 
@@ -239,6 +260,14 @@ export async function getPromptCustomization(
     agent: mergeAgentPrompts(customization.agent),
     backlogPlan: mergeBacklogPlanPrompts(customization.backlogPlan),
     enhancement: mergeEnhancementPrompts(customization.enhancement),
+    commitMessage: mergeCommitMessagePrompts(customization.commitMessage),
+    titleGeneration: mergeTitleGenerationPrompts(customization.titleGeneration),
+    issueValidation: mergeIssueValidationPrompts(customization.issueValidation),
+    ideation: mergeIdeationPrompts(customization.ideation),
+    appSpec: mergeAppSpecPrompts(customization.appSpec),
+    contextDescription: mergeContextDescriptionPrompts(customization.contextDescription),
+    suggestions: mergeSuggestionsPrompts(customization.suggestions),
+    taskExecution: mergeTaskExecutionPrompts(customization.taskExecution),
   };
 }
 
@@ -321,3 +350,56 @@ export async function getCustomSubagents(
 
   return Object.keys(merged).length > 0 ? merged : undefined;
 }
+
+/** Result from getActiveClaudeApiProfile */
+export interface ActiveClaudeApiProfileResult {
+  /** The active profile, or undefined if using direct Anthropic API */
+  profile: ClaudeApiProfile | undefined;
+  /** Credentials for resolving 'credentials' apiKeySource */
+  credentials: import('@automaker/types').Credentials | undefined;
+}
+
+/**
+ * Get the active Claude API profile and credentials from global settings.
+ * Returns both the profile and credentials for resolving 'credentials' apiKeySource.
+ *
+ * @param settingsService - Optional settings service instance
+ * @param logPrefix - Prefix for log messages (e.g., '[AgentService]')
+ * @returns Promise resolving to object with profile and credentials
+ */
+export async function getActiveClaudeApiProfile(
+  settingsService?: SettingsService | null,
+  logPrefix = '[SettingsHelper]'
+): Promise<ActiveClaudeApiProfileResult> {
+  if (!settingsService) {
+    return { profile: undefined, credentials: undefined };
+  }
+
+  try {
+    const globalSettings = await settingsService.getGlobalSettings();
+    const credentials = await settingsService.getCredentials();
+    const profiles = globalSettings.claudeApiProfiles || [];
+    const activeProfileId = globalSettings.activeClaudeApiProfileId;
+
+    // No active profile selected - use direct Anthropic API
+    if (!activeProfileId) {
+      return { profile: undefined, credentials };
+    }
+
+    // Find the active profile by ID
+    const activeProfile = profiles.find((p) => p.id === activeProfileId);
+
+    if (activeProfile) {
+      logger.info(`${logPrefix} Using Claude API profile: ${activeProfile.name}`);
+      return { profile: activeProfile, credentials };
+    } else {
+      logger.warn(
+        `${logPrefix} Active profile ID "${activeProfileId}" not found, falling back to direct Anthropic API`
+      );
+      return { profile: undefined, credentials };
+    }
+  } catch (error) {
+    logger.error(`${logPrefix} Failed to load Claude API profile:`, error);
+    return { profile: undefined, credentials: undefined };
+  }
+}

apps/server/src/lib/worktree-metadata.ts

@@ -5,18 +5,14 @@
 
 import * as secureFs from './secure-fs.js';
 import * as path from 'path';
+import type { PRState, WorktreePRInfo } from '@automaker/types';
+
+// Re-export types for backwards compatibility
+export type { PRState, WorktreePRInfo };
 
 /** Maximum length for sanitized branch names in filesystem paths */
 const MAX_SANITIZED_BRANCH_PATH_LENGTH = 200;
 
-export interface WorktreePRInfo {
-  number: number;
-  url: string;
-  title: string;
-  state: string;
-  createdAt: string;
-}
-
 export interface WorktreeMetadata {
   branch: string;
   createdAt: string;

apps/server/src/lib/xml-extractor.ts

@@ -0,0 +1,611 @@
+/**
+ * XML Extraction Utilities
+ *
+ * Robust XML parsing utilities for extracting and updating sections
+ * from app_spec.txt XML content. Uses regex-based parsing which is
+ * sufficient for our controlled XML structure.
+ *
+ * Note: If more complex XML parsing is needed in the future, consider
+ * using a library like 'fast-xml-parser' or 'xml2js'.
+ */
+
+import { createLogger } from '@automaker/utils';
+import type { SpecOutput } from '@automaker/types';
+
+const logger = createLogger('XmlExtractor');
+
+/**
+ * Represents an implemented feature extracted from XML
+ */
+export interface ImplementedFeature {
+  name: string;
+  description: string;
+  file_locations?: string[];
+}
+
+/**
+ * Logger interface for optional custom logging
+ */
+export interface XmlExtractorLogger {
+  debug: (message: string, ...args: unknown[]) => void;
+  warn?: (message: string, ...args: unknown[]) => void;
+}
+
+/**
+ * Options for XML extraction operations
+ */
+export interface ExtractXmlOptions {
+  /** Custom logger (defaults to internal logger) */
+  logger?: XmlExtractorLogger;
+}
+
+/**
+ * Escape special XML characters
+ * Handles undefined/null values by converting them to empty strings
+ */
+export function escapeXml(str: string | undefined | null): string {
+  if (str == null) {
+    return '';
+  }
+  return str
+    .replace(/&/g, '&')
+    .replace(/</g, '&lt;')
+    .replace(/>/g, '&gt;')
+    .replace(/"/g, '&quot;')
+    .replace(/'/g, '&apos;');
+}
+
+/**
+ * Unescape XML entities back to regular characters
+ */
+export function unescapeXml(str: string): string {
+  return str
+    .replace(/&apos;/g, "'")
+    .replace(/&quot;/g, '"')
+    .replace(/&gt;/g, '>')
+    .replace(/&lt;/g, '<')
+    .replace(/&amp;/g, '&');
+}
+
+/**
+ * Extract the content of a specific XML section
+ *
+ * @param xmlContent - The full XML content
+ * @param tagName - The tag name to extract (e.g., 'implemented_features')
+ * @param options - Optional extraction options
+ * @returns The content between the tags, or null if not found
+ */
+export function extractXmlSection(
+  xmlContent: string,
+  tagName: string,
+  options: ExtractXmlOptions = {}
+): string | null {
+  const log = options.logger || logger;
+
+  const regex = new RegExp(`<${tagName}>([\\s\\S]*?)<\\/${tagName}>`, 'i');
+  const match = xmlContent.match(regex);
+
+  if (match) {
+    log.debug(`Extracted <${tagName}> section`);
+    return match[1];
+  }
+
+  log.debug(`Section <${tagName}> not found`);
+  return null;
+}
+
+/**
+ * Extract all values from repeated XML elements
+ *
+ * @param xmlContent - The XML content to search
+ * @param tagName - The tag name to extract values from
+ * @param options - Optional extraction options
+ * @returns Array of extracted values (unescaped)
+ */
+export function extractXmlElements(
+  xmlContent: string,
+  tagName: string,
+  options: ExtractXmlOptions = {}
+): string[] {
+  const log = options.logger || logger;
+  const values: string[] = [];
+
+  const regex = new RegExp(`<${tagName}>([\\s\\S]*?)<\\/${tagName}>`, 'g');
+  const matches = xmlContent.matchAll(regex);
+
+  for (const match of matches) {
+    values.push(unescapeXml(match[1].trim()));
+  }
+
+  log.debug(`Extracted ${values.length} <${tagName}> elements`);
+  return values;
+}
+
+/**
+ * Extract implemented features from app_spec.txt XML content
+ *
+ * @param specContent - The full XML content of app_spec.txt
+ * @param options - Optional extraction options
+ * @returns Array of implemented features with name, description, and optional file_locations
+ */
+export function extractImplementedFeatures(
+  specContent: string,
+  options: ExtractXmlOptions = {}
+): ImplementedFeature[] {
+  const log = options.logger || logger;
+  const features: ImplementedFeature[] = [];
+
+  // Match <implemented_features>...</implemented_features> section
+  const implementedSection = extractXmlSection(specContent, 'implemented_features', options);
+
+  if (!implementedSection) {
+    log.debug('No implemented_features section found');
+    return features;
+  }
+
+  // Extract individual feature blocks
+  const featureRegex = /<feature>([\s\S]*?)<\/feature>/g;
+  const featureMatches = implementedSection.matchAll(featureRegex);
+
+  for (const featureMatch of featureMatches) {
+    const featureContent = featureMatch[1];
+
+    // Extract name
+    const nameMatch = featureContent.match(/<name>([\s\S]*?)<\/name>/);
+    const name = nameMatch ? unescapeXml(nameMatch[1].trim()) : '';
+
+    // Extract description
+    const descMatch = featureContent.match(/<description>([\s\S]*?)<\/description>/);
+    const description = descMatch ? unescapeXml(descMatch[1].trim()) : '';
+
+    // Extract file_locations if present
+    const locationsSection = extractXmlSection(featureContent, 'file_locations', options);
+    const file_locations = locationsSection
+      ? extractXmlElements(locationsSection, 'location', options)
+      : undefined;
+
+    if (name) {
+      features.push({
+        name,
+        description,
+        ...(file_locations && file_locations.length > 0 ? { file_locations } : {}),
+      });
+    }
+  }
+
+  log.debug(`Extracted ${features.length} implemented features`);
+  return features;
+}
+
+/**
+ * Extract only the feature names from implemented_features section
+ *
+ * @param specContent - The full XML content of app_spec.txt
+ * @param options - Optional extraction options
+ * @returns Array of feature names
+ */
+export function extractImplementedFeatureNames(
+  specContent: string,
+  options: ExtractXmlOptions = {}
+): string[] {
+  const features = extractImplementedFeatures(specContent, options);
+  return features.map((f) => f.name);
+}
+
+/**
+ * Generate XML for a single implemented feature
+ *
+ * @param feature - The feature to convert to XML
+ * @param indent - The base indentation level (default: 2 spaces)
+ * @returns XML string for the feature
+ */
+export function featureToXml(feature: ImplementedFeature, indent: string = '  '): string {
+  const i2 = indent.repeat(2);
+  const i3 = indent.repeat(3);
+  const i4 = indent.repeat(4);
+
+  let xml = `${i2}<feature>
+${i3}<name>${escapeXml(feature.name)}</name>
+${i3}<description>${escapeXml(feature.description)}</description>`;
+
+  if (feature.file_locations && feature.file_locations.length > 0) {
+    xml += `
+${i3}<file_locations>
+${feature.file_locations.map((loc) => `${i4}<location>${escapeXml(loc)}</location>`).join('\n')}
+${i3}</file_locations>`;
+  }
+
+  xml += `
+${i2}</feature>`;
+
+  return xml;
+}
+
+/**
+ * Generate XML for an array of implemented features
+ *
+ * @param features - Array of features to convert to XML
+ * @param indent - The base indentation level (default: 2 spaces)
+ * @returns XML string for the implemented_features section content
+ */
+export function featuresToXml(features: ImplementedFeature[], indent: string = '  '): string {
+  return features.map((f) => featureToXml(f, indent)).join('\n');
+}
+
+/**
+ * Update the implemented_features section in XML content
+ *
+ * @param specContent - The full XML content
+ * @param newFeatures - The new features to set
+ * @param options - Optional extraction options
+ * @returns Updated XML content with the new implemented_features section
+ */
+export function updateImplementedFeaturesSection(
+  specContent: string,
+  newFeatures: ImplementedFeature[],
+  options: ExtractXmlOptions = {}
+): string {
+  const log = options.logger || logger;
+  const indent = '  ';
+
+  // Generate new section content
+  const newSectionContent = featuresToXml(newFeatures, indent);
+
+  // Build the new section
+  const newSection = `<implemented_features>
+${newSectionContent}
+${indent}</implemented_features>`;
+
+  // Check if section exists
+  const sectionRegex = /<implemented_features>[\s\S]*?<\/implemented_features>/;
+
+  if (sectionRegex.test(specContent)) {
+    log.debug('Replacing existing implemented_features section');
+    return specContent.replace(sectionRegex, newSection);
+  }
+
+  // If section doesn't exist, try to insert after core_capabilities
+  const coreCapabilitiesEnd = '</core_capabilities>';
+  const insertIndex = specContent.indexOf(coreCapabilitiesEnd);
+
+  if (insertIndex !== -1) {
+    const insertPosition = insertIndex + coreCapabilitiesEnd.length;
+    log.debug('Inserting implemented_features after core_capabilities');
+    return (
+      specContent.slice(0, insertPosition) +
+      '\n\n' +
+      indent +
+      newSection +
+      specContent.slice(insertPosition)
+    );
+  }
+
+  // As a fallback, insert before </project_specification>
+  const projectSpecEnd = '</project_specification>';
+  const fallbackIndex = specContent.indexOf(projectSpecEnd);
+
+  if (fallbackIndex !== -1) {
+    log.debug('Inserting implemented_features before </project_specification>');
+    return (
+      specContent.slice(0, fallbackIndex) +
+      indent +
+      newSection +
+      '\n' +
+      specContent.slice(fallbackIndex)
+    );
+  }
+
+  log.warn?.('Could not find appropriate insertion point for implemented_features');
+  log.debug('Could not find appropriate insertion point for implemented_features');
+  return specContent;
+}
+
+/**
+ * Add a new feature to the implemented_features section
+ *
+ * @param specContent - The full XML content
+ * @param newFeature - The feature to add
+ * @param options - Optional extraction options
+ * @returns Updated XML content with the new feature added
+ */
+export function addImplementedFeature(
+  specContent: string,
+  newFeature: ImplementedFeature,
+  options: ExtractXmlOptions = {}
+): string {
+  const log = options.logger || logger;
+
+  // Extract existing features
+  const existingFeatures = extractImplementedFeatures(specContent, options);
+
+  // Check for duplicates by name
+  const isDuplicate = existingFeatures.some(
+    (f) => f.name.toLowerCase() === newFeature.name.toLowerCase()
+  );
+
+  if (isDuplicate) {
+    log.debug(`Feature "${newFeature.name}" already exists, skipping`);
+    return specContent;
+  }
+
+  // Add the new feature
+  const updatedFeatures = [...existingFeatures, newFeature];
+
+  log.debug(`Adding feature "${newFeature.name}"`);
+  return updateImplementedFeaturesSection(specContent, updatedFeatures, options);
+}
+
+/**
+ * Remove a feature from the implemented_features section by name
+ *
+ * @param specContent - The full XML content
+ * @param featureName - The name of the feature to remove
+ * @param options - Optional extraction options
+ * @returns Updated XML content with the feature removed
+ */
+export function removeImplementedFeature(
+  specContent: string,
+  featureName: string,
+  options: ExtractXmlOptions = {}
+): string {
+  const log = options.logger || logger;
+
+  // Extract existing features
+  const existingFeatures = extractImplementedFeatures(specContent, options);
+
+  // Filter out the feature to remove
+  const updatedFeatures = existingFeatures.filter(
+    (f) => f.name.toLowerCase() !== featureName.toLowerCase()
+  );
+
+  if (updatedFeatures.length === existingFeatures.length) {
+    log.debug(`Feature "${featureName}" not found, no changes made`);
+    return specContent;
+  }
+
+  log.debug(`Removing feature "${featureName}"`);
+  return updateImplementedFeaturesSection(specContent, updatedFeatures, options);
+}
+
+/**
+ * Update an existing feature in the implemented_features section
+ *
+ * @param specContent - The full XML content
+ * @param featureName - The name of the feature to update
+ * @param updates - Partial updates to apply to the feature
+ * @param options - Optional extraction options
+ * @returns Updated XML content with the feature modified
+ */
+export function updateImplementedFeature(
+  specContent: string,
+  featureName: string,
+  updates: Partial<ImplementedFeature>,
+  options: ExtractXmlOptions = {}
+): string {
+  const log = options.logger || logger;
+
+  // Extract existing features
+  const existingFeatures = extractImplementedFeatures(specContent, options);
+
+  // Find and update the feature
+  let found = false;
+  const updatedFeatures = existingFeatures.map((f) => {
+    if (f.name.toLowerCase() === featureName.toLowerCase()) {
+      found = true;
+      return {
+        ...f,
+        ...updates,
+        // Preserve the original name if not explicitly updated
+        name: updates.name ?? f.name,
+      };
+    }
+    return f;
+  });
+
+  if (!found) {
+    log.debug(`Feature "${featureName}" not found, no changes made`);
+    return specContent;
+  }
+
+  log.debug(`Updating feature "${featureName}"`);
+  return updateImplementedFeaturesSection(specContent, updatedFeatures, options);
+}
+
+/**
+ * Check if a feature exists in the implemented_features section
+ *
+ * @param specContent - The full XML content
+ * @param featureName - The name of the feature to check
+ * @param options - Optional extraction options
+ * @returns True if the feature exists
+ */
+export function hasImplementedFeature(
+  specContent: string,
+  featureName: string,
+  options: ExtractXmlOptions = {}
+): boolean {
+  const features = extractImplementedFeatures(specContent, options);
+  return features.some((f) => f.name.toLowerCase() === featureName.toLowerCase());
+}
+
+/**
+ * Convert extracted features to SpecOutput.implemented_features format
+ *
+ * @param features - Array of extracted features
+ * @returns Features in SpecOutput format
+ */
+export function toSpecOutputFeatures(
+  features: ImplementedFeature[]
+): SpecOutput['implemented_features'] {
+  return features.map((f) => ({
+    name: f.name,
+    description: f.description,
+    ...(f.file_locations && f.file_locations.length > 0
+      ? { file_locations: f.file_locations }
+      : {}),
+  }));
+}
+
+/**
+ * Convert SpecOutput.implemented_features to ImplementedFeature format
+ *
+ * @param specFeatures - Features from SpecOutput
+ * @returns Features in ImplementedFeature format
+ */
+export function fromSpecOutputFeatures(
+  specFeatures: SpecOutput['implemented_features']
+): ImplementedFeature[] {
+  return specFeatures.map((f) => ({
+    name: f.name,
+    description: f.description,
+    ...(f.file_locations && f.file_locations.length > 0
+      ? { file_locations: f.file_locations }
+      : {}),
+  }));
+}
+
+/**
+ * Represents a roadmap phase extracted from XML
+ */
+export interface RoadmapPhase {
+  name: string;
+  status: string;
+  description?: string;
+}
+
+/**
+ * Extract the technology stack from app_spec.txt XML content
+ *
+ * @param specContent - The full XML content
+ * @param options - Optional extraction options
+ * @returns Array of technology names
+ */
+export function extractTechnologyStack(
+  specContent: string,
+  options: ExtractXmlOptions = {}
+): string[] {
+  const log = options.logger || logger;
+
+  const techSection = extractXmlSection(specContent, 'technology_stack', options);
+  if (!techSection) {
+    log.debug('No technology_stack section found');
+    return [];
+  }
+
+  const technologies = extractXmlElements(techSection, 'technology', options);
+  log.debug(`Extracted ${technologies.length} technologies`);
+  return technologies;
+}
+
+/**
+ * Update the technology_stack section in XML content
+ *
+ * @param specContent - The full XML content
+ * @param technologies - The new technology list
+ * @param options - Optional extraction options
+ * @returns Updated XML content
+ */
+export function updateTechnologyStack(
+  specContent: string,
+  technologies: string[],
+  options: ExtractXmlOptions = {}
+): string {
+  const log = options.logger || logger;
+  const indent = '  ';
+  const i2 = indent.repeat(2);
+
+  // Generate new section content
+  const techXml = technologies
+    .map((t) => `${i2}<technology>${escapeXml(t)}</technology>`)
+    .join('\n');
+  const newSection = `<technology_stack>\n${techXml}\n${indent}</technology_stack>`;
+
+  // Check if section exists
+  const sectionRegex = /<technology_stack>[\s\S]*?<\/technology_stack>/;
+
+  if (sectionRegex.test(specContent)) {
+    log.debug('Replacing existing technology_stack section');
+    return specContent.replace(sectionRegex, newSection);
+  }
+
+  log.debug('No technology_stack section found to update');
+  return specContent;
+}
+
+/**
+ * Extract roadmap phases from app_spec.txt XML content
+ *
+ * @param specContent - The full XML content
+ * @param options - Optional extraction options
+ * @returns Array of roadmap phases
+ */
+export function extractRoadmapPhases(
+  specContent: string,
+  options: ExtractXmlOptions = {}
+): RoadmapPhase[] {
+  const log = options.logger || logger;
+  const phases: RoadmapPhase[] = [];
+
+  const roadmapSection = extractXmlSection(specContent, 'implementation_roadmap', options);
+  if (!roadmapSection) {
+    log.debug('No implementation_roadmap section found');
+    return phases;
+  }
+
+  // Extract individual phase blocks
+  const phaseRegex = /<phase>([\s\S]*?)<\/phase>/g;
+  const phaseMatches = roadmapSection.matchAll(phaseRegex);
+
+  for (const phaseMatch of phaseMatches) {
+    const phaseContent = phaseMatch[1];
+
+    const nameMatch = phaseContent.match(/<name>([\s\S]*?)<\/name>/);
+    const name = nameMatch ? unescapeXml(nameMatch[1].trim()) : '';
+
+    const statusMatch = phaseContent.match(/<status>([\s\S]*?)<\/status>/);
+    const status = statusMatch ? unescapeXml(statusMatch[1].trim()) : 'pending';
+
+    const descMatch = phaseContent.match(/<description>([\s\S]*?)<\/description>/);
+    const description = descMatch ? unescapeXml(descMatch[1].trim()) : undefined;
+
+    if (name) {
+      phases.push({ name, status, description });
+    }
+  }
+
+  log.debug(`Extracted ${phases.length} roadmap phases`);
+  return phases;
+}
+
+/**
+ * Update a roadmap phase status in XML content
+ *
+ * @param specContent - The full XML content
+ * @param phaseName - The name of the phase to update
+ * @param newStatus - The new status value
+ * @param options - Optional extraction options
+ * @returns Updated XML content
+ */
+export function updateRoadmapPhaseStatus(
+  specContent: string,
+  phaseName: string,
+  newStatus: string,
+  options: ExtractXmlOptions = {}
+): string {
+  const log = options.logger || logger;
+
+  // Find the phase and update its status
+  // Match the phase block containing the specific name
+  const phaseRegex = new RegExp(
+    `(<phase>\\s*<name>\\s*${escapeXml(phaseName)}\\s*<\\/name>\\s*<status>)[\\s\\S]*?(<\\/status>)`,
+    'i'
+  );
+
+  if (phaseRegex.test(specContent)) {
+    log.debug(`Updating phase "${phaseName}" status to "${newStatus}"`);
+    return specContent.replace(phaseRegex, `$1${escapeXml(newStatus)}$2`);
+  }
+
+  log.debug(`Phase "${phaseName}" not found`);
+  return specContent;
+}

apps/server/src/providers/claude-provider.ts

@@ -10,7 +10,12 @@ import { BaseProvider } from './base-provider.js';
 import { classifyError, getUserFriendlyErrorMessage, createLogger } from '@automaker/utils';
 
 const logger = createLogger('ClaudeProvider');
-import { getThinkingTokenBudget, validateBareModelId } from '@automaker/types';
+import {
+  getThinkingTokenBudget,
+  validateBareModelId,
+  type ClaudeApiProfile,
+  type Credentials,
+} from '@automaker/types';
 import type {
   ExecuteOptions,
   ProviderMessage,
@@ -21,9 +26,19 @@ import type {
 // Explicit allowlist of environment variables to pass to the SDK.
 // Only these vars are passed - nothing else from process.env leaks through.
 const ALLOWED_ENV_VARS = [
+  // Authentication
   'ANTHROPIC_API_KEY',
-  'ANTHROPIC_BASE_URL',
   'ANTHROPIC_AUTH_TOKEN',
+  // Endpoint configuration
+  'ANTHROPIC_BASE_URL',
+  'API_TIMEOUT_MS',
+  // Model mappings
+  'ANTHROPIC_DEFAULT_HAIKU_MODEL',
+  'ANTHROPIC_DEFAULT_SONNET_MODEL',
+  'ANTHROPIC_DEFAULT_OPUS_MODEL',
+  // Traffic control
+  'CLAUDE_CODE_DISABLE_NONESSENTIAL_TRAFFIC',
+  // System vars (always from process.env)
   'PATH',
   'HOME',
   'SHELL',
@@ -33,16 +48,108 @@ const ALLOWED_ENV_VARS = [
   'LC_ALL',
 ];
 
+// System vars are always passed from process.env regardless of profile
+const SYSTEM_ENV_VARS = ['PATH', 'HOME', 'SHELL', 'TERM', 'USER', 'LANG', 'LC_ALL'];
+
 /**
- * Build environment for the SDK with only explicitly allowed variables
+ * Build environment for the SDK with only explicitly allowed variables.
+ * When a profile is provided, uses profile configuration (clean switch - don't inherit from process.env).
+ * When no profile is provided, uses direct Anthropic API settings from process.env.
+ *
+ * @param profile - Optional Claude API profile for alternative endpoint configuration
+ * @param credentials - Optional credentials object for resolving 'credentials' apiKeySource
  */
-function buildEnv(): Record<string, string | undefined> {
+function buildEnv(
+  profile?: ClaudeApiProfile,
+  credentials?: Credentials
+): Record<string, string | undefined> {
   const env: Record<string, string | undefined> = {};
-  for (const key of ALLOWED_ENV_VARS) {
+
+  if (profile) {
+    // Use profile configuration (clean switch - don't inherit non-system vars from process.env)
+    logger.debug('Building environment from Claude API profile:', {
+      name: profile.name,
+      apiKeySource: profile.apiKeySource ?? 'inline',
+    });
+
+    // Resolve API key based on source strategy
+    let apiKey: string | undefined;
+    const source = profile.apiKeySource ?? 'inline'; // Default to inline for backwards compat
+
+    switch (source) {
+      case 'inline':
+        apiKey = profile.apiKey;
+        break;
+      case 'env':
+        apiKey = process.env.ANTHROPIC_API_KEY;
+        break;
+      case 'credentials':
+        apiKey = credentials?.apiKeys?.anthropic;
+        break;
+    }
+
+    // Warn if no API key found
+    if (!apiKey) {
+      logger.warn(`No API key found for profile "${profile.name}" with source "${source}"`);
+    }
+
+    // Authentication
+    if (profile.useAuthToken) {
+      env['ANTHROPIC_AUTH_TOKEN'] = apiKey;
+    } else {
+      env['ANTHROPIC_API_KEY'] = apiKey;
+    }
+
+    // Endpoint configuration
+    env['ANTHROPIC_BASE_URL'] = profile.baseUrl;
+
+    if (profile.timeoutMs) {
+      env['API_TIMEOUT_MS'] = String(profile.timeoutMs);
+    }
+
+    // Model mappings
+    if (profile.modelMappings?.haiku) {
+      env['ANTHROPIC_DEFAULT_HAIKU_MODEL'] = profile.modelMappings.haiku;
+    }
+    if (profile.modelMappings?.sonnet) {
+      env['ANTHROPIC_DEFAULT_SONNET_MODEL'] = profile.modelMappings.sonnet;
+    }
+    if (profile.modelMappings?.opus) {
+      env['ANTHROPIC_DEFAULT_OPUS_MODEL'] = profile.modelMappings.opus;
+    }
+
+    // Traffic control
+    if (profile.disableNonessentialTraffic) {
+      env['CLAUDE_CODE_DISABLE_NONESSENTIAL_TRAFFIC'] = '1';
+    }
+  } else {
+    // Use direct Anthropic API - two modes:
+    // 1. API Key mode: ANTHROPIC_API_KEY from credentials/env
+    // 2. Claude Max plan: Uses CLI OAuth auth (SDK handles this automatically)
+    //
+    // IMPORTANT: Do NOT set any profile vars (base URL, model mappings, etc.)
+    // This ensures clean switching - only pass through what's in process.env
+    if (process.env.ANTHROPIC_API_KEY) {
+      env['ANTHROPIC_API_KEY'] = process.env.ANTHROPIC_API_KEY;
+    }
+    // If using Claude Max plan via CLI auth, the SDK handles auth automatically
+    // when no API key is provided. We don't set ANTHROPIC_AUTH_TOKEN here
+    // unless it was explicitly set in process.env (rare edge case).
+    if (process.env.ANTHROPIC_AUTH_TOKEN) {
+      env['ANTHROPIC_AUTH_TOKEN'] = process.env.ANTHROPIC_AUTH_TOKEN;
+    }
+    // Do NOT set ANTHROPIC_BASE_URL - let SDK use default Anthropic endpoint
+    // Do NOT set model mappings - use standard Claude model names
+    // Do NOT set CLAUDE_CODE_DISABLE_NONESSENTIAL_TRAFFIC
+  }
+
+  // Always add system vars from process.env
+  for (const key of SYSTEM_ENV_VARS) {
     if (process.env[key]) {
       env[key] = process.env[key];
     }
   }
+
   return env;
 }
 
@@ -70,6 +177,8 @@ export class ClaudeProvider extends BaseProvider {
       conversationHistory,
       sdkSessionId,
       thinkingLevel,
+      claudeApiProfile,
+      credentials,
     } = options;
 
     // Convert thinking level to token budget
@@ -82,7 +191,9 @@ export class ClaudeProvider extends BaseProvider {
       maxTurns,
       cwd,
       // Pass only explicitly allowed environment variables to SDK
-      env: buildEnv(),
+      // When a profile is active, uses profile settings (clean switch)
+      // When no profile, uses direct Anthropic API (from process.env or CLI OAuth)
+      env: buildEnv(claudeApiProfile, credentials),
       // Pass through allowedTools if provided by caller (decided by sdk-options.ts)
       ...(allowedTools && { allowedTools }),
       // AUTONOMOUS MODE: Always bypass permissions for fully autonomous operation

apps/server/src/providers/cli-provider.ts

@@ -35,6 +35,7 @@ import {
   type SubprocessOptions,
   type WslCliResult,
 } from '@automaker/platform';
+import { calculateReasoningTimeout } from '@automaker/types';
 import { createLogger, isAbortError } from '@automaker/utils';
 import { execSync } from 'child_process';
 import * as fs from 'fs';
@@ -107,6 +108,15 @@ export interface CliDetectionResult {
 // Create logger for CLI operations
 const cliLogger = createLogger('CliProvider');
 
+/**
+ * Base timeout for CLI operations in milliseconds.
+ * CLI tools have longer startup and processing times compared to direct API calls,
+ * so we use a higher base timeout (120s) than the default provider timeout (30s).
+ * This is multiplied by reasoning effort multipliers when applicable.
+ * @see calculateReasoningTimeout from @automaker/types
+ */
+const CLI_BASE_TIMEOUT_MS = 120000;
+
 /**
  * Abstract base class for CLI-based providers
  *
@@ -450,6 +460,10 @@ export abstract class CliProvider extends BaseProvider {
       }
     }
 
+    // Calculate dynamic timeout based on reasoning effort.
+    // This addresses GitHub issue #530 where reasoning models with 'xhigh' effort would timeout.
+    const timeout = calculateReasoningTimeout(options.reasoningEffort, CLI_BASE_TIMEOUT_MS);
+
     // WSL strategy
     if (this.useWsl && this.wslCliPath) {
       const wslCwd = windowsToWslPath(cwd);
@@ -473,7 +487,7 @@ export abstract class CliProvider extends BaseProvider {
         cwd, // Windows cwd for spawn
         env: filteredEnv,
         abortController: options.abortController,
-        timeout: 120000, // CLI operations may take longer
+        timeout,
       };
     }
 
@@ -488,7 +502,7 @@ export abstract class CliProvider extends BaseProvider {
         cwd,
         env: filteredEnv,
         abortController: options.abortController,
-        timeout: 120000,
+        timeout,
       };
     }
 
@@ -501,7 +515,7 @@ export abstract class CliProvider extends BaseProvider {
       cwd,
       env: filteredEnv,
       abortController: options.abortController,
-      timeout: 120000,
+      timeout,
     };
   }
 

apps/server/src/providers/codex-provider.ts

@@ -33,6 +33,8 @@ import {
   CODEX_MODEL_MAP,
   supportsReasoningEffort,
   validateBareModelId,
+  calculateReasoningTimeout,
+  DEFAULT_TIMEOUT_MS,
   type CodexApprovalPolicy,
   type CodexSandboxMode,
   type CodexAuthStatus,
@@ -91,7 +93,14 @@ const CODEX_ITEM_TYPES = {
 const SYSTEM_PROMPT_LABEL = 'System instructions';
 const HISTORY_HEADER = 'Current request:\n';
 const TEXT_ENCODING = 'utf-8';
-const DEFAULT_TIMEOUT_MS = 30000;
+/**
+ * Default timeout for Codex CLI operations in milliseconds.
+ * This is the "no output" timeout - if the CLI doesn't produce any JSONL output
+ * for this duration, the process is killed. For reasoning models with high
+ * reasoning effort, this timeout is dynamically extended via calculateReasoningTimeout().
+ * @see calculateReasoningTimeout from @automaker/types
+ */
+const CODEX_CLI_TIMEOUT_MS = DEFAULT_TIMEOUT_MS;
 const CONTEXT_WINDOW_256K = 256000;
 const MAX_OUTPUT_32K = 32000;
 const MAX_OUTPUT_16K = 16000;
@@ -814,13 +823,19 @@ export class CodexProvider extends BaseProvider {
         envOverrides[OPENAI_API_KEY_ENV] = executionPlan.openAiApiKey;
       }
 
+      // Calculate dynamic timeout based on reasoning effort.
+      // Higher reasoning effort (e.g., 'xhigh' for "xtra thinking" mode) requires more time
+      // for the model to generate reasoning tokens before producing output.
+      // This fixes GitHub issue #530 where features would get stuck with reasoning models.
+      const timeout = calculateReasoningTimeout(options.reasoningEffort, CODEX_CLI_TIMEOUT_MS);
+
       const stream = spawnJSONLProcess({
         command: commandPath,
         args,
         cwd: options.cwd,
         env: envOverrides,
         abortController: options.abortController,
-        timeout: DEFAULT_TIMEOUT_MS,
+        timeout,
         stdinData: promptText, // Pass prompt via stdin
       });
 

apps/server/src/providers/cursor-config-manager.ts

@@ -44,7 +44,7 @@ export class CursorConfigManager {
 
     // Return default config with all available models
     return {
-      defaultModel: 'auto',
+      defaultModel: 'cursor-auto',
       models: getAllCursorModelIds(),
     };
   }
@@ -77,7 +77,7 @@ export class CursorConfigManager {
    * Get the default model
    */
   getDefaultModel(): CursorModelId {
-    return this.config.defaultModel || 'auto';
+    return this.config.defaultModel || 'cursor-auto';
   }
 
   /**
@@ -93,7 +93,7 @@ export class CursorConfigManager {
    * Get enabled models
    */
   getEnabledModels(): CursorModelId[] {
-    return this.config.models || ['auto'];
+    return this.config.models || ['cursor-auto'];
   }
 
   /**
@@ -174,7 +174,7 @@ export class CursorConfigManager {
    */
   reset(): void {
     this.config = {
-      defaultModel: 'auto',
+      defaultModel: 'cursor-auto',
       models: getAllCursorModelIds(),
     };
     this.saveConfig();

apps/server/src/providers/simple-query-service.ts

@@ -20,6 +20,8 @@ import type {
   ContentBlock,
   ThinkingLevel,
   ReasoningEffort,
+  ClaudeApiProfile,
+  Credentials,
 } from '@automaker/types';
 import { stripProviderPrefix } from '@automaker/types';
 
@@ -54,6 +56,10 @@ export interface SimpleQueryOptions {
   readOnly?: boolean;
   /** Setting sources for CLAUDE.md loading */
   settingSources?: Array<'user' | 'project' | 'local'>;
+  /** Active Claude API profile for alternative endpoint configuration */
+  claudeApiProfile?: ClaudeApiProfile;
+  /** Credentials for resolving 'credentials' apiKeySource in Claude API profiles */
+  credentials?: Credentials;
 }
 
 /**
@@ -125,6 +131,8 @@ export async function simpleQuery(options: SimpleQueryOptions): Promise<SimpleQu
     reasoningEffort: options.reasoningEffort,
     readOnly: options.readOnly,
     settingSources: options.settingSources,
+    claudeApiProfile: options.claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+    credentials: options.credentials, // Pass credentials for resolving 'credentials' apiKeySource
   };
 
   for await (const msg of provider.executeQuery(providerOptions)) {
@@ -207,6 +215,8 @@ export async function streamingQuery(options: StreamingQueryOptions): Promise<Si
     reasoningEffort: options.reasoningEffort,
     readOnly: options.readOnly,
     settingSources: options.settingSources,
+    claudeApiProfile: options.claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+    credentials: options.credentials, // Pass credentials for resolving 'credentials' apiKeySource
   };
 
   for await (const msg of provider.executeQuery(providerOptions)) {

apps/server/src/routes/app-spec/common.ts

@@ -6,8 +6,17 @@ import { createLogger } from '@automaker/utils';
 
 const logger = createLogger('SpecRegeneration');
 
+// Types for running generation
+export type GenerationType = 'spec_regeneration' | 'feature_generation' | 'sync';
+
+interface RunningGeneration {
+  isRunning: boolean;
+  type: GenerationType;
+  startedAt: string;
+}
+
 // Shared state for tracking generation status - scoped by project path
-const runningProjects = new Map<string, boolean>();
+const runningProjects = new Map<string, RunningGeneration>();
 const abortControllers = new Map<string, AbortController>();
 
 /**
@@ -17,16 +26,21 @@ export function getSpecRegenerationStatus(projectPath?: string): {
   isRunning: boolean;
   currentAbortController: AbortController | null;
   projectPath?: string;
+  type?: GenerationType;
+  startedAt?: string;
 } {
   if (projectPath) {
+    const generation = runningProjects.get(projectPath);
     return {
-      isRunning: runningProjects.get(projectPath) || false,
+      isRunning: generation?.isRunning || false,
       currentAbortController: abortControllers.get(projectPath) || null,
       projectPath,
+      type: generation?.type,
+      startedAt: generation?.startedAt,
     };
   }
   // Fallback: check if any project is running (for backward compatibility)
-  const isAnyRunning = Array.from(runningProjects.values()).some((running) => running);
+  const isAnyRunning = Array.from(runningProjects.values()).some((g) => g.isRunning);
   return { isRunning: isAnyRunning, currentAbortController: null };
 }
 
@@ -46,10 +60,15 @@ export function getRunningProjectPath(): string | null {
 export function setRunningState(
   projectPath: string,
   running: boolean,
-  controller: AbortController | null = null
+  controller: AbortController | null = null,
+  type: GenerationType = 'spec_regeneration'
 ): void {
   if (running) {
-    runningProjects.set(projectPath, true);
+    runningProjects.set(projectPath, {
+      isRunning: true,
+      type,
+      startedAt: new Date().toISOString(),
+    });
     if (controller) {
       abortControllers.set(projectPath, controller);
     }
@@ -59,6 +78,33 @@ export function setRunningState(
   }
 }
 
+/**
+ * Get all running spec/feature generations for the running agents view
+ */
+export function getAllRunningGenerations(): Array<{
+  projectPath: string;
+  type: GenerationType;
+  startedAt: string;
+}> {
+  const results: Array<{
+    projectPath: string;
+    type: GenerationType;
+    startedAt: string;
+  }> = [];
+
+  for (const [projectPath, generation] of runningProjects.entries()) {
+    if (generation.isRunning) {
+      results.push({
+        projectPath,
+        type: generation.type,
+        startedAt: generation.startedAt,
+      });
+    }
+  }
+
+  return results;
+}
+
 /**
  * Helper to log authentication status
  */

apps/server/src/routes/app-spec/generate-features-from-spec.ts

@@ -14,7 +14,12 @@ import { streamingQuery } from '../../providers/simple-query-service.js';
 import { parseAndCreateFeatures } from './parse-and-create-features.js';
 import { getAppSpecPath } from '@automaker/platform';
 import type { SettingsService } from '../../services/settings-service.js';
-import { getAutoLoadClaudeMdSetting } from '../../lib/settings-helpers.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getPromptCustomization,
+  getActiveClaudeApiProfile,
+} from '../../lib/settings-helpers.js';
+import { FeatureLoader } from '../../services/feature-loader.js';
 
 const logger = createLogger('SpecRegeneration');
 
@@ -53,38 +58,48 @@ export async function generateFeaturesFromSpec(
     return;
   }
 
+  // Get customized prompts from settings
+  const prompts = await getPromptCustomization(settingsService, '[FeatureGeneration]');
+
+  // Load existing features to prevent duplicates
+  const featureLoader = new FeatureLoader();
+  const existingFeatures = await featureLoader.getAll(projectPath);
+
+  logger.info(`Found ${existingFeatures.length} existing features to exclude from generation`);
+
+  // Build existing features context for the prompt
+  let existingFeaturesContext = '';
+  if (existingFeatures.length > 0) {
+    const featuresList = existingFeatures
+      .map(
+        (f) =>
+          `- "${f.title}" (ID: ${f.id}): ${f.description?.substring(0, 100) || 'No description'}`
+      )
+      .join('\n');
+    existingFeaturesContext = `
+
+## EXISTING FEATURES (DO NOT REGENERATE THESE)
+
+The following ${existingFeatures.length} features already exist in the project. You MUST NOT generate features that duplicate or overlap with these:
+
+${featuresList}
+
+CRITICAL INSTRUCTIONS:
+- DO NOT generate any features with the same or similar titles as the existing features listed above
+- DO NOT generate features that cover the same functionality as existing features
+- ONLY generate NEW features that are not yet in the system
+- If a feature from the roadmap already exists, skip it entirely
+- Generate unique feature IDs that do not conflict with existing IDs: ${existingFeatures.map((f) => f.id).join(', ')}
+`;
+  }
+
   const prompt = `Based on this project specification:
 
 ${spec}
+${existingFeaturesContext}
+${prompts.appSpec.generateFeaturesFromSpecPrompt}
 
-Generate a prioritized list of implementable features. For each feature provide:
-
-1. **id**: A unique lowercase-hyphenated identifier
-2. **category**: Functional category (e.g., "Core", "UI", "API", "Authentication", "Database")
-3. **title**: Short descriptive title
-4. **description**: What this feature does (2-3 sentences)
-5. **priority**: 1 (high), 2 (medium), or 3 (low)
-6. **complexity**: "simple", "moderate", or "complex"
-7. **dependencies**: Array of feature IDs this depends on (can be empty)
-
-Format as JSON:
-{
-  "features": [
-    {
-      "id": "feature-id",
-      "category": "Feature Category",
-      "title": "Feature Title",
-      "description": "What it does",
-      "priority": 1,
-      "complexity": "moderate",
-      "dependencies": []
-    }
-  ]
-}
-
-Generate ${featureCount} features that build on each other logically.
-
-IMPORTANT: Do not ask for clarification. The specification is provided above. Generate the JSON immediately.`;
+Generate ${featureCount} NEW features that build on each other logically. Remember: ONLY generate features that DO NOT already exist.`;
 
   logger.info('========== PROMPT BEING SENT ==========');
   logger.info(`Prompt length: ${prompt.length} chars`);
@@ -112,6 +127,12 @@ IMPORTANT: Do not ask for clarification. The specification is provided above. Ge
 
   logger.info('Using model:', model);
 
+  // Get active Claude API profile for alternative endpoint configuration
+  const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+    settingsService,
+    '[FeatureGeneration]'
+  );
+
   // Use streamingQuery with event callbacks
   const result = await streamingQuery({
     prompt,
@@ -123,6 +144,8 @@ IMPORTANT: Do not ask for clarification. The specification is provided above. Ge
     thinkingLevel,
     readOnly: true, // Feature generation only reads code, doesn't write
     settingSources: autoLoadClaudeMd ? ['user', 'project', 'local'] : undefined,
+    claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+    credentials, // Pass credentials for resolving 'credentials' apiKeySource
     onText: (text) => {
       logger.debug(`Feature text block received (${text.length} chars)`);
       events.emit('spec-regeneration:event', {

apps/server/src/routes/app-spec/generate-spec.ts

@@ -7,12 +7,7 @@
 
 import * as secureFs from '../../lib/secure-fs.js';
 import type { EventEmitter } from '../../lib/events.js';
-import {
-  specOutputSchema,
-  specToXml,
-  getStructuredSpecPromptInstruction,
-  type SpecOutput,
-} from '../../lib/app-spec-format.js';
+import { specOutputSchema, specToXml, type SpecOutput } from '../../lib/app-spec-format.js';
 import { createLogger } from '@automaker/utils';
 import { DEFAULT_PHASE_MODELS, isCursorModel } from '@automaker/types';
 import { resolvePhaseModel } from '@automaker/model-resolver';
@@ -21,7 +16,11 @@ import { streamingQuery } from '../../providers/simple-query-service.js';
 import { generateFeaturesFromSpec } from './generate-features-from-spec.js';
 import { ensureAutomakerDir, getAppSpecPath } from '@automaker/platform';
 import type { SettingsService } from '../../services/settings-service.js';
-import { getAutoLoadClaudeMdSetting } from '../../lib/settings-helpers.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getPromptCustomization,
+  getActiveClaudeApiProfile,
+} from '../../lib/settings-helpers.js';
 
 const logger = createLogger('SpecRegeneration');
 
@@ -43,6 +42,9 @@ export async function generateSpec(
   logger.info('analyzeProject:', analyzeProject);
   logger.info('maxFeatures:', maxFeatures);
 
+  // Get customized prompts from settings
+  const prompts = await getPromptCustomization(settingsService, '[SpecRegeneration]');
+
   // Build the prompt based on whether we should analyze the project
   let analysisInstructions = '';
   let techStackDefaults = '';
@@ -66,9 +68,7 @@ export async function generateSpec(
 Use these technologies as the foundation for the specification.`;
   }
 
-  const prompt = `You are helping to define a software project specification.
-
-IMPORTANT: Never ask for clarification or additional information. Use the information provided and make reasonable assumptions to create the best possible specification. If details are missing, infer them based on common patterns and best practices.
+  const prompt = `${prompts.appSpec.generateSpecSystemPrompt}
 
 Project Overview:
 ${projectOverview}
@@ -77,7 +77,7 @@ ${techStackDefaults}
 
 ${analysisInstructions}
 
-${getStructuredSpecPromptInstruction()}`;
+${prompts.appSpec.structuredSpecInstructions}`;
 
   logger.info('========== PROMPT BEING SENT ==========');
   logger.info(`Prompt length: ${prompt.length} chars`);
@@ -104,6 +104,12 @@ ${getStructuredSpecPromptInstruction()}`;
 
   logger.info('Using model:', model);
 
+  // Get active Claude API profile for alternative endpoint configuration
+  const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+    settingsService,
+    '[SpecRegeneration]'
+  );
+
   let responseText = '';
   let structuredOutput: SpecOutput | null = null;
 
@@ -136,6 +142,8 @@ Your entire response should be valid JSON starting with { and ending with }. No
     thinkingLevel,
     readOnly: true, // Spec generation only reads code, we write the spec ourselves
     settingSources: autoLoadClaudeMd ? ['user', 'project', 'local'] : undefined,
+    claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+    credentials, // Pass credentials for resolving 'credentials' apiKeySource
     outputFormat: useStructuredOutput
       ? {
           type: 'json_schema',
@@ -205,19 +213,33 @@ Your entire response should be valid JSON starting with { and ending with }. No
       xmlContent = responseText.substring(xmlStart, xmlEnd + '</project_specification>'.length);
       logger.info(`Extracted XML content: ${xmlContent.length} chars (from position ${xmlStart})`);
     } else {
-      // No valid XML structure found in the response text
-      // This happens when structured output was expected but not received, and the agent
-      // output conversational text instead of XML (e.g., "The project directory appears to be empty...")
-      // We should NOT save this conversational text as it's not a valid spec
-      logger.error('❌ Response does not contain valid <project_specification> XML structure');
-      logger.error(
-        'This typically happens when structured output failed and the agent produced conversational text instead of XML'
-      );
-      throw new Error(
-        'Failed to generate spec: No valid XML structure found in response. ' +
-          'The response contained conversational text but no <project_specification> tags. ' +
-          'Please try again.'
-      );
+      // No XML found, try JSON extraction
+      logger.warn('⚠️ No XML tags found, attempting JSON extraction...');
+      const extractedJson = extractJson<SpecOutput>(responseText, { logger });
+
+      if (
+        extractedJson &&
+        typeof extractedJson.project_name === 'string' &&
+        typeof extractedJson.overview === 'string' &&
+        Array.isArray(extractedJson.technology_stack) &&
+        Array.isArray(extractedJson.core_capabilities) &&
+        Array.isArray(extractedJson.implemented_features)
+      ) {
+        logger.info('✅ Successfully extracted JSON from response text');
+        xmlContent = specToXml(extractedJson);
+        logger.info(`✅ Converted extracted JSON to XML: ${xmlContent.length} chars`);
+      } else {
+        // Neither XML nor valid JSON found
+        logger.error('❌ Response does not contain valid XML or JSON structure');
+        logger.error(
+          'This typically happens when structured output failed and the agent produced conversational text instead of structured output'
+        );
+        throw new Error(
+          'Failed to generate spec: No valid XML or JSON structure found in response. ' +
+            'The response contained conversational text but no <project_specification> tags or valid JSON. ' +
+            'Please try again.'
+        );
+      }
     }
   }
 

apps/server/src/routes/app-spec/index.ts

@@ -7,6 +7,7 @@ import type { EventEmitter } from '../../lib/events.js';
 import { createCreateHandler } from './routes/create.js';
 import { createGenerateHandler } from './routes/generate.js';
 import { createGenerateFeaturesHandler } from './routes/generate-features.js';
+import { createSyncHandler } from './routes/sync.js';
 import { createStopHandler } from './routes/stop.js';
 import { createStatusHandler } from './routes/status.js';
 import type { SettingsService } from '../../services/settings-service.js';
@@ -20,6 +21,7 @@ export function createSpecRegenerationRoutes(
   router.post('/create', createCreateHandler(events));
   router.post('/generate', createGenerateHandler(events, settingsService));
   router.post('/generate-features', createGenerateFeaturesHandler(events, settingsService));
+  router.post('/sync', createSyncHandler(events, settingsService));
   router.post('/stop', createStopHandler());
   router.get('/status', createStatusHandler());
 

apps/server/src/routes/app-spec/parse-and-create-features.ts

@@ -5,9 +5,10 @@
 import path from 'path';
 import * as secureFs from '../../lib/secure-fs.js';
 import type { EventEmitter } from '../../lib/events.js';
-import { createLogger } from '@automaker/utils';
+import { createLogger, atomicWriteJson, DEFAULT_BACKUP_COUNT } from '@automaker/utils';
 import { getFeaturesDir } from '@automaker/platform';
 import { extractJsonWithArray } from '../../lib/json-extractor.js';
+import { getNotificationService } from '../../services/notification-service.js';
 
 const logger = createLogger('SpecRegeneration');
 
@@ -73,10 +74,10 @@ export async function parseAndCreateFeatures(
         updatedAt: new Date().toISOString(),
       };
 
-      await secureFs.writeFile(
-        path.join(featureDir, 'feature.json'),
-        JSON.stringify(featureData, null, 2)
-      );
+      // Use atomic write with backup support for crash protection
+      await atomicWriteJson(path.join(featureDir, 'feature.json'), featureData, {
+        backupCount: DEFAULT_BACKUP_COUNT,
+      });
 
       createdFeatures.push({ id: feature.id, title: feature.title });
     }
@@ -88,6 +89,15 @@ export async function parseAndCreateFeatures(
       message: `Spec regeneration complete! Created ${createdFeatures.length} features.`,
       projectPath: projectPath,
     });
+
+    // Create notification for spec generation completion
+    const notificationService = getNotificationService();
+    await notificationService.createNotification({
+      type: 'spec_regeneration_complete',
+      title: 'Spec Generation Complete',
+      message: `Created ${createdFeatures.length} features from the project specification.`,
+      projectPath: projectPath,
+    });
   } catch (error) {
     logger.error('❌ parseAndCreateFeatures() failed:');
     logger.error('Error:', error);

apps/server/src/routes/app-spec/routes/generate-features.ts

@@ -50,7 +50,7 @@ export function createGenerateFeaturesHandler(
       logAuthStatus('Before starting feature generation');
 
       const abortController = new AbortController();
-      setRunningState(projectPath, true, abortController);
+      setRunningState(projectPath, true, abortController, 'feature_generation');
       logger.info('Starting background feature generation task...');
 
       generateFeaturesFromSpec(projectPath, events, abortController, maxFeatures, settingsService)

apps/server/src/routes/app-spec/routes/sync.ts

@@ -0,0 +1,76 @@
+/**
+ * POST /sync endpoint - Sync spec with codebase and features
+ */
+
+import type { Request, Response } from 'express';
+import type { EventEmitter } from '../../../lib/events.js';
+import { createLogger } from '@automaker/utils';
+import {
+  getSpecRegenerationStatus,
+  setRunningState,
+  logAuthStatus,
+  logError,
+  getErrorMessage,
+} from '../common.js';
+import { syncSpec } from '../sync-spec.js';
+import type { SettingsService } from '../../../services/settings-service.js';
+
+const logger = createLogger('SpecSync');
+
+export function createSyncHandler(events: EventEmitter, settingsService?: SettingsService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    logger.info('========== /sync endpoint called ==========');
+    logger.debug('Request body:', JSON.stringify(req.body, null, 2));
+
+    try {
+      const { projectPath } = req.body as {
+        projectPath: string;
+      };
+
+      logger.debug('projectPath:', projectPath);
+
+      if (!projectPath) {
+        logger.error('Missing projectPath parameter');
+        res.status(400).json({ success: false, error: 'projectPath required' });
+        return;
+      }
+
+      const { isRunning } = getSpecRegenerationStatus(projectPath);
+      if (isRunning) {
+        logger.warn('Generation/sync already running for project:', projectPath);
+        res.json({ success: false, error: 'Operation already running for this project' });
+        return;
+      }
+
+      logAuthStatus('Before starting spec sync');
+
+      const abortController = new AbortController();
+      setRunningState(projectPath, true, abortController, 'sync');
+      logger.info('Starting background spec sync task...');
+
+      syncSpec(projectPath, events, abortController, settingsService)
+        .then((result) => {
+          logger.info('Spec sync completed successfully');
+          logger.info('Result:', JSON.stringify(result, null, 2));
+        })
+        .catch((error) => {
+          logError(error, 'Spec sync failed with error');
+          events.emit('spec-regeneration:event', {
+            type: 'spec_regeneration_error',
+            error: getErrorMessage(error),
+            projectPath,
+          });
+        })
+        .finally(() => {
+          logger.info('Spec sync task finished (success or error)');
+          setRunningState(projectPath, false, null);
+        });
+
+      logger.info('Returning success response (sync running in background)');
+      res.json({ success: true });
+    } catch (error) {
+      logError(error, 'Sync route handler failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/app-spec/sync-spec.ts

@@ -0,0 +1,318 @@
+/**
+ * Sync spec with current codebase and feature state
+ *
+ * Updates the spec file based on:
+ * - Completed Automaker features
+ * - Code analysis for tech stack and implementations
+ * - Roadmap phase status updates
+ */
+
+import * as secureFs from '../../lib/secure-fs.js';
+import type { EventEmitter } from '../../lib/events.js';
+import { createLogger } from '@automaker/utils';
+import { DEFAULT_PHASE_MODELS } from '@automaker/types';
+import { resolvePhaseModel } from '@automaker/model-resolver';
+import { streamingQuery } from '../../providers/simple-query-service.js';
+import { getAppSpecPath } from '@automaker/platform';
+import type { SettingsService } from '../../services/settings-service.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getActiveClaudeApiProfile,
+} from '../../lib/settings-helpers.js';
+import { FeatureLoader } from '../../services/feature-loader.js';
+import {
+  extractImplementedFeatures,
+  extractTechnologyStack,
+  extractRoadmapPhases,
+  updateImplementedFeaturesSection,
+  updateTechnologyStack,
+  updateRoadmapPhaseStatus,
+  type ImplementedFeature,
+  type RoadmapPhase,
+} from '../../lib/xml-extractor.js';
+import { getNotificationService } from '../../services/notification-service.js';
+
+const logger = createLogger('SpecSync');
+
+/**
+ * Result of a sync operation
+ */
+export interface SyncResult {
+  techStackUpdates: {
+    added: string[];
+    removed: string[];
+  };
+  implementedFeaturesUpdates: {
+    addedFromFeatures: string[];
+    removed: string[];
+  };
+  roadmapUpdates: Array<{ phaseName: string; newStatus: string }>;
+  summary: string;
+}
+
+/**
+ * Sync the spec with current codebase and feature state
+ */
+export async function syncSpec(
+  projectPath: string,
+  events: EventEmitter,
+  abortController: AbortController,
+  settingsService?: SettingsService
+): Promise<SyncResult> {
+  logger.info('========== syncSpec() started ==========');
+  logger.info('projectPath:', projectPath);
+
+  const result: SyncResult = {
+    techStackUpdates: { added: [], removed: [] },
+    implementedFeaturesUpdates: { addedFromFeatures: [], removed: [] },
+    roadmapUpdates: [],
+    summary: '',
+  };
+
+  // Read existing spec
+  const specPath = getAppSpecPath(projectPath);
+  let specContent: string;
+
+  try {
+    specContent = (await secureFs.readFile(specPath, 'utf-8')) as string;
+    logger.info(`Spec loaded successfully (${specContent.length} chars)`);
+  } catch (readError) {
+    logger.error('Failed to read spec file:', readError);
+    events.emit('spec-regeneration:event', {
+      type: 'spec_regeneration_error',
+      error: 'No project spec found. Create or regenerate spec first.',
+      projectPath,
+    });
+    throw new Error('No project spec found');
+  }
+
+  events.emit('spec-regeneration:event', {
+    type: 'spec_regeneration_progress',
+    content: '[Phase: sync] Starting spec sync...\n',
+    projectPath,
+  });
+
+  // Extract current state from spec
+  const currentImplementedFeatures = extractImplementedFeatures(specContent);
+  const currentTechStack = extractTechnologyStack(specContent);
+  const currentRoadmapPhases = extractRoadmapPhases(specContent);
+
+  logger.info(`Current spec has ${currentImplementedFeatures.length} implemented features`);
+  logger.info(`Current spec has ${currentTechStack.length} technologies`);
+  logger.info(`Current spec has ${currentRoadmapPhases.length} roadmap phases`);
+
+  // Load completed Automaker features
+  const featureLoader = new FeatureLoader();
+  const allFeatures = await featureLoader.getAll(projectPath);
+  const completedFeatures = allFeatures.filter(
+    (f) => f.status === 'completed' || f.status === 'verified'
+  );
+
+  logger.info(`Found ${completedFeatures.length} completed/verified features in Automaker`);
+
+  events.emit('spec-regeneration:event', {
+    type: 'spec_regeneration_progress',
+    content: `Found ${completedFeatures.length} completed features to sync...\n`,
+    projectPath,
+  });
+
+  // Build new implemented features list from completed Automaker features
+  const newImplementedFeatures: ImplementedFeature[] = [];
+  const existingNames = new Set(currentImplementedFeatures.map((f) => f.name.toLowerCase()));
+
+  for (const feature of completedFeatures) {
+    const name = feature.title || `Feature: ${feature.id}`;
+    if (!existingNames.has(name.toLowerCase())) {
+      newImplementedFeatures.push({
+        name,
+        description: feature.description || '',
+      });
+      result.implementedFeaturesUpdates.addedFromFeatures.push(name);
+    }
+  }
+
+  // Merge: keep existing + add new from completed features
+  const mergedFeatures = [...currentImplementedFeatures, ...newImplementedFeatures];
+
+  // Update spec with merged features
+  if (result.implementedFeaturesUpdates.addedFromFeatures.length > 0) {
+    specContent = updateImplementedFeaturesSection(specContent, mergedFeatures);
+    logger.info(
+      `Added ${result.implementedFeaturesUpdates.addedFromFeatures.length} features to spec`
+    );
+  }
+
+  // Analyze codebase for tech stack updates using AI
+  events.emit('spec-regeneration:event', {
+    type: 'spec_regeneration_progress',
+    content: 'Analyzing codebase for technology updates...\n',
+    projectPath,
+  });
+
+  const autoLoadClaudeMd = await getAutoLoadClaudeMdSetting(
+    projectPath,
+    settingsService,
+    '[SpecSync]'
+  );
+
+  const settings = await settingsService?.getGlobalSettings();
+  const phaseModelEntry =
+    settings?.phaseModels?.specGenerationModel || DEFAULT_PHASE_MODELS.specGenerationModel;
+  const { model, thinkingLevel } = resolvePhaseModel(phaseModelEntry);
+
+  // Get active Claude API profile for alternative endpoint configuration
+  const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+    settingsService,
+    '[SpecSync]'
+  );
+
+  // Use AI to analyze tech stack
+  const techAnalysisPrompt = `Analyze this project and return ONLY a JSON object with the current technology stack.
+
+Current known technologies: ${currentTechStack.join(', ')}
+
+Look at package.json, config files, and source code to identify:
+- Frameworks (React, Vue, Express, etc.)
+- Languages (TypeScript, JavaScript, Python, etc.)
+- Build tools (Vite, Webpack, etc.)
+- Databases (PostgreSQL, MongoDB, etc.)
+- Key libraries and tools
+
+Return ONLY this JSON format, no other text:
+{
+  "technologies": ["Technology 1", "Technology 2", ...]
+}`;
+
+  try {
+    const techResult = await streamingQuery({
+      prompt: techAnalysisPrompt,
+      model,
+      cwd: projectPath,
+      maxTurns: 10,
+      allowedTools: ['Read', 'Glob', 'Grep'],
+      abortController,
+      thinkingLevel,
+      readOnly: true,
+      settingSources: autoLoadClaudeMd ? ['user', 'project', 'local'] : undefined,
+      claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+      credentials, // Pass credentials for resolving 'credentials' apiKeySource
+      onText: (text) => {
+        logger.debug(`Tech analysis text: ${text.substring(0, 100)}`);
+      },
+    });
+
+    // Parse tech stack from response
+    const jsonMatch = techResult.text.match(/\{[\s\S]*"technologies"[\s\S]*\}/);
+    if (jsonMatch) {
+      const parsed = JSON.parse(jsonMatch[0]);
+      if (Array.isArray(parsed.technologies)) {
+        const newTechStack = parsed.technologies as string[];
+
+        // Calculate differences
+        const currentSet = new Set(currentTechStack.map((t) => t.toLowerCase()));
+        const newSet = new Set(newTechStack.map((t) => t.toLowerCase()));
+
+        for (const tech of newTechStack) {
+          if (!currentSet.has(tech.toLowerCase())) {
+            result.techStackUpdates.added.push(tech);
+          }
+        }
+
+        for (const tech of currentTechStack) {
+          if (!newSet.has(tech.toLowerCase())) {
+            result.techStackUpdates.removed.push(tech);
+          }
+        }
+
+        // Update spec with new tech stack if there are changes
+        if (
+          result.techStackUpdates.added.length > 0 ||
+          result.techStackUpdates.removed.length > 0
+        ) {
+          specContent = updateTechnologyStack(specContent, newTechStack);
+          logger.info(
+            `Updated tech stack: +${result.techStackUpdates.added.length}, -${result.techStackUpdates.removed.length}`
+          );
+        }
+      }
+    }
+  } catch (error) {
+    logger.warn('Failed to analyze tech stack:', error);
+    // Continue with other sync operations
+  }
+
+  // Update roadmap phase statuses based on completed features
+  events.emit('spec-regeneration:event', {
+    type: 'spec_regeneration_progress',
+    content: 'Checking roadmap phase statuses...\n',
+    projectPath,
+  });
+
+  // For each phase, check if all its features are completed
+  // This is a heuristic - we check if the phase name appears in any feature titles/descriptions
+  for (const phase of currentRoadmapPhases) {
+    if (phase.status === 'completed') continue; // Already completed
+
+    // Check if this phase should be marked as completed
+    // A phase is considered complete if we have completed features that mention it
+    const phaseNameLower = phase.name.toLowerCase();
+    const relatedCompletedFeatures = completedFeatures.filter(
+      (f) =>
+        f.title?.toLowerCase().includes(phaseNameLower) ||
+        f.description?.toLowerCase().includes(phaseNameLower) ||
+        f.category?.toLowerCase().includes(phaseNameLower)
+    );
+
+    // If we have related completed features and the phase is still pending/in_progress,
+    // update it to in_progress or completed based on feature count
+    if (relatedCompletedFeatures.length > 0 && phase.status !== 'completed') {
+      const newStatus = 'in_progress';
+      specContent = updateRoadmapPhaseStatus(specContent, phase.name, newStatus);
+      result.roadmapUpdates.push({ phaseName: phase.name, newStatus });
+      logger.info(`Updated phase "${phase.name}" to ${newStatus}`);
+    }
+  }
+
+  // Save updated spec
+  await secureFs.writeFile(specPath, specContent, 'utf-8');
+  logger.info('Spec saved successfully');
+
+  // Build summary
+  const summaryParts: string[] = [];
+  if (result.implementedFeaturesUpdates.addedFromFeatures.length > 0) {
+    summaryParts.push(
+      `Added ${result.implementedFeaturesUpdates.addedFromFeatures.length} implemented features`
+    );
+  }
+  if (result.techStackUpdates.added.length > 0) {
+    summaryParts.push(`Added ${result.techStackUpdates.added.length} technologies`);
+  }
+  if (result.techStackUpdates.removed.length > 0) {
+    summaryParts.push(`Removed ${result.techStackUpdates.removed.length} technologies`);
+  }
+  if (result.roadmapUpdates.length > 0) {
+    summaryParts.push(`Updated ${result.roadmapUpdates.length} roadmap phases`);
+  }
+
+  result.summary = summaryParts.length > 0 ? summaryParts.join(', ') : 'Spec is already up to date';
+
+  // Create notification
+  const notificationService = getNotificationService();
+  await notificationService.createNotification({
+    type: 'spec_regeneration_complete',
+    title: 'Spec Sync Complete',
+    message: result.summary,
+    projectPath,
+  });
+
+  events.emit('spec-regeneration:event', {
+    type: 'spec_regeneration_complete',
+    message: `Spec sync complete! ${result.summary}`,
+    projectPath,
+  });
+
+  logger.info('========== syncSpec() completed ==========');
+  logger.info('Summary:', result.summary);
+
+  return result;
+}

apps/server/src/routes/auth/index.ts

@@ -117,9 +117,27 @@ export function createAuthRoutes(): Router {
    *
    * Returns whether the current request is authenticated.
    * Used by the UI to determine if login is needed.
+   *
+   * If AUTOMAKER_AUTO_LOGIN=true is set, automatically creates a session
+   * for unauthenticated requests (useful for development).
    */
-  router.get('/status', (req, res) => {
-    const authenticated = isRequestAuthenticated(req);
+  router.get('/status', async (req, res) => {
+    let authenticated = isRequestAuthenticated(req);
+
+    // Auto-login for development: create session automatically if enabled
+    // Only works in non-production environments as a safeguard
+    if (
+      !authenticated &&
+      process.env.AUTOMAKER_AUTO_LOGIN === 'true' &&
+      process.env.NODE_ENV !== 'production'
+    ) {
+      const sessionToken = await createSession();
+      const cookieOptions = getSessionCookieOptions();
+      const cookieName = getSessionCookieName();
+      res.cookie(cookieName, sessionToken, cookieOptions);
+      authenticated = true;
+    }
+
     res.json({
       success: true,
       authenticated,

apps/server/src/routes/auto-mode/index.ts

@@ -10,6 +10,8 @@ import { validatePathParams } from '../../middleware/validate-paths.js';
 import { createStopFeatureHandler } from './routes/stop-feature.js';
 import { createStatusHandler } from './routes/status.js';
 import { createRunFeatureHandler } from './routes/run-feature.js';
+import { createStartHandler } from './routes/start.js';
+import { createStopHandler } from './routes/stop.js';
 import { createVerifyFeatureHandler } from './routes/verify-feature.js';
 import { createResumeFeatureHandler } from './routes/resume-feature.js';
 import { createContextExistsHandler } from './routes/context-exists.js';
@@ -22,6 +24,10 @@ import { createResumeInterruptedHandler } from './routes/resume-interrupted.js';
 export function createAutoModeRoutes(autoModeService: AutoModeService): Router {
   const router = Router();
 
+  // Auto loop control routes
+  router.post('/start', validatePathParams('projectPath'), createStartHandler(autoModeService));
+  router.post('/stop', validatePathParams('projectPath'), createStopHandler(autoModeService));
+
   router.post('/stop-feature', createStopFeatureHandler(autoModeService));
   router.post('/status', validatePathParams('projectPath?'), createStatusHandler(autoModeService));
   router.post(

apps/server/src/routes/auto-mode/routes/start.ts

@@ -0,0 +1,54 @@
+/**
+ * POST /start endpoint - Start auto mode loop for a project
+ */
+
+import type { Request, Response } from 'express';
+import type { AutoModeService } from '../../../services/auto-mode-service.js';
+import { createLogger } from '@automaker/utils';
+import { getErrorMessage, logError } from '../common.js';
+
+const logger = createLogger('AutoMode');
+
+export function createStartHandler(autoModeService: AutoModeService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, maxConcurrency } = req.body as {
+        projectPath: string;
+        maxConcurrency?: number;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({
+          success: false,
+          error: 'projectPath is required',
+        });
+        return;
+      }
+
+      // Check if already running
+      if (autoModeService.isAutoLoopRunningForProject(projectPath)) {
+        res.json({
+          success: true,
+          message: 'Auto mode is already running for this project',
+          alreadyRunning: true,
+        });
+        return;
+      }
+
+      // Start the auto loop for this project
+      await autoModeService.startAutoLoopForProject(projectPath, maxConcurrency ?? 3);
+
+      logger.info(
+        `Started auto loop for project: ${projectPath} with maxConcurrency: ${maxConcurrency ?? 3}`
+      );
+
+      res.json({
+        success: true,
+        message: `Auto mode started with max ${maxConcurrency ?? 3} concurrent features`,
+      });
+    } catch (error) {
+      logError(error, 'Start auto mode failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/auto-mode/routes/status.ts

@@ -1,5 +1,8 @@
 /**
  * POST /status endpoint - Get auto mode status
+ *
+ * If projectPath is provided, returns per-project status including autoloop state.
+ * If no projectPath, returns global status for backward compatibility.
  */
 
 import type { Request, Response } from 'express';
@@ -9,10 +12,30 @@ import { getErrorMessage, logError } from '../common.js';
 export function createStatusHandler(autoModeService: AutoModeService) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
+      const { projectPath } = req.body as { projectPath?: string };
+
+      // If projectPath is provided, return per-project status
+      if (projectPath) {
+        const projectStatus = autoModeService.getStatusForProject(projectPath);
+        res.json({
+          success: true,
+          isRunning: projectStatus.runningCount > 0,
+          isAutoLoopRunning: projectStatus.isAutoLoopRunning,
+          runningFeatures: projectStatus.runningFeatures,
+          runningCount: projectStatus.runningCount,
+          maxConcurrency: projectStatus.maxConcurrency,
+          projectPath,
+        });
+        return;
+      }
+
+      // Fall back to global status for backward compatibility
       const status = autoModeService.getStatus();
+      const activeProjects = autoModeService.getActiveAutoLoopProjects();
       res.json({
         success: true,
         ...status,
+        activeAutoLoopProjects: activeProjects,
       });
     } catch (error) {
       logError(error, 'Get status failed');

apps/server/src/routes/auto-mode/routes/stop.ts

@@ -0,0 +1,54 @@
+/**
+ * POST /stop endpoint - Stop auto mode loop for a project
+ */
+
+import type { Request, Response } from 'express';
+import type { AutoModeService } from '../../../services/auto-mode-service.js';
+import { createLogger } from '@automaker/utils';
+import { getErrorMessage, logError } from '../common.js';
+
+const logger = createLogger('AutoMode');
+
+export function createStopHandler(autoModeService: AutoModeService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath } = req.body as {
+        projectPath: string;
+      };
+
+      if (!projectPath) {
+        res.status(400).json({
+          success: false,
+          error: 'projectPath is required',
+        });
+        return;
+      }
+
+      // Check if running
+      if (!autoModeService.isAutoLoopRunningForProject(projectPath)) {
+        res.json({
+          success: true,
+          message: 'Auto mode is not running for this project',
+          wasRunning: false,
+        });
+        return;
+      }
+
+      // Stop the auto loop for this project
+      const runningCount = await autoModeService.stopAutoLoopForProject(projectPath);
+
+      logger.info(
+        `Stopped auto loop for project: ${projectPath}, ${runningCount} features still running`
+      );
+
+      res.json({
+        success: true,
+        message: 'Auto mode stopped',
+        runningFeaturesCount: runningCount,
+      });
+    } catch (error) {
+      logError(error, 'Stop auto mode failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/backlog-plan/common.ts

@@ -3,12 +3,31 @@
  */
 
 import { createLogger } from '@automaker/utils';
+import { ensureAutomakerDir, getAutomakerDir } from '@automaker/platform';
+import * as secureFs from '../../lib/secure-fs.js';
+import path from 'path';
+import type { BacklogPlanResult } from '@automaker/types';
 
 const logger = createLogger('BacklogPlan');
 
 // State for tracking running generation
 let isRunning = false;
 let currentAbortController: AbortController | null = null;
+let runningDetails: {
+  projectPath: string;
+  prompt: string;
+  model?: string;
+  startedAt: string;
+} | null = null;
+
+const BACKLOG_PLAN_FILENAME = 'backlog-plan.json';
+
+export interface StoredBacklogPlan {
+  savedAt: string;
+  prompt: string;
+  model?: string;
+  result: BacklogPlanResult;
+}
 
 export function getBacklogPlanStatus(): { isRunning: boolean } {
   return { isRunning };
@@ -16,20 +35,125 @@ export function getBacklogPlanStatus(): { isRunning: boolean } {
 
 export function setRunningState(running: boolean, abortController?: AbortController | null): void {
   isRunning = running;
+  if (!running) {
+    runningDetails = null;
+  }
   if (abortController !== undefined) {
     currentAbortController = abortController;
   }
 }
 
+export function setRunningDetails(
+  details: {
+    projectPath: string;
+    prompt: string;
+    model?: string;
+    startedAt: string;
+  } | null
+): void {
+  runningDetails = details;
+}
+
+export function getRunningDetails(): {
+  projectPath: string;
+  prompt: string;
+  model?: string;
+  startedAt: string;
+} | null {
+  return runningDetails;
+}
+
+function getBacklogPlanPath(projectPath: string): string {
+  return path.join(getAutomakerDir(projectPath), BACKLOG_PLAN_FILENAME);
+}
+
+export async function saveBacklogPlan(projectPath: string, plan: StoredBacklogPlan): Promise<void> {
+  await ensureAutomakerDir(projectPath);
+  const filePath = getBacklogPlanPath(projectPath);
+  await secureFs.writeFile(filePath, JSON.stringify(plan, null, 2), 'utf-8');
+}
+
+export async function loadBacklogPlan(projectPath: string): Promise<StoredBacklogPlan | null> {
+  try {
+    const filePath = getBacklogPlanPath(projectPath);
+    const raw = await secureFs.readFile(filePath, 'utf-8');
+    const parsed = JSON.parse(raw as string) as StoredBacklogPlan;
+    if (!Array.isArray(parsed?.result?.changes)) {
+      return null;
+    }
+    return parsed;
+  } catch {
+    return null;
+  }
+}
+
+export async function clearBacklogPlan(projectPath: string): Promise<void> {
+  try {
+    const filePath = getBacklogPlanPath(projectPath);
+    await secureFs.unlink(filePath);
+  } catch {
+    // ignore missing file
+  }
+}
+
 export function getAbortController(): AbortController | null {
   return currentAbortController;
 }
 
-export function getErrorMessage(error: unknown): string {
-  if (error instanceof Error) {
-    return error.message;
+/**
+ * Map SDK/CLI errors to user-friendly messages
+ */
+export function mapBacklogPlanError(rawMessage: string): string {
+  // Claude Code spawn failures
+  if (
+    rawMessage.includes('Failed to spawn Claude Code process') ||
+    rawMessage.includes('spawn node ENOENT') ||
+    rawMessage.includes('Claude Code executable not found') ||
+    rawMessage.includes('Claude Code native binary not found')
+  ) {
+    return 'Claude CLI could not be launched. Make sure the Claude CLI is installed and available in PATH, or check that Node.js is correctly installed. Try running "which claude" or "claude --version" in your terminal to verify.';
   }
-  return String(error);
+
+  // Claude Code process crash
+  if (rawMessage.includes('Claude Code process exited')) {
+    return 'Claude exited unexpectedly. Try again. If it keeps happening, re-run `claude login` or update your API key in Setup.';
+  }
+
+  // Rate limiting
+  if (rawMessage.toLowerCase().includes('rate limit') || rawMessage.includes('429')) {
+    return 'Rate limited. Please wait a moment and try again.';
+  }
+
+  // Network errors
+  if (
+    rawMessage.toLowerCase().includes('network') ||
+    rawMessage.toLowerCase().includes('econnrefused') ||
+    rawMessage.toLowerCase().includes('timeout')
+  ) {
+    return 'Network error. Check your internet connection and try again.';
+  }
+
+  // Authentication errors
+  if (
+    rawMessage.toLowerCase().includes('not authenticated') ||
+    rawMessage.toLowerCase().includes('unauthorized') ||
+    rawMessage.includes('401')
+  ) {
+    return 'Authentication failed. Please check your API key or run `claude login` to authenticate.';
+  }
+
+  // Return original message for unknown errors
+  return rawMessage;
+}
+
+export function getErrorMessage(error: unknown): string {
+  let rawMessage: string;
+  if (error instanceof Error) {
+    rawMessage = error.message;
+  } else {
+    rawMessage = String(error);
+  }
+  return mapBacklogPlanError(rawMessage);
 }
 
 export function logError(error: unknown, context: string): void {

apps/server/src/routes/backlog-plan/generate-plan.ts

@@ -17,9 +17,19 @@ import { resolvePhaseModel } from '@automaker/model-resolver';
 import { FeatureLoader } from '../../services/feature-loader.js';
 import { ProviderFactory } from '../../providers/provider-factory.js';
 import { extractJsonWithArray } from '../../lib/json-extractor.js';
-import { logger, setRunningState, getErrorMessage } from './common.js';
+import {
+  logger,
+  setRunningState,
+  setRunningDetails,
+  getErrorMessage,
+  saveBacklogPlan,
+} from './common.js';
 import type { SettingsService } from '../../services/settings-service.js';
-import { getAutoLoadClaudeMdSetting, getPromptCustomization } from '../../lib/settings-helpers.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getPromptCustomization,
+  getActiveClaudeApiProfile,
+} from '../../lib/settings-helpers.js';
 
 const featureLoader = new FeatureLoader();
 
@@ -155,6 +165,12 @@ ${userPrompt}`;
       finalSystemPrompt = undefined; // System prompt is now embedded in the user prompt
     }
 
+    // Get active Claude API profile for alternative endpoint configuration
+    const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+      settingsService,
+      '[BacklogPlan]'
+    );
+
     // Execute the query
     const stream = provider.executeQuery({
       prompt: finalPrompt,
@@ -167,6 +183,8 @@ ${userPrompt}`;
       settingSources: autoLoadClaudeMd ? ['user', 'project'] : undefined,
       readOnly: true, // Plan generation only generates text, doesn't write files
       thinkingLevel, // Pass thinking level for extended thinking
+      claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+      credentials, // Pass credentials for resolving 'credentials' apiKeySource
     });
 
     let responseText = '';
@@ -200,6 +218,13 @@ ${userPrompt}`;
     // Parse the response
     const result = parsePlanResponse(responseText);
 
+    await saveBacklogPlan(projectPath, {
+      savedAt: new Date().toISOString(),
+      prompt,
+      model: effectiveModel,
+      result,
+    });
+
     events.emit('backlog-plan:event', {
       type: 'backlog_plan_complete',
       result,
@@ -218,5 +243,6 @@ ${userPrompt}`;
     throw error;
   } finally {
     setRunningState(false, null);
+    setRunningDetails(null);
   }
 }

apps/server/src/routes/backlog-plan/index.ts

@@ -9,6 +9,7 @@ import { createGenerateHandler } from './routes/generate.js';
 import { createStopHandler } from './routes/stop.js';
 import { createStatusHandler } from './routes/status.js';
 import { createApplyHandler } from './routes/apply.js';
+import { createClearHandler } from './routes/clear.js';
 import type { SettingsService } from '../../services/settings-service.js';
 
 export function createBacklogPlanRoutes(
@@ -23,8 +24,9 @@ export function createBacklogPlanRoutes(
     createGenerateHandler(events, settingsService)
   );
   router.post('/stop', createStopHandler());
-  router.get('/status', createStatusHandler());
+  router.get('/status', validatePathParams('projectPath'), createStatusHandler());
   router.post('/apply', validatePathParams('projectPath'), createApplyHandler());
+  router.post('/clear', validatePathParams('projectPath'), createClearHandler());
 
   return router;
 }

apps/server/src/routes/backlog-plan/routes/apply.ts

@@ -5,7 +5,7 @@
 import type { Request, Response } from 'express';
 import type { BacklogPlanResult, BacklogChange, Feature } from '@automaker/types';
 import { FeatureLoader } from '../../../services/feature-loader.js';
-import { getErrorMessage, logError, logger } from '../common.js';
+import { clearBacklogPlan, getErrorMessage, logError, logger } from '../common.js';
 
 const featureLoader = new FeatureLoader();
 
@@ -147,6 +147,17 @@ export function createApplyHandler() {
         }
       }
 
+      // Clear the plan before responding
+      try {
+        await clearBacklogPlan(projectPath);
+      } catch (error) {
+        logger.warn(
+          `[BacklogPlan] Failed to clear backlog plan after apply:`,
+          getErrorMessage(error)
+        );
+        // Don't throw - operation succeeded, just cleanup failed
+      }
+
       res.json({
         success: true,
         appliedChanges,

apps/server/src/routes/backlog-plan/routes/clear.ts

@@ -0,0 +1,25 @@
+/**
+ * POST /clear endpoint - Clear saved backlog plan
+ */
+
+import type { Request, Response } from 'express';
+import { clearBacklogPlan, getErrorMessage, logError } from '../common.js';
+
+export function createClearHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath } = req.body as { projectPath: string };
+
+      if (!projectPath) {
+        res.status(400).json({ success: false, error: 'projectPath required' });
+        return;
+      }
+
+      await clearBacklogPlan(projectPath);
+      res.json({ success: true });
+    } catch (error) {
+      logError(error, 'Clear backlog plan failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/backlog-plan/routes/generate.ts

@@ -4,7 +4,13 @@
 
 import type { Request, Response } from 'express';
 import type { EventEmitter } from '../../../lib/events.js';
-import { getBacklogPlanStatus, setRunningState, getErrorMessage, logError } from '../common.js';
+import {
+  getBacklogPlanStatus,
+  setRunningState,
+  setRunningDetails,
+  getErrorMessage,
+  logError,
+} from '../common.js';
 import { generateBacklogPlan } from '../generate-plan.js';
 import type { SettingsService } from '../../../services/settings-service.js';
 
@@ -37,20 +43,26 @@ export function createGenerateHandler(events: EventEmitter, settingsService?: Se
       }
 
       setRunningState(true);
+      setRunningDetails({
+        projectPath,
+        prompt,
+        model,
+        startedAt: new Date().toISOString(),
+      });
       const abortController = new AbortController();
       setRunningState(true, abortController);
 
       // Start generation in background
+      // Note: generateBacklogPlan handles its own error event emission,
+      // so we only log here to avoid duplicate error toasts
       generateBacklogPlan(projectPath, prompt, events, abortController, settingsService, model)
         .catch((error) => {
+          // Just log - error event already emitted by generateBacklogPlan
           logError(error, 'Generate backlog plan failed (background)');
-          events.emit('backlog-plan:event', {
-            type: 'backlog_plan_error',
-            error: getErrorMessage(error),
-          });
         })
         .finally(() => {
           setRunningState(false, null);
+          setRunningDetails(null);
         });
 
       res.json({ success: true });

apps/server/src/routes/backlog-plan/routes/status.ts

@@ -3,13 +3,15 @@
  */
 
 import type { Request, Response } from 'express';
-import { getBacklogPlanStatus, getErrorMessage, logError } from '../common.js';
+import { getBacklogPlanStatus, loadBacklogPlan, getErrorMessage, logError } from '../common.js';
 
 export function createStatusHandler() {
-  return async (_req: Request, res: Response): Promise<void> => {
+  return async (req: Request, res: Response): Promise<void> => {
     try {
       const status = getBacklogPlanStatus();
-      res.json({ success: true, ...status });
+      const projectPath = typeof req.query.projectPath === 'string' ? req.query.projectPath : '';
+      const savedPlan = projectPath ? await loadBacklogPlan(projectPath) : null;
+      res.json({ success: true, ...status, savedPlan });
     } catch (error) {
       logError(error, 'Get backlog plan status failed');
       res.status(500).json({ success: false, error: getErrorMessage(error) });

apps/server/src/routes/backlog-plan/routes/stop.ts

@@ -3,7 +3,13 @@
  */
 
 import type { Request, Response } from 'express';
-import { getAbortController, setRunningState, getErrorMessage, logError } from '../common.js';
+import {
+  getAbortController,
+  setRunningState,
+  setRunningDetails,
+  getErrorMessage,
+  logError,
+} from '../common.js';
 
 export function createStopHandler() {
   return async (_req: Request, res: Response): Promise<void> => {
@@ -12,6 +18,7 @@ export function createStopHandler() {
       if (abortController) {
         abortController.abort();
         setRunningState(false, null);
+        setRunningDetails(null);
       }
       res.json({ success: true });
     } catch (error) {

apps/server/src/routes/context/routes/describe-file.ts

@@ -19,7 +19,11 @@ import { simpleQuery } from '../../../providers/simple-query-service.js';
 import * as secureFs from '../../../lib/secure-fs.js';
 import * as path from 'path';
 import type { SettingsService } from '../../../services/settings-service.js';
-import { getAutoLoadClaudeMdSetting } from '../../../lib/settings-helpers.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getPromptCustomization,
+  getActiveClaudeApiProfile,
+} from '../../../lib/settings-helpers.js';
 
 const logger = createLogger('DescribeFile');
 
@@ -130,11 +134,12 @@ export function createDescribeFileHandler(
       // Get the filename for context
       const fileName = path.basename(resolvedPath);
 
+      // Get customized prompts from settings
+      const prompts = await getPromptCustomization(settingsService, '[DescribeFile]');
+
       // Build prompt with file content passed as structured data
       // The file content is included directly, not via tool invocation
-      const prompt = `Analyze the following file and provide a 1-2 sentence description suitable for use as context in an AI coding assistant. Focus on what the file contains, its purpose, and why an AI agent might want to use this context in the future (e.g., "API documentation for the authentication endpoints", "Configuration file for database connections", "Coding style guidelines for the project").
-
-Respond with ONLY the description text, no additional formatting, preamble, or explanation.
+      const prompt = `${prompts.contextDescription.describeFilePrompt}
 
 File: ${fileName}${truncated ? ' (truncated)' : ''}
 
@@ -161,6 +166,12 @@ ${contentToAnalyze}`;
 
       logger.info(`Resolved model: ${model}, thinkingLevel: ${thinkingLevel}`);
 
+      // Get active Claude API profile for alternative endpoint configuration
+      const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+        settingsService,
+        '[DescribeFile]'
+      );
+
       // Use simpleQuery - provider abstraction handles routing to correct provider
       const result = await simpleQuery({
         prompt,
@@ -171,6 +182,8 @@ ${contentToAnalyze}`;
         thinkingLevel,
         readOnly: true, // File description only reads, doesn't write
         settingSources: autoLoadClaudeMd ? ['user', 'project', 'local'] : undefined,
+        claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+        credentials, // Pass credentials for resolving 'credentials' apiKeySource
       });
 
       const description = result.text;

apps/server/src/routes/context/routes/describe-image.ts

@@ -19,7 +19,11 @@ import { simpleQuery } from '../../../providers/simple-query-service.js';
 import * as secureFs from '../../../lib/secure-fs.js';
 import * as path from 'path';
 import type { SettingsService } from '../../../services/settings-service.js';
-import { getAutoLoadClaudeMdSetting } from '../../../lib/settings-helpers.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getPromptCustomization,
+  getActiveClaudeApiProfile,
+} from '../../../lib/settings-helpers.js';
 
 const logger = createLogger('DescribeImage');
 
@@ -278,12 +282,17 @@ export function createDescribeImageHandler(
 
       logger.info(`[${requestId}] Using model: ${model}`);
 
-      // Build the instruction text
-      const instructionText =
-        `Describe this image in 1-2 sentences suitable for use as context in an AI coding assistant. ` +
-        `Focus on what the image shows and its purpose (e.g., "UI mockup showing login form with email/password fields", ` +
-        `"Architecture diagram of microservices", "Screenshot of error message in terminal").\n\n` +
-        `Respond with ONLY the description text, no additional formatting, preamble, or explanation.`;
+      // Get customized prompts from settings
+      const prompts = await getPromptCustomization(settingsService, '[DescribeImage]');
+
+      // Get active Claude API profile for alternative endpoint configuration
+      const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+        settingsService,
+        '[DescribeImage]'
+      );
+
+      // Build the instruction text from centralized prompts
+      const instructionText = prompts.contextDescription.describeImagePrompt;
 
       // Build prompt based on provider capability
       // Some providers (like Cursor) may not support image content blocks
@@ -323,6 +332,8 @@ export function createDescribeImageHandler(
         thinkingLevel,
         readOnly: true, // Image description only reads, doesn't write
         settingSources: autoLoadClaudeMd ? ['user', 'project', 'local'] : undefined,
+        claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+        credentials, // Pass credentials for resolving 'credentials' apiKeySource
       });
 
       logger.info(`[${requestId}] simpleQuery completed in ${Date.now() - queryStart}ms`);

apps/server/src/routes/enhance-prompt/routes/enhance.ts

@@ -12,7 +12,10 @@ import { resolveModelString } from '@automaker/model-resolver';
 import { CLAUDE_MODEL_MAP, type ThinkingLevel } from '@automaker/types';
 import { simpleQuery } from '../../../providers/simple-query-service.js';
 import type { SettingsService } from '../../../services/settings-service.js';
-import { getPromptCustomization } from '../../../lib/settings-helpers.js';
+import {
+  getPromptCustomization,
+  getActiveClaudeApiProfile,
+} from '../../../lib/settings-helpers.js';
 import {
   buildUserPrompt,
   isValidEnhancementMode,
@@ -126,6 +129,12 @@ export function createEnhanceHandler(
 
       logger.debug(`Using model: ${resolvedModel}`);
 
+      // Get active Claude API profile for alternative endpoint configuration
+      const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+        settingsService,
+        '[EnhancePrompt]'
+      );
+
       // Use simpleQuery - provider abstraction handles routing to correct provider
       // The system prompt is combined with user prompt since some providers
       // don't have a separate system prompt concept
@@ -137,6 +146,8 @@ export function createEnhanceHandler(
         allowedTools: [],
         thinkingLevel,
         readOnly: true, // Prompt enhancement only generates text, doesn't write files
+        claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+        credentials, // Pass credentials for resolving 'credentials' apiKeySource
       });
 
       const enhancedText = result.text;

apps/server/src/routes/event-history/common.ts

@@ -0,0 +1,19 @@
+/**
+ * Common utilities for event history routes
+ */
+
+import { createLogger } from '@automaker/utils';
+import { getErrorMessage as getErrorMessageShared, createLogError } from '../common.js';
+
+/** Logger instance for event history operations */
+export const logger = createLogger('EventHistory');
+
+/**
+ * Extract user-friendly error message from error objects
+ */
+export { getErrorMessageShared as getErrorMessage };
+
+/**
+ * Log error with automatic logger binding
+ */
+export const logError = createLogError(logger);

apps/server/src/routes/event-history/index.ts

@@ -0,0 +1,68 @@
+/**
+ * Event History routes - HTTP API for event history management
+ *
+ * Provides endpoints for:
+ * - Listing events with filtering
+ * - Getting individual event details
+ * - Deleting events
+ * - Clearing all events
+ * - Replaying events to test hooks
+ *
+ * Mounted at /api/event-history in the main server.
+ */
+
+import { Router } from 'express';
+import type { EventHistoryService } from '../../services/event-history-service.js';
+import type { SettingsService } from '../../services/settings-service.js';
+import { validatePathParams } from '../../middleware/validate-paths.js';
+import { createListHandler } from './routes/list.js';
+import { createGetHandler } from './routes/get.js';
+import { createDeleteHandler } from './routes/delete.js';
+import { createClearHandler } from './routes/clear.js';
+import { createReplayHandler } from './routes/replay.js';
+
+/**
+ * Create event history router with all endpoints
+ *
+ * Endpoints:
+ * - POST /list - List events with optional filtering
+ * - POST /get - Get a single event by ID
+ * - POST /delete - Delete an event by ID
+ * - POST /clear - Clear all events for a project
+ * - POST /replay - Replay an event to trigger hooks
+ *
+ * @param eventHistoryService - Instance of EventHistoryService
+ * @param settingsService - Instance of SettingsService (for replay)
+ * @returns Express Router configured with all event history endpoints
+ */
+export function createEventHistoryRoutes(
+  eventHistoryService: EventHistoryService,
+  settingsService: SettingsService
+): Router {
+  const router = Router();
+
+  // List events with filtering
+  router.post('/list', validatePathParams('projectPath'), createListHandler(eventHistoryService));
+
+  // Get single event
+  router.post('/get', validatePathParams('projectPath'), createGetHandler(eventHistoryService));
+
+  // Delete event
+  router.post(
+    '/delete',
+    validatePathParams('projectPath'),
+    createDeleteHandler(eventHistoryService)
+  );
+
+  // Clear all events
+  router.post('/clear', validatePathParams('projectPath'), createClearHandler(eventHistoryService));
+
+  // Replay event
+  router.post(
+    '/replay',
+    validatePathParams('projectPath'),
+    createReplayHandler(eventHistoryService, settingsService)
+  );
+
+  return router;
+}

apps/server/src/routes/event-history/routes/clear.ts

@@ -0,0 +1,33 @@
+/**
+ * POST /api/event-history/clear - Clear all events for a project
+ *
+ * Request body: { projectPath: string }
+ * Response: { success: true, cleared: number }
+ */
+
+import type { Request, Response } from 'express';
+import type { EventHistoryService } from '../../../services/event-history-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createClearHandler(eventHistoryService: EventHistoryService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath } = req.body as { projectPath: string };
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      const cleared = await eventHistoryService.clearEvents(projectPath);
+
+      res.json({
+        success: true,
+        cleared,
+      });
+    } catch (error) {
+      logError(error, 'Clear events failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/event-history/routes/delete.ts

@@ -0,0 +1,43 @@
+/**
+ * POST /api/event-history/delete - Delete an event by ID
+ *
+ * Request body: { projectPath: string, eventId: string }
+ * Response: { success: true } or { success: false, error: string }
+ */
+
+import type { Request, Response } from 'express';
+import type { EventHistoryService } from '../../../services/event-history-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createDeleteHandler(eventHistoryService: EventHistoryService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, eventId } = req.body as {
+        projectPath: string;
+        eventId: string;
+      };
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!eventId || typeof eventId !== 'string') {
+        res.status(400).json({ success: false, error: 'eventId is required' });
+        return;
+      }
+
+      const deleted = await eventHistoryService.deleteEvent(projectPath, eventId);
+
+      if (!deleted) {
+        res.status(404).json({ success: false, error: 'Event not found' });
+        return;
+      }
+
+      res.json({ success: true });
+    } catch (error) {
+      logError(error, 'Delete event failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/event-history/routes/get.ts

@@ -0,0 +1,46 @@
+/**
+ * POST /api/event-history/get - Get a single event by ID
+ *
+ * Request body: { projectPath: string, eventId: string }
+ * Response: { success: true, event: StoredEvent } or { success: false, error: string }
+ */
+
+import type { Request, Response } from 'express';
+import type { EventHistoryService } from '../../../services/event-history-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createGetHandler(eventHistoryService: EventHistoryService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, eventId } = req.body as {
+        projectPath: string;
+        eventId: string;
+      };
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!eventId || typeof eventId !== 'string') {
+        res.status(400).json({ success: false, error: 'eventId is required' });
+        return;
+      }
+
+      const event = await eventHistoryService.getEvent(projectPath, eventId);
+
+      if (!event) {
+        res.status(404).json({ success: false, error: 'Event not found' });
+        return;
+      }
+
+      res.json({
+        success: true,
+        event,
+      });
+    } catch (error) {
+      logError(error, 'Get event failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/event-history/routes/list.ts

@@ -0,0 +1,53 @@
+/**
+ * POST /api/event-history/list - List events for a project
+ *
+ * Request body: {
+ *   projectPath: string,
+ *   filter?: {
+ *     trigger?: EventHookTrigger,
+ *     featureId?: string,
+ *     since?: string,
+ *     until?: string,
+ *     limit?: number,
+ *     offset?: number
+ *   }
+ * }
+ * Response: { success: true, events: StoredEventSummary[], total: number }
+ */
+
+import type { Request, Response } from 'express';
+import type { EventHistoryService } from '../../../services/event-history-service.js';
+import type { EventHistoryFilter } from '@automaker/types';
+import { getErrorMessage, logError } from '../common.js';
+
+export function createListHandler(eventHistoryService: EventHistoryService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, filter } = req.body as {
+        projectPath: string;
+        filter?: EventHistoryFilter;
+      };
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      const events = await eventHistoryService.getEvents(projectPath, filter);
+      const total = await eventHistoryService.getEventCount(projectPath, {
+        ...filter,
+        limit: undefined,
+        offset: undefined,
+      });
+
+      res.json({
+        success: true,
+        events,
+        total,
+      });
+    } catch (error) {
+      logError(error, 'List events failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/event-history/routes/replay.ts

@@ -0,0 +1,234 @@
+/**
+ * POST /api/event-history/replay - Replay an event to trigger hooks
+ *
+ * Request body: {
+ *   projectPath: string,
+ *   eventId: string,
+ *   hookIds?: string[]  // Optional: specific hooks to run (if not provided, runs all enabled matching hooks)
+ * }
+ * Response: { success: true, result: EventReplayResult }
+ */
+
+import type { Request, Response } from 'express';
+import type { EventHistoryService } from '../../../services/event-history-service.js';
+import type { SettingsService } from '../../../services/settings-service.js';
+import type { EventReplayResult, EventReplayHookResult, EventHook } from '@automaker/types';
+import { exec } from 'child_process';
+import { promisify } from 'util';
+import { getErrorMessage, logError, logger } from '../common.js';
+
+const execAsync = promisify(exec);
+
+/** Default timeout for shell commands (30 seconds) */
+const DEFAULT_SHELL_TIMEOUT = 30000;
+
+/** Default timeout for HTTP requests (10 seconds) */
+const DEFAULT_HTTP_TIMEOUT = 10000;
+
+interface HookContext {
+  featureId?: string;
+  featureName?: string;
+  projectPath?: string;
+  projectName?: string;
+  error?: string;
+  errorType?: string;
+  timestamp: string;
+  eventType: string;
+}
+
+/**
+ * Substitute {{variable}} placeholders in a string
+ */
+function substituteVariables(template: string, context: HookContext): string {
+  return template.replace(/\{\{(\w+)\}\}/g, (match, variable) => {
+    const value = context[variable as keyof HookContext];
+    if (value === undefined || value === null) {
+      return '';
+    }
+    return String(value);
+  });
+}
+
+/**
+ * Execute a single hook and return the result
+ */
+async function executeHook(hook: EventHook, context: HookContext): Promise<EventReplayHookResult> {
+  const hookName = hook.name || hook.id;
+  const startTime = Date.now();
+
+  try {
+    if (hook.action.type === 'shell') {
+      const command = substituteVariables(hook.action.command, context);
+      const timeout = hook.action.timeout || DEFAULT_SHELL_TIMEOUT;
+
+      logger.info(`Replaying shell hook "${hookName}": ${command}`);
+
+      await execAsync(command, {
+        timeout,
+        maxBuffer: 1024 * 1024,
+      });
+
+      return {
+        hookId: hook.id,
+        hookName: hook.name,
+        success: true,
+        durationMs: Date.now() - startTime,
+      };
+    } else if (hook.action.type === 'http') {
+      const url = substituteVariables(hook.action.url, context);
+      const method = hook.action.method || 'POST';
+
+      const headers: Record<string, string> = {
+        'Content-Type': 'application/json',
+      };
+      if (hook.action.headers) {
+        for (const [key, value] of Object.entries(hook.action.headers)) {
+          headers[key] = substituteVariables(value, context);
+        }
+      }
+
+      let body: string | undefined;
+      if (hook.action.body) {
+        body = substituteVariables(hook.action.body, context);
+      } else if (method !== 'GET') {
+        body = JSON.stringify({
+          eventType: context.eventType,
+          timestamp: context.timestamp,
+          featureId: context.featureId,
+          projectPath: context.projectPath,
+          projectName: context.projectName,
+          error: context.error,
+        });
+      }
+
+      logger.info(`Replaying HTTP hook "${hookName}": ${method} ${url}`);
+
+      const controller = new AbortController();
+      const timeoutId = setTimeout(() => controller.abort(), DEFAULT_HTTP_TIMEOUT);
+
+      const response = await fetch(url, {
+        method,
+        headers,
+        body: method !== 'GET' ? body : undefined,
+        signal: controller.signal,
+      });
+
+      clearTimeout(timeoutId);
+
+      if (!response.ok) {
+        return {
+          hookId: hook.id,
+          hookName: hook.name,
+          success: false,
+          error: `HTTP ${response.status}: ${response.statusText}`,
+          durationMs: Date.now() - startTime,
+        };
+      }
+
+      return {
+        hookId: hook.id,
+        hookName: hook.name,
+        success: true,
+        durationMs: Date.now() - startTime,
+      };
+    }
+
+    return {
+      hookId: hook.id,
+      hookName: hook.name,
+      success: false,
+      error: 'Unknown hook action type',
+      durationMs: Date.now() - startTime,
+    };
+  } catch (error) {
+    const errorMessage =
+      error instanceof Error
+        ? error.name === 'AbortError'
+          ? 'Request timed out'
+          : error.message
+        : String(error);
+
+    return {
+      hookId: hook.id,
+      hookName: hook.name,
+      success: false,
+      error: errorMessage,
+      durationMs: Date.now() - startTime,
+    };
+  }
+}
+
+export function createReplayHandler(
+  eventHistoryService: EventHistoryService,
+  settingsService: SettingsService
+) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, eventId, hookIds } = req.body as {
+        projectPath: string;
+        eventId: string;
+        hookIds?: string[];
+      };
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      if (!eventId || typeof eventId !== 'string') {
+        res.status(400).json({ success: false, error: 'eventId is required' });
+        return;
+      }
+
+      // Get the event
+      const event = await eventHistoryService.getEvent(projectPath, eventId);
+      if (!event) {
+        res.status(404).json({ success: false, error: 'Event not found' });
+        return;
+      }
+
+      // Get hooks from settings
+      const settings = await settingsService.getGlobalSettings();
+      let hooks = settings.eventHooks || [];
+
+      // Filter to matching trigger and enabled hooks
+      hooks = hooks.filter((h) => h.enabled && h.trigger === event.trigger);
+
+      // If specific hook IDs requested, filter to those
+      if (hookIds && hookIds.length > 0) {
+        hooks = hooks.filter((h) => hookIds.includes(h.id));
+      }
+
+      // Build context for variable substitution
+      const context: HookContext = {
+        featureId: event.featureId,
+        featureName: event.featureName,
+        projectPath: event.projectPath,
+        projectName: event.projectName,
+        error: event.error,
+        errorType: event.errorType,
+        timestamp: event.timestamp,
+        eventType: event.trigger,
+      };
+
+      // Execute all hooks in parallel
+      const hookResults = await Promise.all(hooks.map((hook) => executeHook(hook, context)));
+
+      const result: EventReplayResult = {
+        eventId,
+        hooksTriggered: hooks.length,
+        hookResults,
+      };
+
+      logger.info(`Replayed event ${eventId}: ${hooks.length} hooks triggered`);
+
+      res.json({
+        success: true,
+        result,
+      });
+    } catch (error) {
+      logError(error, 'Replay event failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/features/index.ts

@@ -4,6 +4,8 @@
 
 import { Router } from 'express';
 import { FeatureLoader } from '../../services/feature-loader.js';
+import type { SettingsService } from '../../services/settings-service.js';
+import type { EventEmitter } from '../../lib/events.js';
 import { validatePathParams } from '../../middleware/validate-paths.js';
 import { createListHandler } from './routes/list.js';
 import { createGetHandler } from './routes/get.js';
@@ -15,12 +17,20 @@ import { createDeleteHandler } from './routes/delete.js';
 import { createAgentOutputHandler, createRawOutputHandler } from './routes/agent-output.js';
 import { createGenerateTitleHandler } from './routes/generate-title.js';
 
-export function createFeaturesRoutes(featureLoader: FeatureLoader): Router {
+export function createFeaturesRoutes(
+  featureLoader: FeatureLoader,
+  settingsService?: SettingsService,
+  events?: EventEmitter
+): Router {
   const router = Router();
 
   router.post('/list', validatePathParams('projectPath'), createListHandler(featureLoader));
   router.post('/get', validatePathParams('projectPath'), createGetHandler(featureLoader));
-  router.post('/create', validatePathParams('projectPath'), createCreateHandler(featureLoader));
+  router.post(
+    '/create',
+    validatePathParams('projectPath'),
+    createCreateHandler(featureLoader, events)
+  );
   router.post('/update', validatePathParams('projectPath'), createUpdateHandler(featureLoader));
   router.post(
     '/bulk-update',
@@ -35,7 +45,7 @@ export function createFeaturesRoutes(featureLoader: FeatureLoader): Router {
   router.post('/delete', validatePathParams('projectPath'), createDeleteHandler(featureLoader));
   router.post('/agent-output', createAgentOutputHandler(featureLoader));
   router.post('/raw-output', createRawOutputHandler(featureLoader));
-  router.post('/generate-title', createGenerateTitleHandler());
+  router.post('/generate-title', createGenerateTitleHandler(settingsService));
 
   return router;
 }

apps/server/src/routes/features/routes/bulk-delete.ts

@@ -30,19 +30,27 @@ export function createBulkDeleteHandler(featureLoader: FeatureLoader) {
         return;
       }
 
-      const results = await Promise.all(
-        featureIds.map(async (featureId) => {
-          const success = await featureLoader.delete(projectPath, featureId);
-          if (success) {
-            return { featureId, success: true };
-          }
-          return {
-            featureId,
-            success: false,
-            error: 'Deletion failed. Check server logs for details.',
-          };
-        })
-      );
+      // Process in parallel batches of 20 for efficiency
+      const BATCH_SIZE = 20;
+      const results: BulkDeleteResult[] = [];
+
+      for (let i = 0; i < featureIds.length; i += BATCH_SIZE) {
+        const batch = featureIds.slice(i, i + BATCH_SIZE);
+        const batchResults = await Promise.all(
+          batch.map(async (featureId) => {
+            const success = await featureLoader.delete(projectPath, featureId);
+            if (success) {
+              return { featureId, success: true };
+            }
+            return {
+              featureId,
+              success: false,
+              error: 'Deletion failed. Check server logs for details.',
+            };
+          })
+        );
+        results.push(...batchResults);
+      }
 
       const successCount = results.reduce((count, r) => count + (r.success ? 1 : 0), 0);
       const failureCount = results.length - successCount;

apps/server/src/routes/features/routes/bulk-update.ts

@@ -43,17 +43,36 @@ export function createBulkUpdateHandler(featureLoader: FeatureLoader) {
       const results: BulkUpdateResult[] = [];
       const updatedFeatures: Feature[] = [];
 
-      for (const featureId of featureIds) {
-        try {
-          const updated = await featureLoader.update(projectPath, featureId, updates);
-          results.push({ featureId, success: true });
-          updatedFeatures.push(updated);
-        } catch (error) {
-          results.push({
-            featureId,
-            success: false,
-            error: getErrorMessage(error),
-          });
+      // Process in parallel batches of 20 for efficiency
+      const BATCH_SIZE = 20;
+      for (let i = 0; i < featureIds.length; i += BATCH_SIZE) {
+        const batch = featureIds.slice(i, i + BATCH_SIZE);
+        const batchResults = await Promise.all(
+          batch.map(async (featureId) => {
+            try {
+              const updated = await featureLoader.update(projectPath, featureId, updates);
+              return { featureId, success: true as const, feature: updated };
+            } catch (error) {
+              return {
+                featureId,
+                success: false as const,
+                error: getErrorMessage(error),
+              };
+            }
+          })
+        );
+
+        for (const result of batchResults) {
+          if (result.success) {
+            results.push({ featureId: result.featureId, success: true });
+            updatedFeatures.push(result.feature);
+          } else {
+            results.push({
+              featureId: result.featureId,
+              success: false,
+              error: result.error,
+            });
+          }
         }
       }
 

apps/server/src/routes/features/routes/create.ts

@@ -4,10 +4,11 @@
 
 import type { Request, Response } from 'express';
 import { FeatureLoader } from '../../../services/feature-loader.js';
+import type { EventEmitter } from '../../../lib/events.js';
 import type { Feature } from '@automaker/types';
 import { getErrorMessage, logError } from '../common.js';
 
-export function createCreateHandler(featureLoader: FeatureLoader) {
+export function createCreateHandler(featureLoader: FeatureLoader, events?: EventEmitter) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
       const { projectPath, feature } = req.body as {
@@ -23,7 +24,30 @@ export function createCreateHandler(featureLoader: FeatureLoader) {
         return;
       }
 
+      // Check for duplicate title if title is provided
+      if (feature.title && feature.title.trim()) {
+        const duplicate = await featureLoader.findDuplicateTitle(projectPath, feature.title);
+        if (duplicate) {
+          res.status(409).json({
+            success: false,
+            error: `A feature with title "${feature.title}" already exists`,
+            duplicateFeatureId: duplicate.id,
+          });
+          return;
+        }
+      }
+
       const created = await featureLoader.create(projectPath, feature);
+
+      // Emit feature_created event for hooks
+      if (events) {
+        events.emit('feature:created', {
+          featureId: created.id,
+          featureName: created.name,
+          projectPath,
+        });
+      }
+
       res.json({ success: true, feature: created });
     } catch (error) {
       logError(error, 'Create feature failed');

apps/server/src/routes/features/routes/generate-title.ts

@@ -9,6 +9,11 @@ import type { Request, Response } from 'express';
 import { createLogger } from '@automaker/utils';
 import { CLAUDE_MODEL_MAP } from '@automaker/model-resolver';
 import { simpleQuery } from '../../../providers/simple-query-service.js';
+import type { SettingsService } from '../../../services/settings-service.js';
+import {
+  getPromptCustomization,
+  getActiveClaudeApiProfile,
+} from '../../../lib/settings-helpers.js';
 
 const logger = createLogger('GenerateTitle');
 
@@ -26,16 +31,9 @@ interface GenerateTitleErrorResponse {
   error: string;
 }
 
-const SYSTEM_PROMPT = `You are a title generator. Your task is to create a concise, descriptive title (5-10 words max) for a software feature based on its description.
-
-Rules:
-- Output ONLY the title, nothing else
-- Keep it short and action-oriented (e.g., "Add dark mode toggle", "Fix login validation")
-- Start with a verb when possible (Add, Fix, Update, Implement, Create, etc.)
-- No quotes, periods, or extra formatting
-- Capture the essence of the feature in a scannable way`;
-
-export function createGenerateTitleHandler(): (req: Request, res: Response) => Promise<void> {
+export function createGenerateTitleHandler(
+  settingsService?: SettingsService
+): (req: Request, res: Response) => Promise<void> {
   return async (req: Request, res: Response): Promise<void> => {
     try {
       const { description } = req.body as GenerateTitleRequestBody;
@@ -61,15 +59,27 @@ export function createGenerateTitleHandler(): (req: Request, res: Response) => P
 
       logger.info(`Generating title for description: ${trimmedDescription.substring(0, 50)}...`);
 
+      // Get customized prompts from settings
+      const prompts = await getPromptCustomization(settingsService, '[GenerateTitle]');
+      const systemPrompt = prompts.titleGeneration.systemPrompt;
+
+      // Get active Claude API profile for alternative endpoint configuration
+      const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+        settingsService,
+        '[GenerateTitle]'
+      );
+
       const userPrompt = `Generate a concise title for this feature:\n\n${trimmedDescription}`;
 
       // Use simpleQuery - provider abstraction handles all the streaming/extraction
       const result = await simpleQuery({
-        prompt: `${SYSTEM_PROMPT}\n\n${userPrompt}`,
+        prompt: `${systemPrompt}\n\n${userPrompt}`,
         model: CLAUDE_MODEL_MAP.haiku,
         cwd: process.cwd(),
         maxTurns: 1,
         allowedTools: [],
+        claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+        credentials, // Pass credentials for resolving 'credentials' apiKeySource
       });
 
       const title = result.text;

apps/server/src/routes/features/routes/update.ts

@@ -4,8 +4,14 @@
 
 import type { Request, Response } from 'express';
 import { FeatureLoader } from '../../../services/feature-loader.js';
-import type { Feature } from '@automaker/types';
+import type { Feature, FeatureStatus } from '@automaker/types';
 import { getErrorMessage, logError } from '../common.js';
+import { createLogger } from '@automaker/utils';
+
+const logger = createLogger('features/update');
+
+// Statuses that should trigger syncing to app_spec.txt
+const SYNC_TRIGGER_STATUSES: FeatureStatus[] = ['verified', 'completed'];
 
 export function createUpdateHandler(featureLoader: FeatureLoader) {
   return async (req: Request, res: Response): Promise<void> => {
@@ -34,6 +40,28 @@ export function createUpdateHandler(featureLoader: FeatureLoader) {
         return;
       }
 
+      // Check for duplicate title if title is being updated
+      if (updates.title && updates.title.trim()) {
+        const duplicate = await featureLoader.findDuplicateTitle(
+          projectPath,
+          updates.title,
+          featureId // Exclude the current feature from duplicate check
+        );
+        if (duplicate) {
+          res.status(409).json({
+            success: false,
+            error: `A feature with title "${updates.title}" already exists`,
+            duplicateFeatureId: duplicate.id,
+          });
+          return;
+        }
+      }
+
+      // Get the current feature to detect status changes
+      const currentFeature = await featureLoader.get(projectPath, featureId);
+      const previousStatus = currentFeature?.status as FeatureStatus | undefined;
+      const newStatus = updates.status as FeatureStatus | undefined;
+
       const updated = await featureLoader.update(
         projectPath,
         featureId,
@@ -42,6 +70,22 @@ export function createUpdateHandler(featureLoader: FeatureLoader) {
         enhancementMode,
         preEnhancementDescription
       );
+
+      // Trigger sync to app_spec.txt when status changes to verified or completed
+      if (newStatus && SYNC_TRIGGER_STATUSES.includes(newStatus) && previousStatus !== newStatus) {
+        try {
+          const synced = await featureLoader.syncFeatureToAppSpec(projectPath, updated);
+          if (synced) {
+            logger.info(
+              `Synced feature "${updated.title || updated.id}" to app_spec.txt on status change to ${newStatus}`
+            );
+          }
+        } catch (syncError) {
+          // Log the sync error but don't fail the update operation
+          logger.error(`Failed to sync feature to app_spec.txt:`, syncError);
+        }
+      }
+
       res.json({ success: true, feature: updated });
     } catch (error) {
       logError(error, 'Update feature failed');

apps/server/src/routes/fs/routes/image.ts

@@ -1,5 +1,12 @@
 /**
  * GET /image endpoint - Serve image files
+ *
+ * Requires authentication via auth middleware:
+ * - apiKey query parameter (Electron mode)
+ * - token query parameter (web mode)
+ * - session cookie (web mode)
+ * - X-API-Key header (Electron mode)
+ * - X-Session-Token header (web mode)
  */
 
 import type { Request, Response } from 'express';

apps/server/src/routes/github/routes/validate-issue.ts

@@ -30,11 +30,15 @@ import { writeValidation } from '../../../lib/validation-storage.js';
 import { streamingQuery } from '../../../providers/simple-query-service.js';
 import {
   issueValidationSchema,
-  ISSUE_VALIDATION_SYSTEM_PROMPT,
   buildValidationPrompt,
   ValidationComment,
   ValidationLinkedPR,
 } from './validation-schema.js';
+import {
+  getPromptCustomization,
+  getAutoLoadClaudeMdSetting,
+  getActiveClaudeApiProfile,
+} from '../../../lib/settings-helpers.js';
 import {
   trySetValidationRunning,
   clearValidationStatus,
@@ -43,7 +47,6 @@ import {
   logger,
 } from './validation-common.js';
 import type { SettingsService } from '../../../services/settings-service.js';
-import { getAutoLoadClaudeMdSetting } from '../../../lib/settings-helpers.js';
 
 /**
  * Request body for issue validation
@@ -117,13 +120,17 @@ async function runValidation(
 
     let responseText = '';
 
+    // Get customized prompts from settings
+    const prompts = await getPromptCustomization(settingsService, '[ValidateIssue]');
+    const issueValidationSystemPrompt = prompts.issueValidation.systemPrompt;
+
     // Determine if we should use structured output (Claude/Codex support it, Cursor/OpenCode don't)
     const useStructuredOutput = isClaudeModel(model) || isCodexModel(model);
 
     // Build the final prompt - for Cursor, include system prompt and JSON schema instructions
     let finalPrompt = basePrompt;
     if (!useStructuredOutput) {
-      finalPrompt = `${ISSUE_VALIDATION_SYSTEM_PROMPT}
+      finalPrompt = `${issueValidationSystemPrompt}
 
 CRITICAL INSTRUCTIONS:
 1. DO NOT write any files. Return the JSON in your response only.
@@ -162,17 +169,25 @@ ${basePrompt}`;
 
     logger.info(`Using model: ${model}`);
 
+    // Get active Claude API profile for alternative endpoint configuration
+    const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+      settingsService,
+      '[IssueValidation]'
+    );
+
     // Use streamingQuery with event callbacks
     const result = await streamingQuery({
       prompt: finalPrompt,
       model: model as string,
       cwd: projectPath,
-      systemPrompt: useStructuredOutput ? ISSUE_VALIDATION_SYSTEM_PROMPT : undefined,
+      systemPrompt: useStructuredOutput ? issueValidationSystemPrompt : undefined,
       abortController,
       thinkingLevel: effectiveThinkingLevel,
       reasoningEffort: effectiveReasoningEffort,
       readOnly: true, // Issue validation only reads code, doesn't write
       settingSources: autoLoadClaudeMd ? ['user', 'project', 'local'] : undefined,
+      claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+      credentials, // Pass credentials for resolving 'credentials' apiKeySource
       outputFormat: useStructuredOutput
         ? {
             type: 'json_schema',

apps/server/src/routes/github/routes/validation-schema.ts

@@ -1,8 +1,11 @@
 /**
- * Issue Validation Schema and System Prompt
+ * Issue Validation Schema and Prompt Building
  *
  * Defines the JSON schema for Claude's structured output and
- * the system prompt that guides the validation process.
+ * helper functions for building validation prompts.
+ *
+ * Note: The system prompt is now centralized in @automaker/prompts
+ * and accessed via getPromptCustomization() in validate-issue.ts
  */
 
 /**
@@ -82,76 +85,6 @@ export const issueValidationSchema = {
   additionalProperties: false,
 } as const;
 
-/**
- * System prompt that guides Claude in validating GitHub issues.
- * Instructs the model to use read-only tools to analyze the codebase.
- */
-export const ISSUE_VALIDATION_SYSTEM_PROMPT = `You are an expert code analyst validating GitHub issues against a codebase.
-
-Your task is to analyze a GitHub issue and determine if it's valid by scanning the codebase.
-
-## Validation Process
-
-1. **Read the issue carefully** - Understand what is being reported or requested
-2. **Search the codebase** - Use Glob to find relevant files by pattern, Grep to search for keywords
-3. **Examine the code** - Use Read to look at the actual implementation in relevant files
-4. **Check linked PRs** - If there are linked pull requests, use \`gh pr diff <PR_NUMBER>\` to review the changes
-5. **Form your verdict** - Based on your analysis, determine if the issue is valid
-
-## Verdicts
-
-- **valid**: The issue describes a real problem that exists in the codebase, or a clear feature request that can be implemented. The referenced files/components exist and the issue is actionable.
-
-- **invalid**: The issue describes behavior that doesn't exist, references non-existent files or components, is based on a misunderstanding of the code, or the described "bug" is actually expected behavior.
-
-- **needs_clarification**: The issue lacks sufficient detail to verify. Specify what additional information is needed in the missingInfo field.
-
-## For Bug Reports, Check:
-- Do the referenced files/components exist?
-- Does the code match what the issue describes?
-- Is the described behavior actually a bug or expected?
-- Can you locate the code that would cause the reported issue?
-
-## For Feature Requests, Check:
-- Does the feature already exist?
-- Is the implementation location clear?
-- Is the request technically feasible given the codebase structure?
-
-## Analyzing Linked Pull Requests
-
-When an issue has linked PRs (especially open ones), you MUST analyze them:
-
-1. **Run \`gh pr diff <PR_NUMBER>\`** to see what changes the PR makes
-2. **Run \`gh pr view <PR_NUMBER>\`** to see PR description and status
-3. **Evaluate if the PR fixes the issue** - Does the diff address the reported problem?
-4. **Provide a recommendation**:
-   - \`wait_for_merge\`: The PR appears to fix the issue correctly. No additional work needed - just wait for it to be merged.
-   - \`pr_needs_work\`: The PR attempts to fix the issue but is incomplete or has problems.
-   - \`no_pr\`: No relevant PR exists for this issue.
-
-5. **Include prAnalysis in your response** with:
-   - hasOpenPR: true/false
-   - prFixesIssue: true/false (based on diff analysis)
-   - prNumber: the PR number you analyzed
-   - prSummary: brief description of what the PR changes
-   - recommendation: one of the above values
-
-## Response Guidelines
-
-- **Always include relatedFiles** when you find relevant code
-- **Set bugConfirmed to true** only if you can definitively confirm a bug exists in the code
-- **Provide a suggestedFix** when you have a clear idea of how to address the issue
-- **Use missingInfo** when the verdict is needs_clarification to list what's needed
-- **Include prAnalysis** when there are linked PRs - this is critical for avoiding duplicate work
-- **Set estimatedComplexity** to help prioritize:
-  - trivial: Simple text changes, one-line fixes
-  - simple: Small changes to one file
-  - moderate: Changes to multiple files or moderate logic changes
-  - complex: Significant refactoring or new feature implementation
-  - very_complex: Major architectural changes or cross-cutting concerns
-
-Be thorough in your analysis but focus on files that are directly relevant to the issue.`;
-
 /**
  * Comment data structure for validation prompt
  */

apps/server/src/routes/health/routes/environment.ts

@@ -9,12 +9,14 @@ import type { Request, Response } from 'express';
 
 export interface EnvironmentResponse {
   isContainerized: boolean;
+  skipSandboxWarning?: boolean;
 }
 
 export function createEnvironmentHandler() {
   return (_req: Request, res: Response): void => {
     res.json({
       isContainerized: process.env.IS_CONTAINERIZED === 'true',
+      skipSandboxWarning: process.env.AUTOMAKER_SKIP_SANDBOX_WARNING === 'true',
     } satisfies EnvironmentResponse);
   };
 }

apps/server/src/routes/notifications/common.ts

@@ -0,0 +1,21 @@
+/**
+ * Common utilities for notification routes
+ *
+ * Provides logger and error handling utilities shared across all notification endpoints.
+ */
+
+import { createLogger } from '@automaker/utils';
+import { getErrorMessage as getErrorMessageShared, createLogError } from '../common.js';
+
+/** Logger instance for notification-related operations */
+export const logger = createLogger('Notifications');
+
+/**
+ * Extract user-friendly error message from error objects
+ */
+export { getErrorMessageShared as getErrorMessage };
+
+/**
+ * Log error with automatic logger binding
+ */
+export const logError = createLogError(logger);

apps/server/src/routes/notifications/index.ts

@@ -0,0 +1,62 @@
+/**
+ * Notifications routes - HTTP API for project-level notifications
+ *
+ * Provides endpoints for:
+ * - Listing notifications
+ * - Getting unread count
+ * - Marking notifications as read
+ * - Dismissing notifications
+ *
+ * All endpoints use handler factories that receive the NotificationService instance.
+ * Mounted at /api/notifications in the main server.
+ */
+
+import { Router } from 'express';
+import type { NotificationService } from '../../services/notification-service.js';
+import { validatePathParams } from '../../middleware/validate-paths.js';
+import { createListHandler } from './routes/list.js';
+import { createUnreadCountHandler } from './routes/unread-count.js';
+import { createMarkReadHandler } from './routes/mark-read.js';
+import { createDismissHandler } from './routes/dismiss.js';
+
+/**
+ * Create notifications router with all endpoints
+ *
+ * Endpoints:
+ * - POST /list - List all notifications for a project
+ * - POST /unread-count - Get unread notification count
+ * - POST /mark-read - Mark notification(s) as read
+ * - POST /dismiss - Dismiss notification(s)
+ *
+ * @param notificationService - Instance of NotificationService
+ * @returns Express Router configured with all notification endpoints
+ */
+export function createNotificationsRoutes(notificationService: NotificationService): Router {
+  const router = Router();
+
+  // List notifications
+  router.post('/list', validatePathParams('projectPath'), createListHandler(notificationService));
+
+  // Get unread count
+  router.post(
+    '/unread-count',
+    validatePathParams('projectPath'),
+    createUnreadCountHandler(notificationService)
+  );
+
+  // Mark as read (single or all)
+  router.post(
+    '/mark-read',
+    validatePathParams('projectPath'),
+    createMarkReadHandler(notificationService)
+  );
+
+  // Dismiss (single or all)
+  router.post(
+    '/dismiss',
+    validatePathParams('projectPath'),
+    createDismissHandler(notificationService)
+  );
+
+  return router;
+}

apps/server/src/routes/notifications/routes/dismiss.ts

@@ -0,0 +1,53 @@
+/**
+ * POST /api/notifications/dismiss - Dismiss notification(s)
+ *
+ * Request body: { projectPath: string, notificationId?: string }
+ * - If notificationId provided: dismisses that notification
+ * - If notificationId not provided: dismisses all notifications
+ *
+ * Response: { success: true, dismissed: boolean | count: number }
+ */
+
+import type { Request, Response } from 'express';
+import type { NotificationService } from '../../../services/notification-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+/**
+ * Create handler for POST /api/notifications/dismiss
+ *
+ * @param notificationService - Instance of NotificationService
+ * @returns Express request handler
+ */
+export function createDismissHandler(notificationService: NotificationService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, notificationId } = req.body;
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      // If notificationId provided, dismiss single notification
+      if (notificationId) {
+        const dismissed = await notificationService.dismissNotification(
+          projectPath,
+          notificationId
+        );
+        if (!dismissed) {
+          res.status(404).json({ success: false, error: 'Notification not found' });
+          return;
+        }
+        res.json({ success: true, dismissed: true });
+        return;
+      }
+
+      // Otherwise dismiss all
+      const count = await notificationService.dismissAll(projectPath);
+      res.json({ success: true, count });
+    } catch (error) {
+      logError(error, 'Dismiss failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/notifications/routes/list.ts

@@ -0,0 +1,39 @@
+/**
+ * POST /api/notifications/list - List all notifications for a project
+ *
+ * Request body: { projectPath: string }
+ * Response: { success: true, notifications: Notification[] }
+ */
+
+import type { Request, Response } from 'express';
+import type { NotificationService } from '../../../services/notification-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+/**
+ * Create handler for POST /api/notifications/list
+ *
+ * @param notificationService - Instance of NotificationService
+ * @returns Express request handler
+ */
+export function createListHandler(notificationService: NotificationService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath } = req.body;
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      const notifications = await notificationService.getNotifications(projectPath);
+
+      res.json({
+        success: true,
+        notifications,
+      });
+    } catch (error) {
+      logError(error, 'List notifications failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/notifications/routes/mark-read.ts

@@ -0,0 +1,50 @@
+/**
+ * POST /api/notifications/mark-read - Mark notification(s) as read
+ *
+ * Request body: { projectPath: string, notificationId?: string }
+ * - If notificationId provided: marks that notification as read
+ * - If notificationId not provided: marks all notifications as read
+ *
+ * Response: { success: true, count?: number, notification?: Notification }
+ */
+
+import type { Request, Response } from 'express';
+import type { NotificationService } from '../../../services/notification-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+/**
+ * Create handler for POST /api/notifications/mark-read
+ *
+ * @param notificationService - Instance of NotificationService
+ * @returns Express request handler
+ */
+export function createMarkReadHandler(notificationService: NotificationService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath, notificationId } = req.body;
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      // If notificationId provided, mark single notification
+      if (notificationId) {
+        const notification = await notificationService.markAsRead(projectPath, notificationId);
+        if (!notification) {
+          res.status(404).json({ success: false, error: 'Notification not found' });
+          return;
+        }
+        res.json({ success: true, notification });
+        return;
+      }
+
+      // Otherwise mark all as read
+      const count = await notificationService.markAllAsRead(projectPath);
+      res.json({ success: true, count });
+    } catch (error) {
+      logError(error, 'Mark read failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/notifications/routes/unread-count.ts

@@ -0,0 +1,39 @@
+/**
+ * POST /api/notifications/unread-count - Get unread notification count
+ *
+ * Request body: { projectPath: string }
+ * Response: { success: true, count: number }
+ */
+
+import type { Request, Response } from 'express';
+import type { NotificationService } from '../../../services/notification-service.js';
+import { getErrorMessage, logError } from '../common.js';
+
+/**
+ * Create handler for POST /api/notifications/unread-count
+ *
+ * @param notificationService - Instance of NotificationService
+ * @returns Express request handler
+ */
+export function createUnreadCountHandler(notificationService: NotificationService) {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { projectPath } = req.body;
+
+      if (!projectPath || typeof projectPath !== 'string') {
+        res.status(400).json({ success: false, error: 'projectPath is required' });
+        return;
+      }
+
+      const count = await notificationService.getUnreadCount(projectPath);
+
+      res.json({
+        success: true,
+        count,
+      });
+    } catch (error) {
+      logError(error, 'Get unread count failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/routes/running-agents/routes/index.ts

@@ -4,12 +4,58 @@
 
 import type { Request, Response } from 'express';
 import type { AutoModeService } from '../../../services/auto-mode-service.js';
+import { getBacklogPlanStatus, getRunningDetails } from '../../backlog-plan/common.js';
+import { getAllRunningGenerations } from '../../app-spec/common.js';
+import path from 'path';
 import { getErrorMessage, logError } from '../common.js';
 
 export function createIndexHandler(autoModeService: AutoModeService) {
   return async (_req: Request, res: Response): Promise<void> => {
     try {
-      const runningAgents = await autoModeService.getRunningAgents();
+      const runningAgents = [...(await autoModeService.getRunningAgents())];
+      const backlogPlanStatus = getBacklogPlanStatus();
+      const backlogPlanDetails = getRunningDetails();
+
+      if (backlogPlanStatus.isRunning && backlogPlanDetails) {
+        runningAgents.push({
+          featureId: `backlog-plan:${backlogPlanDetails.projectPath}`,
+          projectPath: backlogPlanDetails.projectPath,
+          projectName: path.basename(backlogPlanDetails.projectPath),
+          isAutoMode: false,
+          title: 'Backlog plan',
+          description: backlogPlanDetails.prompt,
+        });
+      }
+
+      // Add spec/feature generation tasks
+      const specGenerations = getAllRunningGenerations();
+      for (const generation of specGenerations) {
+        let title: string;
+        let description: string;
+
+        switch (generation.type) {
+          case 'feature_generation':
+            title = 'Generating features from spec';
+            description = 'Creating features from the project specification';
+            break;
+          case 'sync':
+            title = 'Syncing spec with code';
+            description = 'Updating spec from codebase and completed features';
+            break;
+          default:
+            title = 'Regenerating spec';
+            description = 'Analyzing project and generating specification';
+        }
+
+        runningAgents.push({
+          featureId: `spec-generation:${generation.projectPath}`,
+          projectPath: generation.projectPath,
+          projectName: path.basename(generation.projectPath),
+          isAutoMode: false,
+          title,
+          description,
+        });
+      }
 
       res.json({
         success: true,

apps/server/src/routes/settings/routes/update-global.ts

@@ -12,6 +12,18 @@ import type { Request, Response } from 'express';
 import type { SettingsService } from '../../../services/settings-service.js';
 import type { GlobalSettings } from '../../../types/settings.js';
 import { getErrorMessage, logError, logger } from '../common.js';
+import { setLogLevel, LogLevel } from '@automaker/utils';
+import { setRequestLoggingEnabled } from '../../../index.js';
+
+/**
+ * Map server log level string to LogLevel enum
+ */
+const LOG_LEVEL_MAP: Record<string, LogLevel> = {
+  error: LogLevel.ERROR,
+  warn: LogLevel.WARN,
+  info: LogLevel.INFO,
+  debug: LogLevel.DEBUG,
+};
 
 /**
  * Create handler factory for PUT /api/settings/global
@@ -33,18 +45,41 @@ export function createUpdateGlobalHandler(settingsService: SettingsService) {
       }
 
       // Minimal debug logging to help diagnose accidental wipes.
-      if ('projects' in updates || 'theme' in updates || 'localStorageMigrated' in updates) {
-        const projectsLen = Array.isArray((updates as any).projects)
-          ? (updates as any).projects.length
-          : undefined;
-        logger.info(
-          `Update global settings request: projects=${projectsLen ?? 'n/a'}, theme=${
-            (updates as any).theme ?? 'n/a'
-          }, localStorageMigrated=${(updates as any).localStorageMigrated ?? 'n/a'}`
-        );
+      const projectsLen = Array.isArray((updates as any).projects)
+        ? (updates as any).projects.length
+        : undefined;
+      const trashedLen = Array.isArray((updates as any).trashedProjects)
+        ? (updates as any).trashedProjects.length
+        : undefined;
+      logger.info(
+        `[SERVER_SETTINGS_UPDATE] Request received: projects=${projectsLen ?? 'n/a'}, trashedProjects=${trashedLen ?? 'n/a'}, theme=${
+          (updates as any).theme ?? 'n/a'
+        }, localStorageMigrated=${(updates as any).localStorageMigrated ?? 'n/a'}`
+      );
+
+      logger.info('[SERVER_SETTINGS_UPDATE] Calling updateGlobalSettings...');
+      const settings = await settingsService.updateGlobalSettings(updates);
+      logger.info(
+        '[SERVER_SETTINGS_UPDATE] Update complete, projects count:',
+        settings.projects?.length ?? 0
+      );
+
+      // Apply server log level if it was updated
+      if ('serverLogLevel' in updates && updates.serverLogLevel) {
+        const level = LOG_LEVEL_MAP[updates.serverLogLevel];
+        if (level !== undefined) {
+          setLogLevel(level);
+          logger.info(`Server log level changed to: ${updates.serverLogLevel}`);
+        }
       }
 
-      const settings = await settingsService.updateGlobalSettings(updates);
+      // Apply request logging setting if it was updated
+      if ('enableRequestLogging' in updates && typeof updates.enableRequestLogging === 'boolean') {
+        setRequestLoggingEnabled(updates.enableRequestLogging);
+        logger.info(
+          `HTTP request logging ${updates.enableRequestLogging ? 'enabled' : 'disabled'}`
+        );
+      }
 
       res.json({
         success: true,

apps/server/src/routes/suggestions/generate-suggestions.ts

@@ -15,7 +15,11 @@ import { FeatureLoader } from '../../services/feature-loader.js';
 import { getAppSpecPath } from '@automaker/platform';
 import * as secureFs from '../../lib/secure-fs.js';
 import type { SettingsService } from '../../services/settings-service.js';
-import { getAutoLoadClaudeMdSetting } from '../../lib/settings-helpers.js';
+import {
+  getAutoLoadClaudeMdSetting,
+  getPromptCustomization,
+  getActiveClaudeApiProfile,
+} from '../../lib/settings-helpers.js';
 
 const logger = createLogger('Suggestions');
 
@@ -137,11 +141,15 @@ export async function generateSuggestions(
   modelOverride?: string,
   thinkingLevelOverride?: ThinkingLevel
 ): Promise<void> {
+  // Get customized prompts from settings
+  const prompts = await getPromptCustomization(settingsService, '[Suggestions]');
+
+  // Map suggestion types to their prompts
   const typePrompts: Record<string, string> = {
-    features: 'Analyze this project and suggest new features that would add value.',
-    refactoring: 'Analyze this project and identify refactoring opportunities.',
-    security: 'Analyze this project for security vulnerabilities and suggest fixes.',
-    performance: 'Analyze this project for performance issues and suggest optimizations.',
+    features: prompts.suggestions.featuresPrompt,
+    refactoring: prompts.suggestions.refactoringPrompt,
+    security: prompts.suggestions.securityPrompt,
+    performance: prompts.suggestions.performancePrompt,
   };
 
   // Load existing context to avoid duplicates
@@ -151,15 +159,7 @@ export async function generateSuggestions(
 ${existingContext}
 
 ${existingContext ? '\nIMPORTANT: Do NOT suggest features that are already implemented or already in the backlog above. Focus on NEW ideas that complement what already exists.\n' : ''}
-Look at the codebase and provide 3-5 concrete suggestions.
-
-For each suggestion, provide:
-1. A category (e.g., "User Experience", "Security", "Performance")
-2. A clear description of what to implement
-3. Priority (1=high, 2=medium, 3=low)
-4. Brief reasoning for why this would help
-
-The response will be automatically formatted as structured JSON.`;
+${prompts.suggestions.baseTemplate}`;
 
   // Don't send initial message - let the agent output speak for itself
   // The first agent message will be captured as an info entry
@@ -196,6 +196,12 @@ The response will be automatically formatted as structured JSON.`;
 
   logger.info('[Suggestions] Using model:', model);
 
+  // Get active Claude API profile for alternative endpoint configuration
+  const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+    settingsService,
+    '[Suggestions]'
+  );
+
   let responseText = '';
 
   // Determine if we should use structured output (Claude supports it, Cursor doesn't)
@@ -227,6 +233,8 @@ Your entire response should be valid JSON starting with { and ending with }. No
     thinkingLevel,
     readOnly: true, // Suggestions only reads code, doesn't write
     settingSources: autoLoadClaudeMd ? ['user', 'project', 'local'] : undefined,
+    claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+    credentials, // Pass credentials for resolving 'credentials' apiKeySource
     outputFormat: useStructuredOutput
       ? {
           type: 'json_schema',

apps/server/src/routes/worktree/index.ts

@@ -29,6 +29,13 @@ import {
   createGetAvailableEditorsHandler,
   createRefreshEditorsHandler,
 } from './routes/open-in-editor.js';
+import {
+  createOpenInTerminalHandler,
+  createGetAvailableTerminalsHandler,
+  createGetDefaultTerminalHandler,
+  createRefreshTerminalsHandler,
+  createOpenInExternalTerminalHandler,
+} from './routes/open-in-terminal.js';
 import { createInitGitHandler } from './routes/init-git.js';
 import { createMigrateHandler } from './routes/migrate.js';
 import { createStartDevHandler } from './routes/start-dev.js';
@@ -97,9 +104,25 @@ export function createWorktreeRoutes(
   );
   router.post('/switch-branch', requireValidWorktree, createSwitchBranchHandler());
   router.post('/open-in-editor', validatePathParams('worktreePath'), createOpenInEditorHandler());
+  router.post(
+    '/open-in-terminal',
+    validatePathParams('worktreePath'),
+    createOpenInTerminalHandler()
+  );
   router.get('/default-editor', createGetDefaultEditorHandler());
   router.get('/available-editors', createGetAvailableEditorsHandler());
   router.post('/refresh-editors', createRefreshEditorsHandler());
+
+  // External terminal routes
+  router.get('/available-terminals', createGetAvailableTerminalsHandler());
+  router.get('/default-terminal', createGetDefaultTerminalHandler());
+  router.post('/refresh-terminals', createRefreshTerminalsHandler());
+  router.post(
+    '/open-in-external-terminal',
+    validatePathParams('worktreePath'),
+    createOpenInExternalTerminalHandler()
+  );
+
   router.post('/init-git', validatePathParams('projectPath'), createInitGitHandler());
   router.post('/migrate', createMigrateHandler());
   router.post(

apps/server/src/routes/worktree/routes/create-pr.ts

@@ -13,6 +13,7 @@ import {
 } from '../common.js';
 import { updateWorktreePRInfo } from '../../../lib/worktree-metadata.js';
 import { createLogger } from '@automaker/utils';
+import { validatePRState } from '@automaker/types';
 
 const logger = createLogger('CreatePR');
 
@@ -268,11 +269,12 @@ export function createCreatePRHandler() {
             prAlreadyExisted = true;
 
             // Store the existing PR info in metadata
+            // GitHub CLI returns uppercase states: OPEN, MERGED, CLOSED
             await updateWorktreePRInfo(effectiveProjectPath, branchName, {
               number: existingPr.number,
               url: existingPr.url,
               title: existingPr.title || title,
-              state: existingPr.state || 'open',
+              state: validatePRState(existingPr.state),
               createdAt: new Date().toISOString(),
             });
             logger.debug(
@@ -319,11 +321,12 @@ export function createCreatePRHandler() {
 
               if (prNumber) {
                 try {
+                  // Note: GitHub doesn't have a 'DRAFT' state - drafts still show as 'OPEN'
                   await updateWorktreePRInfo(effectiveProjectPath, branchName, {
                     number: prNumber,
                     url: prUrl,
                     title,
-                    state: draft ? 'draft' : 'open',
+                    state: 'OPEN',
                     createdAt: new Date().toISOString(),
                   });
                   logger.debug(`Stored PR info for branch ${branchName}: PR #${prNumber}`);
@@ -352,11 +355,12 @@ export function createCreatePRHandler() {
                   prNumber = existingPr.number;
                   prAlreadyExisted = true;
 
+                  // GitHub CLI returns uppercase states: OPEN, MERGED, CLOSED
                   await updateWorktreePRInfo(effectiveProjectPath, branchName, {
                     number: existingPr.number,
                     url: existingPr.url,
                     title: existingPr.title || title,
-                    state: existingPr.state || 'open',
+                    state: validatePRState(existingPr.state),
                     createdAt: new Date().toISOString(),
                   });
                   logger.debug(`Fetched and stored existing PR: #${existingPr.number}`);

apps/server/src/routes/worktree/routes/dev-server-logs.ts

@@ -34,6 +34,7 @@ export function createGetDevServerLogsHandler() {
           result: {
             worktreePath: result.result.worktreePath,
             port: result.result.port,
+            url: result.result.url,
             logs: result.result.logs,
             startedAt: result.result.startedAt,
           },

apps/server/src/routes/worktree/routes/generate-commit-message.ts

@@ -10,7 +10,6 @@ import { exec } from 'child_process';
 import { promisify } from 'util';
 import { existsSync } from 'fs';
 import { join } from 'path';
-import { query } from '@anthropic-ai/claude-agent-sdk';
 import { createLogger } from '@automaker/utils';
 import { DEFAULT_PHASE_MODELS, isCursorModel, stripProviderPrefix } from '@automaker/types';
 import { resolvePhaseModel } from '@automaker/model-resolver';
@@ -18,6 +17,7 @@ import { mergeCommitMessagePrompts } from '@automaker/prompts';
 import { ProviderFactory } from '../../../providers/provider-factory.js';
 import type { SettingsService } from '../../../services/settings-service.js';
 import { getErrorMessage, logError } from '../common.js';
+import { getActiveClaudeApiProfile } from '../../../lib/settings-helpers.js';
 
 const logger = createLogger('GenerateCommitMessage');
 const execAsync = promisify(exec);
@@ -74,33 +74,6 @@ interface GenerateCommitMessageErrorResponse {
   error: string;
 }
 
-async function extractTextFromStream(
-  stream: AsyncIterable<{
-    type: string;
-    subtype?: string;
-    result?: string;
-    message?: {
-      content?: Array<{ type: string; text?: string }>;
-    };
-  }>
-): Promise<string> {
-  let responseText = '';
-
-  for await (const msg of stream) {
-    if (msg.type === 'assistant' && msg.message?.content) {
-      for (const block of msg.message.content) {
-        if (block.type === 'text' && block.text) {
-          responseText += block.text;
-        }
-      }
-    } else if (msg.type === 'result' && msg.subtype === 'success') {
-      responseText = msg.result || responseText;
-    }
-  }
-
-  return responseText;
-}
-
 export function createGenerateCommitMessageHandler(
   settingsService?: SettingsService
 ): (req: Request, res: Response) => Promise<void> {
@@ -195,57 +168,53 @@ export function createGenerateCommitMessageHandler(
       // Get the effective system prompt (custom or default)
       const systemPrompt = await getSystemPrompt(settingsService);
 
-      let message: string;
+      // Get active Claude API profile for alternative endpoint configuration
+      const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+        settingsService,
+        '[GenerateCommitMessage]'
+      );
 
-      // Route to appropriate provider based on model type
-      if (isCursorModel(model)) {
-        // Use Cursor provider for Cursor models
-        logger.info(`Using Cursor provider for model: ${model}`);
+      // Get provider for the model type
+      const provider = ProviderFactory.getProviderForModel(model);
+      const bareModel = stripProviderPrefix(model);
 
-        const provider = ProviderFactory.getProviderForModel(model);
-        const bareModel = stripProviderPrefix(model);
+      // For Cursor models, combine prompts since Cursor doesn't support systemPrompt separation
+      const effectivePrompt = isCursorModel(model)
+        ? `${systemPrompt}\n\n${userPrompt}`
+        : userPrompt;
+      const effectiveSystemPrompt = isCursorModel(model) ? undefined : systemPrompt;
 
-        const cursorPrompt = `${systemPrompt}\n\n${userPrompt}`;
+      logger.info(`Using ${provider.getName()} provider for model: ${model}`);
 
-        let responseText = '';
-        const cursorStream = provider.executeQuery({
-          prompt: cursorPrompt,
-          model: bareModel,
-          cwd: worktreePath,
-          maxTurns: 1,
-          allowedTools: [],
-          readOnly: true,
-        });
+      let responseText = '';
+      const stream = provider.executeQuery({
+        prompt: effectivePrompt,
+        model: bareModel,
+        cwd: worktreePath,
+        systemPrompt: effectiveSystemPrompt,
+        maxTurns: 1,
+        allowedTools: [],
+        readOnly: true,
+        claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+        credentials, // Pass credentials for resolving 'credentials' apiKeySource
+      });
 
-        // Wrap with timeout to prevent indefinite hangs
-        for await (const msg of withTimeout(cursorStream, AI_TIMEOUT_MS)) {
-          if (msg.type === 'assistant' && msg.message?.content) {
-            for (const block of msg.message.content) {
-              if (block.type === 'text' && block.text) {
-                responseText += block.text;
-              }
+      // Wrap with timeout to prevent indefinite hangs
+      for await (const msg of withTimeout(stream, AI_TIMEOUT_MS)) {
+        if (msg.type === 'assistant' && msg.message?.content) {
+          for (const block of msg.message.content) {
+            if (block.type === 'text' && block.text) {
+              responseText += block.text;
             }
           }
+        } else if (msg.type === 'result' && msg.subtype === 'success' && msg.result) {
+          // Use result if available (some providers return final text here)
+          responseText = msg.result;
         }
-
-        message = responseText.trim();
-      } else {
-        // Use Claude SDK for Claude models
-        const stream = query({
-          prompt: userPrompt,
-          options: {
-            model,
-            systemPrompt,
-            maxTurns: 1,
-            allowedTools: [],
-            permissionMode: 'default',
-          },
-        });
-
-        // Wrap with timeout to prevent indefinite hangs
-        message = await extractTextFromStream(withTimeout(stream, AI_TIMEOUT_MS));
       }
 
+      const message = responseText.trim();
+
       if (!message || message.trim().length === 0) {
         logger.warn('Received empty response from model');
         const response: GenerateCommitMessageErrorResponse = {

apps/server/src/routes/worktree/routes/list.ts

@@ -14,12 +14,34 @@ import path from 'path';
 import * as secureFs from '../../../lib/secure-fs.js';
 import { isGitRepo } from '@automaker/git-utils';
 import { getErrorMessage, logError, normalizePath, execEnv, isGhCliAvailable } from '../common.js';
-import { readAllWorktreeMetadata, type WorktreePRInfo } from '../../../lib/worktree-metadata.js';
+import {
+  readAllWorktreeMetadata,
+  updateWorktreePRInfo,
+  type WorktreePRInfo,
+} from '../../../lib/worktree-metadata.js';
 import { createLogger } from '@automaker/utils';
+import { validatePRState } from '@automaker/types';
+import {
+  checkGitHubRemote,
+  type GitHubRemoteStatus,
+} from '../../github/routes/check-github-remote.js';
 
 const execAsync = promisify(exec);
 const logger = createLogger('Worktree');
 
+/**
+ * Cache for GitHub remote status per project path.
+ * This prevents repeated "no git remotes found" warnings when polling
+ * projects that don't have a GitHub remote configured.
+ */
+interface GitHubRemoteCacheEntry {
+  status: GitHubRemoteStatus;
+  checkedAt: number;
+}
+
+const githubRemoteCache = new Map<string, GitHubRemoteCacheEntry>();
+const GITHUB_REMOTE_CACHE_TTL_MS = 5 * 60 * 1000; // 5 minutes
+
 interface WorktreeInfo {
   path: string;
   branch: string;
@@ -122,22 +144,65 @@ async function scanWorktreesDirectory(
 }
 
 /**
- * Fetch open PRs from GitHub and create a map of branch name to PR info.
- * This allows detecting PRs that were created outside the app.
+ * Get cached GitHub remote status for a project, or check and cache it.
+ * Returns null if gh CLI is not available.
+ */
+async function getGitHubRemoteStatus(projectPath: string): Promise<GitHubRemoteStatus | null> {
+  // Check if gh CLI is available first
+  const ghAvailable = await isGhCliAvailable();
+  if (!ghAvailable) {
+    return null;
+  }
+
+  const now = Date.now();
+  const cached = githubRemoteCache.get(projectPath);
+
+  // Return cached result if still valid
+  if (cached && now - cached.checkedAt < GITHUB_REMOTE_CACHE_TTL_MS) {
+    return cached.status;
+  }
+
+  // Check GitHub remote and cache the result
+  const status = await checkGitHubRemote(projectPath);
+  githubRemoteCache.set(projectPath, {
+    status,
+    checkedAt: Date.now(),
+  });
+
+  return status;
+}
+
+/**
+ * Fetch all PRs from GitHub and create a map of branch name to PR info.
+ * Uses --state all to include merged/closed PRs, allowing detection of
+ * state changes (e.g., when a PR is merged on GitHub).
+ *
+ * This also allows detecting PRs that were created outside the app.
+ *
+ * Uses cached GitHub remote status to avoid repeated warnings when the
+ * project doesn't have a GitHub remote configured.
  */
 async function fetchGitHubPRs(projectPath: string): Promise<Map<string, WorktreePRInfo>> {
   const prMap = new Map<string, WorktreePRInfo>();
 
   try {
-    // Check if gh CLI is available
-    const ghAvailable = await isGhCliAvailable();
-    if (!ghAvailable) {
+    // Check GitHub remote status (uses cache to avoid repeated warnings)
+    const remoteStatus = await getGitHubRemoteStatus(projectPath);
+
+    // If gh CLI not available or no GitHub remote, return empty silently
+    if (!remoteStatus || !remoteStatus.hasGitHubRemote) {
       return prMap;
     }
 
-    // Fetch open PRs from GitHub
+    // Use -R flag with owner/repo for more reliable PR fetching
+    const repoFlag =
+      remoteStatus.owner && remoteStatus.repo
+        ? `-R ${remoteStatus.owner}/${remoteStatus.repo}`
+        : '';
+
+    // Fetch all PRs from GitHub (including merged/closed to detect state changes)
     const { stdout } = await execAsync(
-      'gh pr list --state open --json number,title,url,state,headRefName,createdAt --limit 1000',
+      `gh pr list ${repoFlag} --state all --json number,title,url,state,headRefName,createdAt --limit 1000`,
       { cwd: projectPath, env: execEnv, timeout: 15000 }
     );
 
@@ -155,7 +220,8 @@ async function fetchGitHubPRs(projectPath: string): Promise<Map<string, Worktree
         number: pr.number,
         url: pr.url,
         title: pr.title,
-        state: pr.state,
+        // GitHub CLI returns state as uppercase: OPEN, MERGED, CLOSED
+        state: validatePRState(pr.state),
         createdAt: pr.createdAt,
       });
     }
@@ -170,9 +236,10 @@ async function fetchGitHubPRs(projectPath: string): Promise<Map<string, Worktree
 export function createListHandler() {
   return async (req: Request, res: Response): Promise<void> => {
     try {
-      const { projectPath, includeDetails } = req.body as {
+      const { projectPath, includeDetails, forceRefreshGitHub } = req.body as {
         projectPath: string;
         includeDetails?: boolean;
+        forceRefreshGitHub?: boolean;
       };
 
       if (!projectPath) {
@@ -180,6 +247,12 @@ export function createListHandler() {
         return;
       }
 
+      // Clear GitHub remote cache if force refresh requested
+      // This allows users to re-check for GitHub remote after adding one
+      if (forceRefreshGitHub) {
+        githubRemoteCache.delete(projectPath);
+      }
+
       if (!(await isGitRepo(projectPath))) {
         res.json({ success: true, worktrees: [] });
         return;
@@ -287,23 +360,43 @@ export function createListHandler() {
         }
       }
 
-      // Add PR info from metadata or GitHub for each worktree
-      // Only fetch GitHub PRs if includeDetails is requested (performance optimization)
+      // Assign PR info to each worktree, preferring fresh GitHub data over cached metadata.
+      // Only fetch GitHub PRs if includeDetails is requested (performance optimization).
+      // Uses --state all to detect merged/closed PRs, limited to 1000 recent PRs.
       const githubPRs = includeDetails
         ? await fetchGitHubPRs(projectPath)
         : new Map<string, WorktreePRInfo>();
 
       for (const worktree of worktrees) {
+        // Skip PR assignment for the main worktree - it's not meaningful to show
+        // PRs on the main branch tab, and can be confusing if someone created
+        // a PR from main to another branch
+        if (worktree.isMain) {
+          continue;
+        }
+
         const metadata = allMetadata.get(worktree.branch);
-        if (metadata?.pr) {
-          // Use stored metadata (more complete info)
-          worktree.pr = metadata.pr;
-        } else if (includeDetails) {
-          // Fall back to GitHub PR detection only when includeDetails is requested
-          const githubPR = githubPRs.get(worktree.branch);
-          if (githubPR) {
-            worktree.pr = githubPR;
+        const githubPR = githubPRs.get(worktree.branch);
+
+        if (githubPR) {
+          // Prefer fresh GitHub data (it has the current state)
+          worktree.pr = githubPR;
+
+          // Sync metadata with GitHub state when:
+          // 1. No metadata exists for this PR (PR created externally)
+          // 2. State has changed (e.g., merged/closed on GitHub)
+          const needsSync = !metadata?.pr || metadata.pr.state !== githubPR.state;
+          if (needsSync) {
+            // Fire and forget - don't block the response
+            updateWorktreePRInfo(projectPath, worktree.branch, githubPR).catch((err) => {
+              logger.warn(
+                `Failed to update PR info for ${worktree.branch}: ${getErrorMessage(err)}`
+              );
+            });
           }
+        } else if (metadata?.pr && metadata.pr.state === 'OPEN') {
+          // Fall back to stored metadata only if the PR is still OPEN
+          worktree.pr = metadata.pr;
         }
       }
 

apps/server/src/routes/worktree/routes/open-in-terminal.ts

@@ -0,0 +1,181 @@
+/**
+ * Terminal endpoints for opening worktree directories in terminals
+ *
+ * POST /open-in-terminal - Open in system default terminal (integrated)
+ * GET /available-terminals - List all available external terminals
+ * GET /default-terminal - Get the default external terminal
+ * POST /refresh-terminals - Clear terminal cache and re-detect
+ * POST /open-in-external-terminal - Open a directory in an external terminal
+ */
+
+import type { Request, Response } from 'express';
+import { isAbsolute } from 'path';
+import {
+  openInTerminal,
+  clearTerminalCache,
+  detectAllTerminals,
+  detectDefaultTerminal,
+  openInExternalTerminal,
+} from '@automaker/platform';
+import { createLogger } from '@automaker/utils';
+import { getErrorMessage, logError } from '../common.js';
+
+const logger = createLogger('open-in-terminal');
+
+/**
+ * Handler to open in system default terminal (integrated terminal behavior)
+ */
+export function createOpenInTerminalHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { worktreePath } = req.body as {
+        worktreePath: string;
+      };
+
+      if (!worktreePath || typeof worktreePath !== 'string') {
+        res.status(400).json({
+          success: false,
+          error: 'worktreePath required and must be a string',
+        });
+        return;
+      }
+
+      // Security: Validate that worktreePath is an absolute path
+      if (!isAbsolute(worktreePath)) {
+        res.status(400).json({
+          success: false,
+          error: 'worktreePath must be an absolute path',
+        });
+        return;
+      }
+
+      // Use the platform utility to open in terminal
+      const result = await openInTerminal(worktreePath);
+      res.json({
+        success: true,
+        result: {
+          message: `Opened terminal in ${worktreePath}`,
+          terminalName: result.terminalName,
+        },
+      });
+    } catch (error) {
+      logError(error, 'Open in terminal failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+
+/**
+ * Handler to get all available external terminals
+ */
+export function createGetAvailableTerminalsHandler() {
+  return async (_req: Request, res: Response): Promise<void> => {
+    try {
+      const terminals = await detectAllTerminals();
+      res.json({
+        success: true,
+        result: {
+          terminals,
+        },
+      });
+    } catch (error) {
+      logError(error, 'Get available terminals failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+
+/**
+ * Handler to get the default external terminal
+ */
+export function createGetDefaultTerminalHandler() {
+  return async (_req: Request, res: Response): Promise<void> => {
+    try {
+      const terminal = await detectDefaultTerminal();
+      res.json({
+        success: true,
+        result: terminal
+          ? {
+              terminalId: terminal.id,
+              terminalName: terminal.name,
+              terminalCommand: terminal.command,
+            }
+          : null,
+      });
+    } catch (error) {
+      logError(error, 'Get default terminal failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+
+/**
+ * Handler to refresh the terminal cache and re-detect available terminals
+ * Useful when the user has installed/uninstalled terminals
+ */
+export function createRefreshTerminalsHandler() {
+  return async (_req: Request, res: Response): Promise<void> => {
+    try {
+      // Clear the cache
+      clearTerminalCache();
+
+      // Re-detect terminals (this will repopulate the cache)
+      const terminals = await detectAllTerminals();
+
+      logger.info(`Terminal cache refreshed, found ${terminals.length} terminals`);
+
+      res.json({
+        success: true,
+        result: {
+          terminals,
+          message: `Found ${terminals.length} available external terminals`,
+        },
+      });
+    } catch (error) {
+      logError(error, 'Refresh terminals failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}
+
+/**
+ * Handler to open a directory in an external terminal
+ */
+export function createOpenInExternalTerminalHandler() {
+  return async (req: Request, res: Response): Promise<void> => {
+    try {
+      const { worktreePath, terminalId } = req.body as {
+        worktreePath: string;
+        terminalId?: string;
+      };
+
+      if (!worktreePath || typeof worktreePath !== 'string') {
+        res.status(400).json({
+          success: false,
+          error: 'worktreePath required and must be a string',
+        });
+        return;
+      }
+
+      if (!isAbsolute(worktreePath)) {
+        res.status(400).json({
+          success: false,
+          error: 'worktreePath must be an absolute path',
+        });
+        return;
+      }
+
+      const result = await openInExternalTerminal(worktreePath, terminalId);
+      res.json({
+        success: true,
+        result: {
+          message: `Opened ${worktreePath} in ${result.terminalName}`,
+          terminalName: result.terminalName,
+        },
+      });
+    } catch (error) {
+      logError(error, 'Open in external terminal failed');
+      res.status(500).json({ success: false, error: getErrorMessage(error) });
+    }
+  };
+}

apps/server/src/services/agent-service.ts

@@ -29,6 +29,7 @@ import {
   getSkillsConfiguration,
   getSubagentsConfiguration,
   getCustomSubagents,
+  getActiveClaudeApiProfile,
 } from '../lib/settings-helpers.js';
 
 interface Message {
@@ -274,6 +275,12 @@ export class AgentService {
           ? await getCustomSubagents(this.settingsService, effectiveWorkDir)
           : undefined;
 
+      // Get active Claude API profile for alternative endpoint configuration
+      const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+        this.settingsService,
+        '[AgentService]'
+      );
+
       // Load project context files (CLAUDE.md, CODE_QUALITY.md, etc.) and memory files
       // Use the user's message as task context for smart memory selection
       const contextResult = await loadContextFiles({
@@ -378,6 +385,8 @@ export class AgentService {
         agents: customSubagents, // Pass custom subagents for task delegation
         thinkingLevel: effectiveThinkingLevel, // Pass thinking level for Claude models
         reasoningEffort: effectiveReasoningEffort, // Pass reasoning effort for Codex models
+        claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+        credentials, // Pass credentials for resolving 'credentials' apiKeySource
       };
 
       // Build prompt content with images

apps/server/src/services/claude-usage-service.ts

@@ -22,6 +22,29 @@ export class ClaudeUsageService {
   private timeout = 30000; // 30 second timeout
   private isWindows = os.platform() === 'win32';
   private isLinux = os.platform() === 'linux';
+  // On Windows, ConPTY requires AttachConsole which fails in Electron/service mode
+  // Detect Electron by checking for electron-specific env vars or process properties
+  // When in Electron, always use winpty to avoid ConPTY's AttachConsole errors
+  private isElectron =
+    !!(process.versions && (process.versions as Record<string, string>).electron) ||
+    !!process.env.ELECTRON_RUN_AS_NODE;
+  private useConptyFallback = false; // Track if we need to use winpty fallback on Windows
+
+  /**
+   * Kill a PTY process with platform-specific handling.
+   * Windows doesn't support Unix signals like SIGTERM, so we call kill() without arguments.
+   * On Unix-like systems (macOS, Linux), we can specify the signal.
+   *
+   * @param ptyProcess - The PTY process to kill
+   * @param signal - The signal to send on Unix-like systems (default: 'SIGTERM')
+   */
+  private killPtyProcess(ptyProcess: pty.IPty, signal: string = 'SIGTERM'): void {
+    if (this.isWindows) {
+      ptyProcess.kill();
+    } else {
+      ptyProcess.kill(signal);
+    }
+  }
 
   /**
    * Check if Claude CLI is available on the system
@@ -181,37 +204,94 @@ export class ClaudeUsageService {
         ? ['/c', 'claude', '--add-dir', workingDirectory]
         : ['-c', `claude --add-dir "${workingDirectory}"`];
 
+      // Using 'any' for ptyProcess because node-pty types don't include 'killed' property
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
       let ptyProcess: any = null;
 
+      // Build PTY spawn options
+      const ptyOptions: pty.IPtyForkOptions = {
+        name: 'xterm-256color',
+        cols: 120,
+        rows: 30,
+        cwd: workingDirectory,
+        env: {
+          ...process.env,
+          TERM: 'xterm-256color',
+        } as Record<string, string>,
+      };
+
+      // On Windows, always use winpty instead of ConPTY
+      // ConPTY requires AttachConsole which fails in many contexts:
+      // - Electron apps without a console
+      // - VS Code integrated terminal
+      // - Spawned from other applications
+      // The error happens in a subprocess so we can't catch it - must proactively disable
+      if (this.isWindows) {
+        (ptyOptions as pty.IWindowsPtyForkOptions).useConpty = false;
+        logger.info(
+          '[executeClaudeUsageCommandPty] Using winpty on Windows (ConPTY disabled for compatibility)'
+        );
+      }
+
       try {
-        ptyProcess = pty.spawn(shell, args, {
-          name: 'xterm-256color',
-          cols: 120,
-          rows: 30,
-          cwd: workingDirectory,
-          env: {
-            ...process.env,
-            TERM: 'xterm-256color',
-          } as Record<string, string>,
-        });
+        ptyProcess = pty.spawn(shell, args, ptyOptions);
       } catch (spawnError) {
         const errorMessage = spawnError instanceof Error ? spawnError.message : String(spawnError);
-        logger.error('[executeClaudeUsageCommandPty] Failed to spawn PTY:', errorMessage);
 
-        // Return a user-friendly error instead of crashing
-        reject(
-          new Error(
-            `Unable to access terminal: ${errorMessage}. Claude CLI may not be available or PTY support is limited in this environment.`
-          )
-        );
-        return;
+        // Check for Windows ConPTY-specific errors
+        if (this.isWindows && errorMessage.includes('AttachConsole failed')) {
+          // ConPTY failed - try winpty fallback
+          if (!this.useConptyFallback) {
+            logger.warn(
+              '[executeClaudeUsageCommandPty] ConPTY AttachConsole failed, retrying with winpty fallback'
+            );
+            this.useConptyFallback = true;
+
+            try {
+              (ptyOptions as pty.IWindowsPtyForkOptions).useConpty = false;
+              ptyProcess = pty.spawn(shell, args, ptyOptions);
+              logger.info(
+                '[executeClaudeUsageCommandPty] Successfully spawned with winpty fallback'
+              );
+            } catch (fallbackError) {
+              const fallbackMessage =
+                fallbackError instanceof Error ? fallbackError.message : String(fallbackError);
+              logger.error(
+                '[executeClaudeUsageCommandPty] Winpty fallback also failed:',
+                fallbackMessage
+              );
+              reject(
+                new Error(
+                  `Windows PTY unavailable: Both ConPTY and winpty failed. This typically happens when running in Electron without a console. ConPTY error: ${errorMessage}. Winpty error: ${fallbackMessage}`
+                )
+              );
+              return;
+            }
+          } else {
+            logger.error('[executeClaudeUsageCommandPty] Winpty fallback failed:', errorMessage);
+            reject(
+              new Error(
+                `Windows PTY unavailable: ${errorMessage}. The application is running without console access (common in Electron). Try running from a terminal window.`
+              )
+            );
+            return;
+          }
+        } else {
+          logger.error('[executeClaudeUsageCommandPty] Failed to spawn PTY:', errorMessage);
+          reject(
+            new Error(
+              `Unable to access terminal: ${errorMessage}. Claude CLI may not be available or PTY support is limited in this environment.`
+            )
+          );
+          return;
+        }
       }
 
       const timeoutId = setTimeout(() => {
         if (!settled) {
           settled = true;
           if (ptyProcess && !ptyProcess.killed) {
-            ptyProcess.kill();
+            this.killPtyProcess(ptyProcess);
           }
           // Don't fail if we have data - return it instead
           if (output.includes('Current session')) {
@@ -244,16 +324,23 @@ export class ClaudeUsageService {
         const cleanOutput = output.replace(/\x1B\[[0-9;]*[A-Za-z]/g, '');
 
         // Check for specific authentication/permission errors
-        if (
-          cleanOutput.includes('OAuth token does not meet scope requirement') ||
-          cleanOutput.includes('permission_error') ||
-          cleanOutput.includes('token_expired') ||
-          cleanOutput.includes('authentication_error')
-        ) {
+        // Must be very specific to avoid false positives from garbled terminal encoding
+        // Removed permission_error check as it was causing false positives with winpty encoding
+        const authChecks = {
+          oauth: cleanOutput.includes('OAuth token does not meet scope requirement'),
+          tokenExpired: cleanOutput.includes('token_expired'),
+          // Only match if it looks like a JSON API error response
+          authError:
+            cleanOutput.includes('"type":"authentication_error"') ||
+            cleanOutput.includes('"type": "authentication_error"'),
+        };
+        const hasAuthError = authChecks.oauth || authChecks.tokenExpired || authChecks.authError;
+
+        if (hasAuthError) {
           if (!settled) {
             settled = true;
             if (ptyProcess && !ptyProcess.killed) {
-              ptyProcess.kill();
+              this.killPtyProcess(ptyProcess);
             }
             reject(
               new Error(
@@ -265,11 +352,16 @@ export class ClaudeUsageService {
         }
 
         // Check if we've seen the usage data (look for "Current session" or the TUI Usage header)
-        if (
-          !hasSeenUsageData &&
-          (cleanOutput.includes('Current session') ||
-            (cleanOutput.includes('Usage') && cleanOutput.includes('% left')))
-        ) {
+        // Also check for percentage patterns that appear in usage output
+        const hasUsageIndicators =
+          cleanOutput.includes('Current session') ||
+          (cleanOutput.includes('Usage') && cleanOutput.includes('% left')) ||
+          // Additional patterns for winpty - look for percentage patterns
+          /\d+%\s*(left|used|remaining)/i.test(cleanOutput) ||
+          cleanOutput.includes('Resets in') ||
+          cleanOutput.includes('Current week');
+
+        if (!hasSeenUsageData && hasUsageIndicators) {
           hasSeenUsageData = true;
           // Wait for full output, then send escape to exit
           setTimeout(() => {
@@ -277,9 +369,10 @@ export class ClaudeUsageService {
               ptyProcess.write('\x1b'); // Send escape key
 
               // Fallback: if ESC doesn't exit (Linux), use SIGTERM after 2s
+              // Windows doesn't support signals, so killPtyProcess handles platform differences
               setTimeout(() => {
                 if (!settled && ptyProcess && !ptyProcess.killed) {
-                  ptyProcess.kill('SIGTERM');
+                  this.killPtyProcess(ptyProcess);
                 }
               }, 2000);
             }
@@ -307,10 +400,18 @@ export class ClaudeUsageService {
         }
 
         // Detect REPL prompt and send /usage command
-        if (
-          !hasSentCommand &&
-          (cleanOutput.includes('❯') || cleanOutput.includes('? for shortcuts'))
-        ) {
+        // On Windows with winpty, Unicode prompt char ❯ gets garbled, so also check for ASCII indicators
+        const isReplReady =
+          cleanOutput.includes('❯') ||
+          cleanOutput.includes('? for shortcuts') ||
+          // Fallback for winpty garbled encoding - detect CLI welcome screen elements
+          (cleanOutput.includes('Welcome back') && cleanOutput.includes('Claude')) ||
+          (cleanOutput.includes('Tips for getting started') && cleanOutput.includes('Claude')) ||
+          // Detect model indicator which appears when REPL is ready
+          (cleanOutput.includes('Opus') && cleanOutput.includes('Claude API')) ||
+          (cleanOutput.includes('Sonnet') && cleanOutput.includes('Claude API'));
+
+        if (!hasSentCommand && isReplReady) {
           hasSentCommand = true;
           // Wait for REPL to fully settle
           setTimeout(() => {
@@ -347,11 +448,9 @@ export class ClaudeUsageService {
         if (settled) return;
         settled = true;
 
-        if (
-          output.includes('token_expired') ||
-          output.includes('authentication_error') ||
-          output.includes('permission_error')
-        ) {
+        // Check for auth errors - must be specific to avoid false positives
+        // Removed permission_error check as it was causing false positives with winpty encoding
+        if (output.includes('token_expired') || output.includes('"type":"authentication_error"')) {
           reject(new Error("Authentication required - please run 'claude login'"));
           return;
         }

apps/server/src/services/dev-server-service.ts

@@ -379,10 +379,11 @@ class DevServerService {
 
     // Create server info early so we can reference it in handlers
     // We'll add it to runningServers after verifying the process started successfully
+    const hostname = process.env.HOSTNAME || 'localhost';
     const serverInfo: DevServerInfo = {
       worktreePath,
       port,
-      url: `http://localhost:${port}`,
+      url: `http://${hostname}:${port}`,
       process: devProcess,
       startedAt: new Date(),
       scrollbackBuffer: '',
@@ -474,7 +475,7 @@ class DevServerService {
       result: {
         worktreePath,
         port,
-        url: `http://localhost:${port}`,
+        url: `http://${hostname}:${port}`,
         message: `Dev server started on port ${port}`,
       },
     };
@@ -594,6 +595,7 @@ class DevServerService {
     result?: {
       worktreePath: string;
       port: number;
+      url: string;
       logs: string;
       startedAt: string;
     };
@@ -613,6 +615,7 @@ class DevServerService {
       result: {
         worktreePath: server.worktreePath,
         port: server.port,
+        url: server.url,
         logs: server.scrollbackBuffer,
         startedAt: server.startedAt.toISOString(),
       },

apps/server/src/services/event-history-service.ts

@@ -0,0 +1,338 @@
+/**
+ * Event History Service - Stores and retrieves event records for debugging and replay
+ *
+ * Provides persistent storage for events in {projectPath}/.automaker/events/
+ * Each event is stored as a separate JSON file with an index for quick listing.
+ *
+ * Features:
+ * - Store events when they occur
+ * - List and filter historical events
+ * - Replay events to test hook configurations
+ * - Delete old events to manage disk space
+ */
+
+import { createLogger } from '@automaker/utils';
+import * as secureFs from '../lib/secure-fs.js';
+import {
+  getEventHistoryDir,
+  getEventHistoryIndexPath,
+  getEventPath,
+  ensureEventHistoryDir,
+} from '@automaker/platform';
+import type {
+  StoredEvent,
+  StoredEventIndex,
+  StoredEventSummary,
+  EventHistoryFilter,
+  EventHookTrigger,
+} from '@automaker/types';
+import { DEFAULT_EVENT_HISTORY_INDEX } from '@automaker/types';
+import { randomUUID } from 'crypto';
+
+const logger = createLogger('EventHistoryService');
+
+/** Maximum events to keep in the index (oldest are pruned) */
+const MAX_EVENTS_IN_INDEX = 1000;
+
+/**
+ * Atomic file write - write to temp file then rename
+ */
+async function atomicWriteJson(filePath: string, data: unknown): Promise<void> {
+  const tempPath = `${filePath}.tmp.${Date.now()}`;
+  const content = JSON.stringify(data, null, 2);
+
+  try {
+    await secureFs.writeFile(tempPath, content, 'utf-8');
+    await secureFs.rename(tempPath, filePath);
+  } catch (error) {
+    try {
+      await secureFs.unlink(tempPath);
+    } catch {
+      // Ignore cleanup errors
+    }
+    throw error;
+  }
+}
+
+/**
+ * Safely read JSON file with fallback to default
+ */
+async function readJsonFile<T>(filePath: string, defaultValue: T): Promise<T> {
+  try {
+    const content = (await secureFs.readFile(filePath, 'utf-8')) as string;
+    return JSON.parse(content) as T;
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
+      return defaultValue;
+    }
+    logger.error(`Error reading ${filePath}:`, error);
+    return defaultValue;
+  }
+}
+
+/**
+ * Input for storing a new event
+ */
+export interface StoreEventInput {
+  trigger: EventHookTrigger;
+  projectPath: string;
+  featureId?: string;
+  featureName?: string;
+  error?: string;
+  errorType?: string;
+  passes?: boolean;
+  metadata?: Record<string, unknown>;
+}
+
+/**
+ * EventHistoryService - Manages persistent storage of events
+ */
+export class EventHistoryService {
+  /**
+   * Store a new event to history
+   *
+   * @param input - Event data to store
+   * @returns Promise resolving to the stored event
+   */
+  async storeEvent(input: StoreEventInput): Promise<StoredEvent> {
+    const { projectPath, trigger, featureId, featureName, error, errorType, passes, metadata } =
+      input;
+
+    // Ensure events directory exists
+    await ensureEventHistoryDir(projectPath);
+
+    const eventId = `evt-${Date.now()}-${randomUUID().slice(0, 8)}`;
+    const timestamp = new Date().toISOString();
+    const projectName = this.extractProjectName(projectPath);
+
+    const event: StoredEvent = {
+      id: eventId,
+      trigger,
+      timestamp,
+      projectPath,
+      projectName,
+      featureId,
+      featureName,
+      error,
+      errorType,
+      passes,
+      metadata,
+    };
+
+    // Write the full event to its own file
+    const eventPath = getEventPath(projectPath, eventId);
+    await atomicWriteJson(eventPath, event);
+
+    // Update the index
+    await this.addToIndex(projectPath, event);
+
+    logger.info(`Stored event ${eventId} (${trigger}) for project ${projectName}`);
+
+    return event;
+  }
+
+  /**
+   * Get all events for a project with optional filtering
+   *
+   * @param projectPath - Absolute path to project directory
+   * @param filter - Optional filter criteria
+   * @returns Promise resolving to array of event summaries
+   */
+  async getEvents(projectPath: string, filter?: EventHistoryFilter): Promise<StoredEventSummary[]> {
+    const indexPath = getEventHistoryIndexPath(projectPath);
+    const index = await readJsonFile<StoredEventIndex>(indexPath, DEFAULT_EVENT_HISTORY_INDEX);
+
+    let events = [...index.events];
+
+    // Apply filters
+    if (filter) {
+      if (filter.trigger) {
+        events = events.filter((e) => e.trigger === filter.trigger);
+      }
+      if (filter.featureId) {
+        events = events.filter((e) => e.featureId === filter.featureId);
+      }
+      if (filter.since) {
+        const sinceDate = new Date(filter.since).getTime();
+        events = events.filter((e) => new Date(e.timestamp).getTime() >= sinceDate);
+      }
+      if (filter.until) {
+        const untilDate = new Date(filter.until).getTime();
+        events = events.filter((e) => new Date(e.timestamp).getTime() <= untilDate);
+      }
+    }
+
+    // Sort by timestamp (newest first)
+    events.sort((a, b) => new Date(b.timestamp).getTime() - new Date(a.timestamp).getTime());
+
+    // Apply pagination
+    if (filter?.offset) {
+      events = events.slice(filter.offset);
+    }
+    if (filter?.limit) {
+      events = events.slice(0, filter.limit);
+    }
+
+    return events;
+  }
+
+  /**
+   * Get a single event by ID
+   *
+   * @param projectPath - Absolute path to project directory
+   * @param eventId - Event identifier
+   * @returns Promise resolving to the full event or null if not found
+   */
+  async getEvent(projectPath: string, eventId: string): Promise<StoredEvent | null> {
+    const eventPath = getEventPath(projectPath, eventId);
+    try {
+      const content = (await secureFs.readFile(eventPath, 'utf-8')) as string;
+      return JSON.parse(content) as StoredEvent;
+    } catch (error) {
+      if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
+        return null;
+      }
+      logger.error(`Error reading event ${eventId}:`, error);
+      return null;
+    }
+  }
+
+  /**
+   * Delete an event by ID
+   *
+   * @param projectPath - Absolute path to project directory
+   * @param eventId - Event identifier
+   * @returns Promise resolving to true if deleted
+   */
+  async deleteEvent(projectPath: string, eventId: string): Promise<boolean> {
+    // Remove from index
+    const indexPath = getEventHistoryIndexPath(projectPath);
+    const index = await readJsonFile<StoredEventIndex>(indexPath, DEFAULT_EVENT_HISTORY_INDEX);
+
+    const initialLength = index.events.length;
+    index.events = index.events.filter((e) => e.id !== eventId);
+
+    if (index.events.length === initialLength) {
+      return false; // Event not found in index
+    }
+
+    await atomicWriteJson(indexPath, index);
+
+    // Delete the event file
+    const eventPath = getEventPath(projectPath, eventId);
+    try {
+      await secureFs.unlink(eventPath);
+    } catch (error) {
+      if ((error as NodeJS.ErrnoException).code !== 'ENOENT') {
+        logger.error(`Error deleting event file ${eventId}:`, error);
+      }
+    }
+
+    logger.info(`Deleted event ${eventId}`);
+    return true;
+  }
+
+  /**
+   * Clear all events for a project
+   *
+   * @param projectPath - Absolute path to project directory
+   * @returns Promise resolving to number of events cleared
+   */
+  async clearEvents(projectPath: string): Promise<number> {
+    const indexPath = getEventHistoryIndexPath(projectPath);
+    const index = await readJsonFile<StoredEventIndex>(indexPath, DEFAULT_EVENT_HISTORY_INDEX);
+
+    const count = index.events.length;
+
+    // Delete all event files
+    for (const event of index.events) {
+      const eventPath = getEventPath(projectPath, event.id);
+      try {
+        await secureFs.unlink(eventPath);
+      } catch (error) {
+        if ((error as NodeJS.ErrnoException).code !== 'ENOENT') {
+          logger.error(`Error deleting event file ${event.id}:`, error);
+        }
+      }
+    }
+
+    // Reset the index
+    await atomicWriteJson(indexPath, DEFAULT_EVENT_HISTORY_INDEX);
+
+    logger.info(`Cleared ${count} events for project`);
+    return count;
+  }
+
+  /**
+   * Get event count for a project
+   *
+   * @param projectPath - Absolute path to project directory
+   * @param filter - Optional filter criteria
+   * @returns Promise resolving to event count
+   */
+  async getEventCount(projectPath: string, filter?: EventHistoryFilter): Promise<number> {
+    const events = await this.getEvents(projectPath, {
+      ...filter,
+      limit: undefined,
+      offset: undefined,
+    });
+    return events.length;
+  }
+
+  /**
+   * Add an event to the index (internal)
+   */
+  private async addToIndex(projectPath: string, event: StoredEvent): Promise<void> {
+    const indexPath = getEventHistoryIndexPath(projectPath);
+    const index = await readJsonFile<StoredEventIndex>(indexPath, DEFAULT_EVENT_HISTORY_INDEX);
+
+    const summary: StoredEventSummary = {
+      id: event.id,
+      trigger: event.trigger,
+      timestamp: event.timestamp,
+      featureName: event.featureName,
+      featureId: event.featureId,
+    };
+
+    // Add to beginning (newest first)
+    index.events.unshift(summary);
+
+    // Prune old events if over limit
+    if (index.events.length > MAX_EVENTS_IN_INDEX) {
+      const removed = index.events.splice(MAX_EVENTS_IN_INDEX);
+      // Delete the pruned event files
+      for (const oldEvent of removed) {
+        const eventPath = getEventPath(projectPath, oldEvent.id);
+        try {
+          await secureFs.unlink(eventPath);
+        } catch {
+          // Ignore deletion errors for pruned events
+        }
+      }
+      logger.info(`Pruned ${removed.length} old events from history`);
+    }
+
+    await atomicWriteJson(indexPath, index);
+  }
+
+  /**
+   * Extract project name from path
+   */
+  private extractProjectName(projectPath: string): string {
+    const parts = projectPath.split(/[/\\]/);
+    return parts[parts.length - 1] || projectPath;
+  }
+}
+
+// Singleton instance
+let eventHistoryServiceInstance: EventHistoryService | null = null;
+
+/**
+ * Get the singleton event history service instance
+ */
+export function getEventHistoryService(): EventHistoryService {
+  if (!eventHistoryServiceInstance) {
+    eventHistoryServiceInstance = new EventHistoryService();
+  }
+  return eventHistoryServiceInstance;
+}

apps/server/src/services/event-hook-service.ts

@@ -0,0 +1,373 @@
+/**
+ * Event Hook Service - Executes custom actions when system events occur
+ *
+ * Listens to the event emitter and triggers configured hooks:
+ * - Shell commands: Executed with configurable timeout
+ * - HTTP webhooks: POST/GET/PUT/PATCH requests with variable substitution
+ *
+ * Also stores events to history for debugging and replay.
+ *
+ * Supported events:
+ * - feature_created: A new feature was created
+ * - feature_success: Feature completed successfully
+ * - feature_error: Feature failed with an error
+ * - auto_mode_complete: Auto mode finished all features (idle state)
+ * - auto_mode_error: Auto mode encountered a critical error
+ */
+
+import { exec } from 'child_process';
+import { promisify } from 'util';
+import { createLogger } from '@automaker/utils';
+import type { EventEmitter } from '../lib/events.js';
+import type { SettingsService } from './settings-service.js';
+import type { EventHistoryService } from './event-history-service.js';
+import type {
+  EventHook,
+  EventHookTrigger,
+  EventHookShellAction,
+  EventHookHttpAction,
+} from '@automaker/types';
+
+const execAsync = promisify(exec);
+const logger = createLogger('EventHooks');
+
+/** Default timeout for shell commands (30 seconds) */
+const DEFAULT_SHELL_TIMEOUT = 30000;
+
+/** Default timeout for HTTP requests (10 seconds) */
+const DEFAULT_HTTP_TIMEOUT = 10000;
+
+/**
+ * Context available for variable substitution in hooks
+ */
+interface HookContext {
+  featureId?: string;
+  featureName?: string;
+  projectPath?: string;
+  projectName?: string;
+  error?: string;
+  errorType?: string;
+  timestamp: string;
+  eventType: EventHookTrigger;
+}
+
+/**
+ * Auto-mode event payload structure
+ */
+interface AutoModeEventPayload {
+  type?: string;
+  featureId?: string;
+  passes?: boolean;
+  message?: string;
+  error?: string;
+  errorType?: string;
+  projectPath?: string;
+}
+
+/**
+ * Feature created event payload structure
+ */
+interface FeatureCreatedPayload {
+  featureId: string;
+  featureName?: string;
+  projectPath: string;
+}
+
+/**
+ * Event Hook Service
+ *
+ * Manages execution of user-configured event hooks in response to system events.
+ * Also stores events to history for debugging and replay.
+ */
+export class EventHookService {
+  private emitter: EventEmitter | null = null;
+  private settingsService: SettingsService | null = null;
+  private eventHistoryService: EventHistoryService | null = null;
+  private unsubscribe: (() => void) | null = null;
+
+  /**
+   * Initialize the service with event emitter, settings service, and event history service
+   */
+  initialize(
+    emitter: EventEmitter,
+    settingsService: SettingsService,
+    eventHistoryService?: EventHistoryService
+  ): void {
+    this.emitter = emitter;
+    this.settingsService = settingsService;
+    this.eventHistoryService = eventHistoryService || null;
+
+    // Subscribe to events
+    this.unsubscribe = emitter.subscribe((type, payload) => {
+      if (type === 'auto-mode:event') {
+        this.handleAutoModeEvent(payload as AutoModeEventPayload);
+      } else if (type === 'feature:created') {
+        this.handleFeatureCreatedEvent(payload as FeatureCreatedPayload);
+      }
+    });
+
+    logger.info('Event hook service initialized');
+  }
+
+  /**
+   * Cleanup subscriptions
+   */
+  destroy(): void {
+    if (this.unsubscribe) {
+      this.unsubscribe();
+      this.unsubscribe = null;
+    }
+    this.emitter = null;
+    this.settingsService = null;
+    this.eventHistoryService = null;
+  }
+
+  /**
+   * Handle auto-mode events and trigger matching hooks
+   */
+  private async handleAutoModeEvent(payload: AutoModeEventPayload): Promise<void> {
+    if (!payload.type) return;
+
+    // Map internal event types to hook triggers
+    let trigger: EventHookTrigger | null = null;
+
+    switch (payload.type) {
+      case 'auto_mode_feature_complete':
+        trigger = payload.passes ? 'feature_success' : 'feature_error';
+        break;
+      case 'auto_mode_error':
+        // Feature-level error (has featureId) vs auto-mode level error
+        trigger = payload.featureId ? 'feature_error' : 'auto_mode_error';
+        break;
+      case 'auto_mode_idle':
+        trigger = 'auto_mode_complete';
+        break;
+      default:
+        // Other event types don't trigger hooks
+        return;
+    }
+
+    if (!trigger) return;
+
+    // Build context for variable substitution
+    const context: HookContext = {
+      featureId: payload.featureId,
+      projectPath: payload.projectPath,
+      projectName: payload.projectPath ? this.extractProjectName(payload.projectPath) : undefined,
+      error: payload.error || payload.message,
+      errorType: payload.errorType,
+      timestamp: new Date().toISOString(),
+      eventType: trigger,
+    };
+
+    // Execute matching hooks (pass passes for feature completion events)
+    await this.executeHooksForTrigger(trigger, context, { passes: payload.passes });
+  }
+
+  /**
+   * Handle feature:created events and trigger matching hooks
+   */
+  private async handleFeatureCreatedEvent(payload: FeatureCreatedPayload): Promise<void> {
+    const context: HookContext = {
+      featureId: payload.featureId,
+      featureName: payload.featureName,
+      projectPath: payload.projectPath,
+      projectName: this.extractProjectName(payload.projectPath),
+      timestamp: new Date().toISOString(),
+      eventType: 'feature_created',
+    };
+
+    await this.executeHooksForTrigger('feature_created', context);
+  }
+
+  /**
+   * Execute all enabled hooks matching the given trigger and store event to history
+   */
+  private async executeHooksForTrigger(
+    trigger: EventHookTrigger,
+    context: HookContext,
+    additionalData?: { passes?: boolean }
+  ): Promise<void> {
+    // Store event to history (even if no hooks match)
+    if (this.eventHistoryService && context.projectPath) {
+      try {
+        await this.eventHistoryService.storeEvent({
+          trigger,
+          projectPath: context.projectPath,
+          featureId: context.featureId,
+          featureName: context.featureName,
+          error: context.error,
+          errorType: context.errorType,
+          passes: additionalData?.passes,
+        });
+      } catch (error) {
+        logger.error('Failed to store event to history:', error);
+      }
+    }
+
+    if (!this.settingsService) {
+      logger.warn('Settings service not available');
+      return;
+    }
+
+    try {
+      const settings = await this.settingsService.getGlobalSettings();
+      const hooks = settings.eventHooks || [];
+
+      // Filter to enabled hooks matching this trigger
+      const matchingHooks = hooks.filter((hook) => hook.enabled && hook.trigger === trigger);
+
+      if (matchingHooks.length === 0) {
+        return;
+      }
+
+      logger.info(`Executing ${matchingHooks.length} hook(s) for trigger: ${trigger}`);
+
+      // Execute hooks in parallel (don't wait for one to finish before starting next)
+      await Promise.allSettled(matchingHooks.map((hook) => this.executeHook(hook, context)));
+    } catch (error) {
+      logger.error('Error executing hooks:', error);
+    }
+  }
+
+  /**
+   * Execute a single hook
+   */
+  private async executeHook(hook: EventHook, context: HookContext): Promise<void> {
+    const hookName = hook.name || hook.id;
+
+    try {
+      if (hook.action.type === 'shell') {
+        await this.executeShellHook(hook.action, context, hookName);
+      } else if (hook.action.type === 'http') {
+        await this.executeHttpHook(hook.action, context, hookName);
+      }
+    } catch (error) {
+      logger.error(`Hook "${hookName}" failed:`, error);
+    }
+  }
+
+  /**
+   * Execute a shell command hook
+   */
+  private async executeShellHook(
+    action: EventHookShellAction,
+    context: HookContext,
+    hookName: string
+  ): Promise<void> {
+    const command = this.substituteVariables(action.command, context);
+    const timeout = action.timeout || DEFAULT_SHELL_TIMEOUT;
+
+    logger.info(`Executing shell hook "${hookName}": ${command}`);
+
+    try {
+      const { stdout, stderr } = await execAsync(command, {
+        timeout,
+        maxBuffer: 1024 * 1024, // 1MB buffer
+      });
+
+      if (stdout) {
+        logger.debug(`Hook "${hookName}" stdout: ${stdout.trim()}`);
+      }
+      if (stderr) {
+        logger.warn(`Hook "${hookName}" stderr: ${stderr.trim()}`);
+      }
+
+      logger.info(`Shell hook "${hookName}" completed successfully`);
+    } catch (error) {
+      if ((error as NodeJS.ErrnoException).code === 'ETIMEDOUT') {
+        logger.error(`Shell hook "${hookName}" timed out after ${timeout}ms`);
+      }
+      throw error;
+    }
+  }
+
+  /**
+   * Execute an HTTP webhook hook
+   */
+  private async executeHttpHook(
+    action: EventHookHttpAction,
+    context: HookContext,
+    hookName: string
+  ): Promise<void> {
+    const url = this.substituteVariables(action.url, context);
+    const method = action.method || 'POST';
+
+    // Substitute variables in headers
+    const headers: Record<string, string> = {
+      'Content-Type': 'application/json',
+    };
+    if (action.headers) {
+      for (const [key, value] of Object.entries(action.headers)) {
+        headers[key] = this.substituteVariables(value, context);
+      }
+    }
+
+    // Substitute variables in body
+    let body: string | undefined;
+    if (action.body) {
+      body = this.substituteVariables(action.body, context);
+    } else if (method !== 'GET') {
+      // Default body with context information
+      body = JSON.stringify({
+        eventType: context.eventType,
+        timestamp: context.timestamp,
+        featureId: context.featureId,
+        projectPath: context.projectPath,
+        projectName: context.projectName,
+        error: context.error,
+      });
+    }
+
+    logger.info(`Executing HTTP hook "${hookName}": ${method} ${url}`);
+
+    try {
+      const controller = new AbortController();
+      const timeoutId = setTimeout(() => controller.abort(), DEFAULT_HTTP_TIMEOUT);
+
+      const response = await fetch(url, {
+        method,
+        headers,
+        body: method !== 'GET' ? body : undefined,
+        signal: controller.signal,
+      });
+
+      clearTimeout(timeoutId);
+
+      if (!response.ok) {
+        logger.warn(`HTTP hook "${hookName}" received status ${response.status}`);
+      } else {
+        logger.info(`HTTP hook "${hookName}" completed successfully (status: ${response.status})`);
+      }
+    } catch (error) {
+      if ((error as Error).name === 'AbortError') {
+        logger.error(`HTTP hook "${hookName}" timed out after ${DEFAULT_HTTP_TIMEOUT}ms`);
+      }
+      throw error;
+    }
+  }
+
+  /**
+   * Substitute {{variable}} placeholders in a string
+   */
+  private substituteVariables(template: string, context: HookContext): string {
+    return template.replace(/\{\{(\w+)\}\}/g, (match, variable) => {
+      const value = context[variable as keyof HookContext];
+      if (value === undefined || value === null) {
+        return '';
+      }
+      return String(value);
+    });
+  }
+
+  /**
+   * Extract project name from path
+   */
+  private extractProjectName(projectPath: string): string {
+    const parts = projectPath.split(/[/\\]/);
+    return parts[parts.length - 1] || projectPath;
+  }
+}
+
+// Singleton instance
+export const eventHookService = new EventHookService();

apps/server/src/services/feature-loader.ts

@@ -5,14 +5,22 @@
 
 import path from 'path';
 import type { Feature, DescriptionHistoryEntry } from '@automaker/types';
-import { createLogger } from '@automaker/utils';
+import {
+  createLogger,
+  atomicWriteJson,
+  readJsonWithRecovery,
+  logRecoveryWarning,
+  DEFAULT_BACKUP_COUNT,
+} from '@automaker/utils';
 import * as secureFs from '../lib/secure-fs.js';
 import {
   getFeaturesDir,
   getFeatureDir,
   getFeatureImagesDir,
+  getAppSpecPath,
   ensureAutomakerDir,
 } from '@automaker/platform';
+import { addImplementedFeature, type ImplementedFeature } from '../lib/xml-extractor.js';
 
 const logger = createLogger('FeatureLoader');
 
@@ -192,31 +200,31 @@ export class FeatureLoader {
       })) as any[];
       const featureDirs = entries.filter((entry) => entry.isDirectory());
 
-      // Load all features concurrently (secureFs has built-in concurrency limiting)
+      // Load all features concurrently with automatic recovery from backups
       const featurePromises = featureDirs.map(async (dir) => {
         const featureId = dir.name;
         const featureJsonPath = this.getFeatureJsonPath(projectPath, featureId);
 
-        try {
-          const content = (await secureFs.readFile(featureJsonPath, 'utf-8')) as string;
-          const feature = JSON.parse(content);
+        // Use recovery-enabled read to handle corrupted files
+        const result = await readJsonWithRecovery<Feature | null>(featureJsonPath, null, {
+          maxBackups: DEFAULT_BACKUP_COUNT,
+          autoRestore: true,
+        });
 
-          if (!feature.id) {
-            logger.warn(`Feature ${featureId} missing required 'id' field, skipping`);
-            return null;
-          }
+        logRecoveryWarning(result, `Feature ${featureId}`, logger);
 
-          return feature as Feature;
-        } catch (error) {
-          if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
-            return null;
-          } else if (error instanceof SyntaxError) {
-            logger.warn(`Failed to parse feature.json for ${featureId}: ${error.message}`);
-          } else {
-            logger.error(`Failed to load feature ${featureId}:`, (error as Error).message);
-          }
+        const feature = result.data;
+
+        if (!feature) {
           return null;
         }
+
+        if (!feature.id) {
+          logger.warn(`Feature ${featureId} missing required 'id' field, skipping`);
+          return null;
+        }
+
+        return feature;
       });
 
       const results = await Promise.all(featurePromises);
@@ -236,21 +244,85 @@ export class FeatureLoader {
     }
   }
 
+  /**
+   * Normalize a title for comparison (case-insensitive, trimmed)
+   */
+  private normalizeTitle(title: string): string {
+    return title.toLowerCase().trim();
+  }
+
+  /**
+   * Find a feature by its title (case-insensitive match)
+   * @param projectPath - Path to the project
+   * @param title - Title to search for
+   * @returns The matching feature or null if not found
+   */
+  async findByTitle(projectPath: string, title: string): Promise<Feature | null> {
+    if (!title || !title.trim()) {
+      return null;
+    }
+
+    const normalizedTitle = this.normalizeTitle(title);
+    const features = await this.getAll(projectPath);
+
+    for (const feature of features) {
+      if (feature.title && this.normalizeTitle(feature.title) === normalizedTitle) {
+        return feature;
+      }
+    }
+
+    return null;
+  }
+
+  /**
+   * Check if a title already exists on another feature (for duplicate detection)
+   * @param projectPath - Path to the project
+   * @param title - Title to check
+   * @param excludeFeatureId - Optional feature ID to exclude from the check (for updates)
+   * @returns The duplicate feature if found, null otherwise
+   */
+  async findDuplicateTitle(
+    projectPath: string,
+    title: string,
+    excludeFeatureId?: string
+  ): Promise<Feature | null> {
+    if (!title || !title.trim()) {
+      return null;
+    }
+
+    const normalizedTitle = this.normalizeTitle(title);
+    const features = await this.getAll(projectPath);
+
+    for (const feature of features) {
+      // Skip the feature being updated (if provided)
+      if (excludeFeatureId && feature.id === excludeFeatureId) {
+        continue;
+      }
+
+      if (feature.title && this.normalizeTitle(feature.title) === normalizedTitle) {
+        return feature;
+      }
+    }
+
+    return null;
+  }
+
   /**
    * Get a single feature by ID
+   * Uses automatic recovery from backups if the main file is corrupted
    */
   async get(projectPath: string, featureId: string): Promise<Feature | null> {
-    try {
-      const featureJsonPath = this.getFeatureJsonPath(projectPath, featureId);
-      const content = (await secureFs.readFile(featureJsonPath, 'utf-8')) as string;
-      return JSON.parse(content);
-    } catch (error) {
-      if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
-        return null;
-      }
-      logger.error(`Failed to get feature ${featureId}:`, error);
-      throw error;
-    }
+    const featureJsonPath = this.getFeatureJsonPath(projectPath, featureId);
+
+    // Use recovery-enabled read to handle corrupted files
+    const result = await readJsonWithRecovery<Feature | null>(featureJsonPath, null, {
+      maxBackups: DEFAULT_BACKUP_COUNT,
+      autoRestore: true,
+    });
+
+    logRecoveryWarning(result, `Feature ${featureId}`, logger);
+
+    return result.data;
   }
 
   /**
@@ -294,8 +366,8 @@ export class FeatureLoader {
       descriptionHistory: initialHistory,
     };
 
-    // Write feature.json
-    await secureFs.writeFile(featureJsonPath, JSON.stringify(feature, null, 2), 'utf-8');
+    // Write feature.json atomically with backup support
+    await atomicWriteJson(featureJsonPath, feature, { backupCount: DEFAULT_BACKUP_COUNT });
 
     logger.info(`Created feature ${featureId}`);
     return feature;
@@ -379,9 +451,9 @@ export class FeatureLoader {
       descriptionHistory: updatedHistory,
     };
 
-    // Write back to file
+    // Write back to file atomically with backup support
     const featureJsonPath = this.getFeatureJsonPath(projectPath, featureId);
-    await secureFs.writeFile(featureJsonPath, JSON.stringify(updatedFeature, null, 2), 'utf-8');
+    await atomicWriteJson(featureJsonPath, updatedFeature, { backupCount: DEFAULT_BACKUP_COUNT });
 
     logger.info(`Updated feature ${featureId}`);
     return updatedFeature;
@@ -460,4 +532,64 @@ export class FeatureLoader {
       }
     }
   }
+
+  /**
+   * Sync a completed feature to the app_spec.txt implemented_features section
+   *
+   * When a feature is completed, this method adds it to the implemented_features
+   * section of the project's app_spec.txt file. This keeps the spec in sync
+   * with the actual state of the codebase.
+   *
+   * @param projectPath - Path to the project
+   * @param feature - The feature to sync (must have title or description)
+   * @param fileLocations - Optional array of file paths where the feature was implemented
+   * @returns True if the spec was updated, false if no spec exists or feature was skipped
+   */
+  async syncFeatureToAppSpec(
+    projectPath: string,
+    feature: Feature,
+    fileLocations?: string[]
+  ): Promise<boolean> {
+    try {
+      const appSpecPath = getAppSpecPath(projectPath);
+
+      // Read the current app_spec.txt
+      let specContent: string;
+      try {
+        specContent = (await secureFs.readFile(appSpecPath, 'utf-8')) as string;
+      } catch (error) {
+        if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
+          logger.info(`No app_spec.txt found for project, skipping sync for feature ${feature.id}`);
+          return false;
+        }
+        throw error;
+      }
+
+      // Build the implemented feature entry
+      const featureName = feature.title || `Feature: ${feature.id}`;
+      const implementedFeature: ImplementedFeature = {
+        name: featureName,
+        description: feature.description,
+        ...(fileLocations && fileLocations.length > 0 ? { file_locations: fileLocations } : {}),
+      };
+
+      // Add the feature to the implemented_features section
+      const updatedSpecContent = addImplementedFeature(specContent, implementedFeature);
+
+      // Check if the content actually changed (feature might already exist)
+      if (updatedSpecContent === specContent) {
+        logger.info(`Feature "${featureName}" already exists in app_spec.txt, skipping`);
+        return false;
+      }
+
+      // Write the updated spec back to the file
+      await secureFs.writeFile(appSpecPath, updatedSpecContent, 'utf-8');
+
+      logger.info(`Synced feature "${featureName}" to app_spec.txt`);
+      return true;
+    } catch (error) {
+      logger.error(`Failed to sync feature ${feature.id} to app_spec.txt:`, error);
+      throw error;
+    }
+  }
 }

apps/server/src/services/ideation-service.ts

@@ -41,6 +41,7 @@ import type { FeatureLoader } from './feature-loader.js';
 import { createChatOptions, validateWorkingDirectory } from '../lib/sdk-options.js';
 import { resolveModelString } from '@automaker/model-resolver';
 import { stripProviderPrefix } from '@automaker/types';
+import { getPromptCustomization, getActiveClaudeApiProfile } from '../lib/settings-helpers.js';
 
 const logger = createLogger('IdeationService');
 
@@ -195,8 +196,12 @@ export class IdeationService {
       // Gather existing features and ideas to prevent duplicate suggestions
       const existingWorkContext = await this.gatherExistingWorkContext(projectPath);
 
+      // Get customized prompts from settings
+      const prompts = await getPromptCustomization(this.settingsService, '[IdeationService]');
+
       // Build system prompt for ideation
       const systemPrompt = this.buildIdeationSystemPrompt(
+        prompts.ideation.ideationSystemPrompt,
         contextResult.formattedPrompt,
         activeSession.session.promptCategory,
         existingWorkContext
@@ -218,6 +223,12 @@ export class IdeationService {
       // Strip provider prefix - providers need bare model IDs
       const bareModel = stripProviderPrefix(modelId);
 
+      // Get active Claude API profile for alternative endpoint configuration
+      const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+        this.settingsService,
+        '[IdeationService]'
+      );
+
       const executeOptions: ExecuteOptions = {
         prompt: message,
         model: bareModel,
@@ -227,6 +238,8 @@ export class IdeationService {
         maxTurns: 1, // Single turn for ideation
         abortController: activeSession.abortController!,
         conversationHistory: conversationHistory.length > 0 ? conversationHistory : undefined,
+        claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+        credentials, // Pass credentials for resolving 'credentials' apiKeySource
       };
 
       const stream = provider.executeQuery(executeOptions);
@@ -645,8 +658,12 @@ export class IdeationService {
       // Gather existing features and ideas to prevent duplicates
       const existingWorkContext = await this.gatherExistingWorkContext(projectPath);
 
+      // Get customized prompts from settings
+      const prompts = await getPromptCustomization(this.settingsService, '[IdeationService]');
+
       // Build system prompt for structured suggestions
       const systemPrompt = this.buildSuggestionsSystemPrompt(
+        prompts.ideation.suggestionsSystemPrompt,
         contextPrompt,
         category,
         count,
@@ -669,6 +686,12 @@ export class IdeationService {
       // Strip provider prefix - providers need bare model IDs
       const bareModel = stripProviderPrefix(modelId);
 
+      // Get active Claude API profile for alternative endpoint configuration
+      const { profile: claudeApiProfile, credentials } = await getActiveClaudeApiProfile(
+        this.settingsService,
+        '[IdeationService]'
+      );
+
       const executeOptions: ExecuteOptions = {
         prompt: prompt.prompt,
         model: bareModel,
@@ -679,6 +702,8 @@ export class IdeationService {
         // Disable all tools - we just want text generation, not codebase analysis
         allowedTools: [],
         abortController: new AbortController(),
+        claudeApiProfile, // Pass active Claude API profile for alternative endpoint configuration
+        credentials, // Pass credentials for resolving 'credentials' apiKeySource
       };
 
       const stream = provider.executeQuery(executeOptions);
@@ -721,8 +746,14 @@ export class IdeationService {
 
   /**
    * Build system prompt for structured suggestion generation
+   * @param basePrompt - The base system prompt from settings
+   * @param contextFilesPrompt - Project context from loaded files
+   * @param category - The idea category to focus on
+   * @param count - Number of suggestions to generate
+   * @param existingWorkContext - Context about existing features/ideas
    */
   private buildSuggestionsSystemPrompt(
+    basePrompt: string,
     contextFilesPrompt: string | undefined,
     category: IdeaCategory,
     count: number = 10,
@@ -734,35 +765,18 @@ export class IdeationService {
 
     const existingWorkSection = existingWorkContext ? `\n\n${existingWorkContext}` : '';
 
-    return `You are an AI product strategist helping brainstorm feature ideas for a software project.
+    // Replace placeholder {{count}} if present, otherwise append count instruction
+    let prompt = basePrompt;
+    if (prompt.includes('{{count}}')) {
+      prompt = prompt.replace(/\{\{count\}\}/g, String(count));
+    } else {
+      prompt += `\n\nGenerate exactly ${count} suggestions.`;
+    }
 
-IMPORTANT: You do NOT have access to any tools. You CANNOT read files, search code, or run commands.
-You must generate suggestions based ONLY on the project context provided below.
-Do NOT say "I'll analyze" or "Let me explore" - you cannot do those things.
-
-Based on the project context and the user's prompt, generate exactly ${count} creative and actionable feature suggestions.
-
-YOUR RESPONSE MUST BE ONLY A JSON ARRAY - nothing else. No explanation, no preamble, no markdown code fences.
-
-Each suggestion must have this structure:
-{
-  "title": "Short, actionable title (max 60 chars)",
-  "description": "Clear description of what to build or improve (2-3 sentences)",
-  "rationale": "Why this is valuable - the problem it solves or opportunity it creates",
-  "priority": "high" | "medium" | "low"
-}
+    return `${prompt}
 
 Focus area: ${this.getCategoryDescription(category)}
 
-Guidelines:
-- Generate exactly ${count} suggestions
-- Be specific and actionable - avoid vague ideas
-- Mix different priority levels (some high, some medium, some low)
-- Each suggestion should be independently implementable
-- Think creatively - include both obvious improvements and innovative ideas
-- Consider the project's domain and target users
-- IMPORTANT: Do NOT suggest features or ideas that already exist in the "Existing Features" or "Existing Ideas" sections below
-
 ${contextSection}${existingWorkSection}`;
   }
 
@@ -1269,30 +1283,11 @@ ${contextSection}${existingWorkSection}`;
   // ============================================================================
 
   private buildIdeationSystemPrompt(
+    basePrompt: string,
     contextFilesPrompt: string | undefined,
     category?: IdeaCategory,
     existingWorkContext?: string
   ): string {
-    const basePrompt = `You are an AI product strategist and UX expert helping brainstorm ideas for improving a software project.
-
-Your role is to:
-- Analyze the codebase structure and patterns
-- Identify opportunities for improvement
-- Suggest actionable ideas with clear rationale
-- Consider user experience, technical feasibility, and business value
-- Be specific and reference actual files/components when possible
-
-When suggesting ideas:
-1. Provide a clear, concise title
-2. Explain the problem or opportunity
-3. Describe the proposed solution
-4. Highlight the expected benefit
-5. Note any dependencies or considerations
-
-IMPORTANT: Do NOT suggest features or ideas that already exist in the project. Check the "Existing Features" and "Existing Ideas" sections below to avoid duplicates.
-
-Focus on practical, implementable suggestions that would genuinely improve the product.`;
-
     const categoryContext = category
       ? `\n\nFocus area: ${this.getCategoryDescription(category)}`
       : '';

apps/server/src/services/notification-service.ts

@@ -0,0 +1,280 @@
+/**
+ * Notification Service - Handles reading/writing notifications to JSON files
+ *
+ * Provides persistent storage for project-level notifications in
+ * {projectPath}/.automaker/notifications.json
+ *
+ * Notifications alert users when:
+ * - Features reach specific statuses (waiting_approval, verified)
+ * - Long-running operations complete (spec generation)
+ */
+
+import { createLogger } from '@automaker/utils';
+import * as secureFs from '../lib/secure-fs.js';
+import { getNotificationsPath, ensureAutomakerDir } from '@automaker/platform';
+import type { Notification, NotificationsFile, NotificationType } from '@automaker/types';
+import { DEFAULT_NOTIFICATIONS_FILE } from '@automaker/types';
+import type { EventEmitter } from '../lib/events.js';
+import { randomUUID } from 'crypto';
+
+const logger = createLogger('NotificationService');
+
+/**
+ * Atomic file write - write to temp file then rename
+ */
+async function atomicWriteJson(filePath: string, data: unknown): Promise<void> {
+  const tempPath = `${filePath}.tmp.${Date.now()}`;
+  const content = JSON.stringify(data, null, 2);
+
+  try {
+    await secureFs.writeFile(tempPath, content, 'utf-8');
+    await secureFs.rename(tempPath, filePath);
+  } catch (error) {
+    // Clean up temp file if it exists
+    try {
+      await secureFs.unlink(tempPath);
+    } catch {
+      // Ignore cleanup errors
+    }
+    throw error;
+  }
+}
+
+/**
+ * Safely read JSON file with fallback to default
+ */
+async function readJsonFile<T>(filePath: string, defaultValue: T): Promise<T> {
+  try {
+    const content = (await secureFs.readFile(filePath, 'utf-8')) as string;
+    return JSON.parse(content) as T;
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
+      return defaultValue;
+    }
+    logger.error(`Error reading ${filePath}:`, error);
+    return defaultValue;
+  }
+}
+
+/**
+ * Input for creating a new notification
+ */
+export interface CreateNotificationInput {
+  type: NotificationType;
+  title: string;
+  message: string;
+  featureId?: string;
+  projectPath: string;
+}
+
+/**
+ * NotificationService - Manages persistent storage of notifications
+ *
+ * Handles reading and writing notifications to JSON files with atomic operations
+ * for reliability. Each project has its own notifications.json file.
+ */
+export class NotificationService {
+  private events: EventEmitter | null = null;
+
+  /**
+   * Set the event emitter for broadcasting notification events
+   */
+  setEventEmitter(events: EventEmitter): void {
+    this.events = events;
+  }
+
+  /**
+   * Get all notifications for a project
+   *
+   * @param projectPath - Absolute path to project directory
+   * @returns Promise resolving to array of notifications
+   */
+  async getNotifications(projectPath: string): Promise<Notification[]> {
+    const notificationsPath = getNotificationsPath(projectPath);
+    const file = await readJsonFile<NotificationsFile>(
+      notificationsPath,
+      DEFAULT_NOTIFICATIONS_FILE
+    );
+    // Filter out dismissed notifications and sort by date (newest first)
+    return file.notifications
+      .filter((n) => !n.dismissed)
+      .sort((a, b) => new Date(b.createdAt).getTime() - new Date(a.createdAt).getTime());
+  }
+
+  /**
+   * Get unread notification count for a project
+   *
+   * @param projectPath - Absolute path to project directory
+   * @returns Promise resolving to unread count
+   */
+  async getUnreadCount(projectPath: string): Promise<number> {
+    const notifications = await this.getNotifications(projectPath);
+    return notifications.filter((n) => !n.read).length;
+  }
+
+  /**
+   * Create a new notification
+   *
+   * @param input - Notification creation input
+   * @returns Promise resolving to the created notification
+   */
+  async createNotification(input: CreateNotificationInput): Promise<Notification> {
+    const { projectPath, type, title, message, featureId } = input;
+
+    // Ensure automaker directory exists
+    await ensureAutomakerDir(projectPath);
+
+    const notificationsPath = getNotificationsPath(projectPath);
+    const file = await readJsonFile<NotificationsFile>(
+      notificationsPath,
+      DEFAULT_NOTIFICATIONS_FILE
+    );
+
+    const notification: Notification = {
+      id: randomUUID(),
+      type,
+      title,
+      message,
+      createdAt: new Date().toISOString(),
+      read: false,
+      dismissed: false,
+      featureId,
+      projectPath,
+    };
+
+    file.notifications.push(notification);
+    await atomicWriteJson(notificationsPath, file);
+
+    logger.info(`Created notification: ${title} for project ${projectPath}`);
+
+    // Emit event for real-time updates
+    if (this.events) {
+      this.events.emit('notification:created', notification);
+    }
+
+    return notification;
+  }
+
+  /**
+   * Mark a notification as read
+   *
+   * @param projectPath - Absolute path to project directory
+   * @param notificationId - ID of the notification to mark as read
+   * @returns Promise resolving to the updated notification or null if not found
+   */
+  async markAsRead(projectPath: string, notificationId: string): Promise<Notification | null> {
+    const notificationsPath = getNotificationsPath(projectPath);
+    const file = await readJsonFile<NotificationsFile>(
+      notificationsPath,
+      DEFAULT_NOTIFICATIONS_FILE
+    );
+
+    const notification = file.notifications.find((n) => n.id === notificationId);
+    if (!notification) {
+      return null;
+    }
+
+    notification.read = true;
+    await atomicWriteJson(notificationsPath, file);
+
+    logger.info(`Marked notification ${notificationId} as read`);
+    return notification;
+  }
+
+  /**
+   * Mark all notifications as read for a project
+   *
+   * @param projectPath - Absolute path to project directory
+   * @returns Promise resolving to number of notifications marked as read
+   */
+  async markAllAsRead(projectPath: string): Promise<number> {
+    const notificationsPath = getNotificationsPath(projectPath);
+    const file = await readJsonFile<NotificationsFile>(
+      notificationsPath,
+      DEFAULT_NOTIFICATIONS_FILE
+    );
+
+    let count = 0;
+    for (const notification of file.notifications) {
+      if (!notification.read && !notification.dismissed) {
+        notification.read = true;
+        count++;
+      }
+    }
+
+    if (count > 0) {
+      await atomicWriteJson(notificationsPath, file);
+      logger.info(`Marked ${count} notifications as read`);
+    }
+
+    return count;
+  }
+
+  /**
+   * Dismiss a notification
+   *
+   * @param projectPath - Absolute path to project directory
+   * @param notificationId - ID of the notification to dismiss
+   * @returns Promise resolving to true if notification was dismissed
+   */
+  async dismissNotification(projectPath: string, notificationId: string): Promise<boolean> {
+    const notificationsPath = getNotificationsPath(projectPath);
+    const file = await readJsonFile<NotificationsFile>(
+      notificationsPath,
+      DEFAULT_NOTIFICATIONS_FILE
+    );
+
+    const notification = file.notifications.find((n) => n.id === notificationId);
+    if (!notification) {
+      return false;
+    }
+
+    notification.dismissed = true;
+    await atomicWriteJson(notificationsPath, file);
+
+    logger.info(`Dismissed notification ${notificationId}`);
+    return true;
+  }
+
+  /**
+   * Dismiss all notifications for a project
+   *
+   * @param projectPath - Absolute path to project directory
+   * @returns Promise resolving to number of notifications dismissed
+   */
+  async dismissAll(projectPath: string): Promise<number> {
+    const notificationsPath = getNotificationsPath(projectPath);
+    const file = await readJsonFile<NotificationsFile>(
+      notificationsPath,
+      DEFAULT_NOTIFICATIONS_FILE
+    );
+
+    let count = 0;
+    for (const notification of file.notifications) {
+      if (!notification.dismissed) {
+        notification.dismissed = true;
+        count++;
+      }
+    }
+
+    if (count > 0) {
+      await atomicWriteJson(notificationsPath, file);
+      logger.info(`Dismissed ${count} notifications`);
+    }
+
+    return count;
+  }
+}
+
+// Singleton instance
+let notificationServiceInstance: NotificationService | null = null;
+
+/**
+ * Get the singleton notification service instance
+ */
+export function getNotificationService(): NotificationService {
+  if (!notificationServiceInstance) {
+    notificationServiceInstance = new NotificationService();
+  }
+  return notificationServiceInstance;
+}

apps/server/src/services/settings-service.ts

@@ -7,8 +7,11 @@
  * - Per-project settings ({projectPath}/.automaker/settings.json)
  */
 
-import { createLogger } from '@automaker/utils';
+import { createLogger, atomicWriteJson, DEFAULT_BACKUP_COUNT } from '@automaker/utils';
 import * as secureFs from '../lib/secure-fs.js';
+import os from 'os';
+import path from 'path';
+import fs from 'fs/promises';
 
 import {
   getGlobalSettingsPath,
@@ -38,32 +41,13 @@ import {
   CREDENTIALS_VERSION,
   PROJECT_SETTINGS_VERSION,
 } from '../types/settings.js';
+import { migrateModelId, migrateCursorModelIds, migrateOpencodeModelIds } from '@automaker/types';
 
 const logger = createLogger('SettingsService');
 
 /**
- * Atomic file write - write to temp file then rename
- */
-async function atomicWriteJson(filePath: string, data: unknown): Promise<void> {
-  const tempPath = `${filePath}.tmp.${Date.now()}`;
-  const content = JSON.stringify(data, null, 2);
-
-  try {
-    await secureFs.writeFile(tempPath, content, 'utf-8');
-    await secureFs.rename(tempPath, filePath);
-  } catch (error) {
-    // Clean up temp file if it exists
-    try {
-      await secureFs.unlink(tempPath);
-    } catch {
-      // Ignore cleanup errors
-    }
-    throw error;
-  }
-}
-
-/**
- * Safely read JSON file with fallback to default
+ * Wrapper for readJsonFile from utils that uses the local secureFs
+ * to maintain compatibility with the server's secure file system
  */
 async function readJsonFile<T>(filePath: string, defaultValue: T): Promise<T> {
   try {
@@ -90,6 +74,13 @@ async function fileExists(filePath: string): Promise<boolean> {
   }
 }
 
+/**
+ * Write settings atomically with backup support
+ */
+async function writeSettingsJson(filePath: string, data: unknown): Promise<void> {
+  await atomicWriteJson(filePath, data, { backupCount: DEFAULT_BACKUP_COUNT });
+}
+
 /**
  * SettingsService - Manages persistent storage of user settings and credentials
  *
@@ -137,10 +128,14 @@ export class SettingsService {
     // Migrate legacy enhancementModel/validationModel to phaseModels
     const migratedPhaseModels = this.migratePhaseModels(settings);
 
+    // Migrate model IDs to canonical format
+    const migratedModelSettings = this.migrateModelSettings(settings);
+
     // Apply any missing defaults (for backwards compatibility)
     let result: GlobalSettings = {
       ...DEFAULT_GLOBAL_SETTINGS,
       ...settings,
+      ...migratedModelSettings,
       keyboardShortcuts: {
         ...DEFAULT_GLOBAL_SETTINGS.keyboardShortcuts,
         ...settings.keyboardShortcuts,
@@ -171,6 +166,41 @@ export class SettingsService {
       needsSave = true;
     }
 
+    // Migration v4 -> v5: Auto-create "Direct Anthropic" profile for existing users
+    // If user has an Anthropic API key in credentials but no profiles, create a
+    // "Direct Anthropic" profile that references the credentials and set it as active.
+    if (storedVersion < 5) {
+      try {
+        const credentials = await this.getCredentials();
+        const hasAnthropicKey = !!credentials.apiKeys?.anthropic;
+        const hasNoProfiles = !result.claudeApiProfiles || result.claudeApiProfiles.length === 0;
+        const hasNoActiveProfile = !result.activeClaudeApiProfileId;
+
+        if (hasAnthropicKey && hasNoProfiles && hasNoActiveProfile) {
+          const directAnthropicProfile = {
+            id: `profile-${Date.now()}-direct-anthropic`,
+            name: 'Direct Anthropic',
+            baseUrl: 'https://api.anthropic.com',
+            apiKeySource: 'credentials' as const,
+            useAuthToken: false,
+          };
+
+          result.claudeApiProfiles = [directAnthropicProfile];
+          result.activeClaudeApiProfileId = directAnthropicProfile.id;
+
+          logger.info(
+            'Migration v4->v5: Created "Direct Anthropic" profile using existing credentials'
+          );
+        }
+      } catch (error) {
+        logger.warn(
+          'Migration v4->v5: Could not check credentials for auto-profile creation:',
+          error
+        );
+      }
+      needsSave = true;
+    }
+
     // Update version if any migration occurred
     if (needsSave) {
       result.version = SETTINGS_VERSION;
@@ -180,7 +210,7 @@ export class SettingsService {
     if (needsSave) {
       try {
         await ensureDataDir(this.dataDir);
-        await atomicWriteJson(settingsPath, result);
+        await writeSettingsJson(settingsPath, result);
         logger.info('Settings migration complete');
       } catch (error) {
         logger.error('Failed to save migrated settings:', error);
@@ -236,19 +266,70 @@ export class SettingsService {
    * Convert a phase model value to PhaseModelEntry format
    *
    * Handles migration from string format (v2) to object format (v3).
-   * - String values like 'sonnet' become { model: 'sonnet' }
-   * - Object values are returned as-is (with type assertion)
+   * Also migrates legacy model IDs to canonical prefixed format.
+   * - String values like 'sonnet' become { model: 'claude-sonnet' }
+   * - Object values have their model ID migrated if needed
    *
    * @param value - Phase model value (string or PhaseModelEntry)
-   * @returns PhaseModelEntry object
+   * @returns PhaseModelEntry object with canonical model ID
    */
   private toPhaseModelEntry(value: string | PhaseModelEntry): PhaseModelEntry {
     if (typeof value === 'string') {
-      // v2 format: just a model string
-      return { model: value as PhaseModelEntry['model'] };
+      // v2 format: just a model string - migrate to canonical ID
+      return { model: migrateModelId(value) as PhaseModelEntry['model'] };
     }
-    // v3 format: already a PhaseModelEntry object
-    return value;
+    // v3 format: PhaseModelEntry object - migrate model ID if needed
+    return {
+      ...value,
+      model: migrateModelId(value.model) as PhaseModelEntry['model'],
+    };
+  }
+
+  /**
+   * Migrate model-related settings to canonical format
+   *
+   * Migrates:
+   * - enabledCursorModels: legacy IDs to cursor- prefixed
+   * - enabledOpencodeModels: legacy slash format to dash format
+   * - cursorDefaultModel: legacy ID to cursor- prefixed
+   *
+   * @param settings - Settings to migrate
+   * @returns Settings with migrated model IDs
+   */
+  private migrateModelSettings(settings: Partial<GlobalSettings>): Partial<GlobalSettings> {
+    const migrated: Partial<GlobalSettings> = { ...settings };
+
+    // Migrate Cursor models
+    if (settings.enabledCursorModels) {
+      migrated.enabledCursorModels = migrateCursorModelIds(
+        settings.enabledCursorModels as string[]
+      );
+    }
+
+    // Migrate Cursor default model
+    if (settings.cursorDefaultModel) {
+      const migratedDefault = migrateCursorModelIds([settings.cursorDefaultModel as string]);
+      if (migratedDefault.length > 0) {
+        migrated.cursorDefaultModel = migratedDefault[0];
+      }
+    }
+
+    // Migrate OpenCode models
+    if (settings.enabledOpencodeModels) {
+      migrated.enabledOpencodeModels = migrateOpencodeModelIds(
+        settings.enabledOpencodeModels as string[]
+      );
+    }
+
+    // Migrate OpenCode default model
+    if (settings.opencodeDefaultModel) {
+      const migratedDefault = migrateOpencodeModelIds([settings.opencodeDefaultModel as string]);
+      if (migratedDefault.length > 0) {
+        migrated.opencodeDefaultModel = migratedDefault[0];
+      }
+    }
+
+    return migrated;
   }
 
   /**
@@ -286,13 +367,39 @@ export class SettingsService {
     };
 
     const currentProjectsLen = Array.isArray(current.projects) ? current.projects.length : 0;
+    // Check if this is a legitimate project removal (moved to trash) vs accidental wipe
+    const newTrashedProjectsLen = Array.isArray(sanitizedUpdates.trashedProjects)
+      ? sanitizedUpdates.trashedProjects.length
+      : Array.isArray(current.trashedProjects)
+        ? current.trashedProjects.length
+        : 0;
+
     if (
       Array.isArray(sanitizedUpdates.projects) &&
       sanitizedUpdates.projects.length === 0 &&
       currentProjectsLen > 0
     ) {
-      attemptedProjectWipe = true;
-      delete sanitizedUpdates.projects;
+      // Only treat as accidental wipe if trashedProjects is also empty
+      // (If projects are moved to trash, they appear in trashedProjects)
+      if (newTrashedProjectsLen === 0) {
+        logger.warn(
+          '[WIPE_PROTECTION] Attempted to set projects to empty array with no trash! Ignoring update.',
+          {
+            currentProjectsLen,
+            newProjectsLen: 0,
+            newTrashedProjectsLen,
+            currentProjects: current.projects?.map((p) => p.name),
+          }
+        );
+        attemptedProjectWipe = true;
+        delete sanitizedUpdates.projects;
+      } else {
+        logger.info('[LEGITIMATE_REMOVAL] Removing all projects to trash', {
+          currentProjectsLen,
+          newProjectsLen: 0,
+          movedToTrash: newTrashedProjectsLen,
+        });
+      }
     }
 
     ignoreEmptyArrayOverwrite('trashedProjects');
@@ -340,7 +447,7 @@ export class SettingsService {
       };
     }
 
-    await atomicWriteJson(settingsPath, updated);
+    await writeSettingsJson(settingsPath, updated);
     logger.info('Global settings updated');
 
     return updated;
@@ -414,7 +521,7 @@ export class SettingsService {
       };
     }
 
-    await atomicWriteJson(credentialsPath, updated);
+    await writeSettingsJson(credentialsPath, updated);
     logger.info('Credentials updated');
 
     return updated;
@@ -525,7 +632,7 @@ export class SettingsService {
       };
     }
 
-    await atomicWriteJson(settingsPath, updated);
+    await writeSettingsJson(settingsPath, updated);
     logger.info(`Project settings updated for ${projectPath}`);
 
     return updated;
@@ -779,4 +886,203 @@ export class SettingsService {
   getDataDir(): string {
     return this.dataDir;
   }
+
+  /**
+   * Get the legacy Electron userData directory path
+   *
+   * Returns the platform-specific path where Electron previously stored settings
+   * before the migration to shared data directories.
+   *
+   * @returns Absolute path to legacy userData directory
+   */
+  private getLegacyElectronUserDataPath(): string {
+    const homeDir = os.homedir();
+
+    switch (process.platform) {
+      case 'darwin':
+        // macOS: ~/Library/Application Support/Automaker
+        return path.join(homeDir, 'Library', 'Application Support', 'Automaker');
+      case 'win32':
+        // Windows: %APPDATA%\Automaker
+        return path.join(
+          process.env.APPDATA || path.join(homeDir, 'AppData', 'Roaming'),
+          'Automaker'
+        );
+      default:
+        // Linux and others: ~/.config/Automaker
+        return path.join(process.env.XDG_CONFIG_HOME || path.join(homeDir, '.config'), 'Automaker');
+    }
+  }
+
+  /**
+   * Migrate entire data directory from legacy Electron userData location to new shared data directory
+   *
+   * This handles the migration from when Electron stored data in the platform-specific
+   * userData directory (e.g., ~/.config/Automaker) to the new shared ./data directory.
+   *
+   * Migration only occurs if:
+   * 1. The new location does NOT have settings.json
+   * 2. The legacy location DOES have settings.json
+   *
+   * Migrates all files and directories including:
+   * - settings.json (global settings)
+   * - credentials.json (API keys)
+   * - sessions-metadata.json (chat session metadata)
+   * - agent-sessions/ (conversation histories)
+   * - Any other files in the data directory
+   *
+   * @returns Promise resolving to migration result
+   */
+  async migrateFromLegacyElectronPath(): Promise<{
+    migrated: boolean;
+    migratedFiles: string[];
+    legacyPath: string;
+    errors: string[];
+  }> {
+    const legacyPath = this.getLegacyElectronUserDataPath();
+    const migratedFiles: string[] = [];
+    const errors: string[] = [];
+
+    // Skip if legacy path is the same as current data dir (no migration needed)
+    if (path.resolve(legacyPath) === path.resolve(this.dataDir)) {
+      logger.debug('Legacy path same as current data dir, skipping migration');
+      return { migrated: false, migratedFiles, legacyPath, errors };
+    }
+
+    logger.info(`Checking for legacy data migration from: ${legacyPath}`);
+    logger.info(`Current data directory: ${this.dataDir}`);
+
+    // Check if new settings already exist
+    const newSettingsPath = getGlobalSettingsPath(this.dataDir);
+    let newSettingsExist = false;
+    try {
+      await fs.access(newSettingsPath);
+      newSettingsExist = true;
+    } catch {
+      // New settings don't exist, migration may be needed
+    }
+
+    if (newSettingsExist) {
+      logger.debug('Settings already exist in new location, skipping migration');
+      return { migrated: false, migratedFiles, legacyPath, errors };
+    }
+
+    // Check if legacy directory exists and has settings
+    const legacySettingsPath = path.join(legacyPath, 'settings.json');
+    let legacySettingsExist = false;
+    try {
+      await fs.access(legacySettingsPath);
+      legacySettingsExist = true;
+    } catch {
+      // Legacy settings don't exist
+    }
+
+    if (!legacySettingsExist) {
+      logger.debug('No legacy settings found, skipping migration');
+      return { migrated: false, migratedFiles, legacyPath, errors };
+    }
+
+    // Perform migration of specific application data files only
+    // (not Electron internal caches like Code Cache, GPU Cache, etc.)
+    logger.info('Found legacy data directory, migrating application data to new location...');
+
+    // Ensure new data directory exists
+    try {
+      await ensureDataDir(this.dataDir);
+    } catch (error) {
+      const msg = `Failed to create data directory: ${error}`;
+      logger.error(msg);
+      errors.push(msg);
+      return { migrated: false, migratedFiles, legacyPath, errors };
+    }
+
+    // Only migrate specific application data files/directories
+    const itemsToMigrate = [
+      'settings.json',
+      'credentials.json',
+      'sessions-metadata.json',
+      'agent-sessions',
+      '.api-key',
+      '.sessions',
+    ];
+
+    for (const item of itemsToMigrate) {
+      const srcPath = path.join(legacyPath, item);
+      const destPath = path.join(this.dataDir, item);
+
+      // Check if source exists
+      try {
+        await fs.access(srcPath);
+      } catch {
+        // Source doesn't exist, skip
+        continue;
+      }
+
+      // Check if destination already exists
+      try {
+        await fs.access(destPath);
+        logger.debug(`Skipping ${item} - already exists in destination`);
+        continue;
+      } catch {
+        // Destination doesn't exist, proceed with copy
+      }
+
+      // Copy file or directory
+      try {
+        const stat = await fs.stat(srcPath);
+        if (stat.isDirectory()) {
+          await this.copyDirectory(srcPath, destPath);
+          migratedFiles.push(item + '/');
+          logger.info(`Migrated directory: ${item}/`);
+        } else {
+          const content = await fs.readFile(srcPath);
+          await fs.writeFile(destPath, content);
+          migratedFiles.push(item);
+          logger.info(`Migrated file: ${item}`);
+        }
+      } catch (error) {
+        const msg = `Failed to migrate ${item}: ${error}`;
+        logger.error(msg);
+        errors.push(msg);
+      }
+    }
+
+    if (migratedFiles.length > 0) {
+      logger.info(
+        `Migration complete. Migrated ${migratedFiles.length} item(s): ${migratedFiles.join(', ')}`
+      );
+      logger.info(`Legacy path: ${legacyPath}`);
+      logger.info(`New path: ${this.dataDir}`);
+    }
+
+    return {
+      migrated: migratedFiles.length > 0,
+      migratedFiles,
+      legacyPath,
+      errors,
+    };
+  }
+
+  /**
+   * Recursively copy a directory from source to destination
+   *
+   * @param srcDir - Source directory path
+   * @param destDir - Destination directory path
+   */
+  private async copyDirectory(srcDir: string, destDir: string): Promise<void> {
+    await fs.mkdir(destDir, { recursive: true });
+    const entries = await fs.readdir(srcDir, { withFileTypes: true });
+
+    for (const entry of entries) {
+      const srcPath = path.join(srcDir, entry.name);
+      const destPath = path.join(destDir, entry.name);
+
+      if (entry.isDirectory()) {
+        await this.copyDirectory(srcPath, destPath);
+      } else if (entry.isFile()) {
+        const content = await fs.readFile(srcPath);
+        await fs.writeFile(destPath, content);
+      }
+    }
+  }
 }

apps/server/src/services/terminal-service.ts

@@ -70,6 +70,29 @@ export class TerminalService extends EventEmitter {
   private sessions: Map<string, TerminalSession> = new Map();
   private dataCallbacks: Set<DataCallback> = new Set();
   private exitCallbacks: Set<ExitCallback> = new Set();
+  private isWindows = os.platform() === 'win32';
+  // On Windows, ConPTY requires AttachConsole which fails in Electron/service mode
+  // Detect Electron by checking for electron-specific env vars or process properties
+  private isElectron =
+    !!(process.versions && (process.versions as Record<string, string>).electron) ||
+    !!process.env.ELECTRON_RUN_AS_NODE;
+  private useConptyFallback = false; // Track if we need to use winpty fallback on Windows
+
+  /**
+   * Kill a PTY process with platform-specific handling.
+   * Windows doesn't support Unix signals like SIGTERM/SIGKILL, so we call kill() without arguments.
+   * On Unix-like systems (macOS, Linux), we can specify the signal.
+   *
+   * @param ptyProcess - The PTY process to kill
+   * @param signal - The signal to send on Unix-like systems (default: 'SIGTERM')
+   */
+  private killPtyProcess(ptyProcess: pty.IPty, signal: string = 'SIGTERM'): void {
+    if (this.isWindows) {
+      ptyProcess.kill();
+    } else {
+      ptyProcess.kill(signal);
+    }
+  }
 
   /**
    * Detect the best shell for the current platform
@@ -322,13 +345,60 @@ export class TerminalService extends EventEmitter {
 
     logger.info(`Creating session ${id} with shell: ${shell} in ${cwd}`);
 
-    const ptyProcess = pty.spawn(shell, shellArgs, {
+    // Build PTY spawn options
+    const ptyOptions: pty.IPtyForkOptions = {
       name: 'xterm-256color',
       cols: options.cols || 80,
       rows: options.rows || 24,
       cwd,
       env,
-    });
+    };
+
+    // On Windows, always use winpty instead of ConPTY
+    // ConPTY requires AttachConsole which fails in many contexts:
+    // - Electron apps without a console
+    // - VS Code integrated terminal
+    // - Spawned from other applications
+    // The error happens in a subprocess so we can't catch it - must proactively disable
+    if (this.isWindows) {
+      (ptyOptions as pty.IWindowsPtyForkOptions).useConpty = false;
+      logger.info(
+        `[createSession] Using winpty for session ${id} (ConPTY disabled for compatibility)`
+      );
+    }
+
+    let ptyProcess: pty.IPty;
+    try {
+      ptyProcess = pty.spawn(shell, shellArgs, ptyOptions);
+    } catch (spawnError) {
+      const errorMessage = spawnError instanceof Error ? spawnError.message : String(spawnError);
+
+      // Check for Windows ConPTY-specific errors
+      if (this.isWindows && errorMessage.includes('AttachConsole failed')) {
+        // ConPTY failed - try winpty fallback
+        if (!this.useConptyFallback) {
+          logger.warn(`[createSession] ConPTY AttachConsole failed, retrying with winpty fallback`);
+          this.useConptyFallback = true;
+
+          try {
+            (ptyOptions as pty.IWindowsPtyForkOptions).useConpty = false;
+            ptyProcess = pty.spawn(shell, shellArgs, ptyOptions);
+            logger.info(`[createSession] Successfully spawned session ${id} with winpty fallback`);
+          } catch (fallbackError) {
+            const fallbackMessage =
+              fallbackError instanceof Error ? fallbackError.message : String(fallbackError);
+            logger.error(`[createSession] Winpty fallback also failed:`, fallbackMessage);
+            return null;
+          }
+        } else {
+          logger.error(`[createSession] PTY spawn failed (winpty):`, errorMessage);
+          return null;
+        }
+      } else {
+        logger.error(`[createSession] PTY spawn failed:`, errorMessage);
+        return null;
+      }
+    }
 
     const session: TerminalSession = {
       id,
@@ -392,7 +462,11 @@ export class TerminalService extends EventEmitter {
 
     // Handle exit
     ptyProcess.onExit(({ exitCode }) => {
-      logger.info(`Session ${id} exited with code ${exitCode}`);
+      const exitMessage =
+        exitCode === undefined || exitCode === null
+          ? 'Session terminated'
+          : `Session exited with code ${exitCode}`;
+      logger.info(`${exitMessage} (${id})`);
       this.sessions.delete(id);
       this.exitCallbacks.forEach((cb) => cb(id, exitCode));
       this.emit('exit', id, exitCode);
@@ -477,8 +551,9 @@ export class TerminalService extends EventEmitter {
       }
 
       // First try graceful SIGTERM to allow process cleanup
+      // On Windows, killPtyProcess calls kill() without signal since Windows doesn't support Unix signals
       logger.info(`Session ${sessionId} sending SIGTERM`);
-      session.pty.kill('SIGTERM');
+      this.killPtyProcess(session.pty, 'SIGTERM');
 
       // Schedule SIGKILL fallback if process doesn't exit gracefully
       // The onExit handler will remove session from map when it actually exits
@@ -486,7 +561,7 @@ export class TerminalService extends EventEmitter {
         if (this.sessions.has(sessionId)) {
           logger.info(`Session ${sessionId} still alive after SIGTERM, sending SIGKILL`);
           try {
-            session.pty.kill('SIGKILL');
+            this.killPtyProcess(session.pty, 'SIGKILL');
           } catch {
             // Process may have already exited
           }
@@ -588,7 +663,8 @@ export class TerminalService extends EventEmitter {
         if (session.flushTimeout) {
           clearTimeout(session.flushTimeout);
         }
-        session.pty.kill();
+        // Use platform-specific kill to ensure proper termination on Windows
+        this.killPtyProcess(session.pty);
       } catch {
         // Ignore errors during cleanup
       }

apps/server/tests/unit/lib/model-resolver.test.ts

@@ -37,7 +37,7 @@ describe('model-resolver.ts', () => {
       const result = resolveModelString('opus');
       expect(result).toBe('claude-opus-4-5-20251101');
       expect(consoleSpy.log).toHaveBeenCalledWith(
-        expect.stringContaining('Resolved Claude model alias: "opus"')
+        expect.stringContaining('Migrated legacy ID: "opus" -> "claude-opus"')
       );
     });
 

apps/server/tests/unit/lib/worktree-metadata.test.ts

@@ -121,7 +121,7 @@ describe('worktree-metadata.ts', () => {
           number: 123,
           url: 'https://github.com/owner/repo/pull/123',
           title: 'Test PR',
-          state: 'open',
+          state: 'OPEN',
           createdAt: new Date().toISOString(),
         },
       };
@@ -158,7 +158,7 @@ describe('worktree-metadata.ts', () => {
           number: 456,
           url: 'https://github.com/owner/repo/pull/456',
           title: 'Updated PR',
-          state: 'closed',
+          state: 'CLOSED',
           createdAt: new Date().toISOString(),
         },
       };
@@ -177,7 +177,7 @@ describe('worktree-metadata.ts', () => {
         number: 789,
         url: 'https://github.com/owner/repo/pull/789',
         title: 'New PR',
-        state: 'open',
+        state: 'OPEN',
         createdAt: new Date().toISOString(),
       };
 
@@ -201,7 +201,7 @@ describe('worktree-metadata.ts', () => {
         number: 999,
         url: 'https://github.com/owner/repo/pull/999',
         title: 'Updated PR',
-        state: 'merged',
+        state: 'MERGED',
         createdAt: new Date().toISOString(),
       };
 
@@ -224,7 +224,7 @@ describe('worktree-metadata.ts', () => {
         number: 111,
         url: 'https://github.com/owner/repo/pull/111',
         title: 'PR',
-        state: 'open',
+        state: 'OPEN',
         createdAt: new Date().toISOString(),
       };
 
@@ -259,7 +259,7 @@ describe('worktree-metadata.ts', () => {
         number: 222,
         url: 'https://github.com/owner/repo/pull/222',
         title: 'Has PR',
-        state: 'open',
+        state: 'OPEN',
         createdAt: new Date().toISOString(),
       };
 
@@ -297,7 +297,7 @@ describe('worktree-metadata.ts', () => {
           number: 333,
           url: 'https://github.com/owner/repo/pull/333',
           title: 'PR 3',
-          state: 'open',
+          state: 'OPEN',
           createdAt: new Date().toISOString(),
         },
       };

apps/server/tests/unit/providers/claude-provider.test.ts

@@ -286,6 +286,7 @@ describe('claude-provider.ts', () => {
 
       const generator = provider.executeQuery({
         prompt: 'Test',
+        model: 'claude-opus-4-5-20251101',
         cwd: '/test',
       });
 
@@ -312,6 +313,7 @@ describe('claude-provider.ts', () => {
 
       const generator = provider.executeQuery({
         prompt: 'Test',
+        model: 'claude-opus-4-5-20251101',
         cwd: '/test',
       });
 
@@ -339,6 +341,7 @@ describe('claude-provider.ts', () => {
 
       const generator = provider.executeQuery({
         prompt: 'Test',
+        model: 'claude-opus-4-5-20251101',
         cwd: '/test',
       });
 

apps/server/tests/unit/providers/codex-provider.test.ts

@@ -11,6 +11,11 @@ import {
   getCodexConfigDir,
   getCodexAuthIndicators,
 } from '@automaker/platform';
+import {
+  calculateReasoningTimeout,
+  REASONING_TIMEOUT_MULTIPLIERS,
+  DEFAULT_TIMEOUT_MS,
+} from '@automaker/types';
 
 const OPENAI_API_KEY_ENV = 'OPENAI_API_KEY';
 const originalOpenAIKey = process.env[OPENAI_API_KEY_ENV];
@@ -289,5 +294,121 @@ describe('codex-provider.ts', () => {
       expect(codexRunMock).not.toHaveBeenCalled();
       expect(spawnJSONLProcess).toHaveBeenCalled();
     });
+
+    it('passes extended timeout for high reasoning effort', async () => {
+      vi.mocked(spawnJSONLProcess).mockReturnValue((async function* () {})());
+
+      await collectAsyncGenerator(
+        provider.executeQuery({
+          prompt: 'Complex reasoning task',
+          model: 'gpt-5.1-codex-max',
+          cwd: '/tmp',
+          reasoningEffort: 'high',
+        })
+      );
+
+      const call = vi.mocked(spawnJSONLProcess).mock.calls[0][0];
+      // High reasoning effort should have 3x the default timeout (90000ms)
+      expect(call.timeout).toBe(DEFAULT_TIMEOUT_MS * REASONING_TIMEOUT_MULTIPLIERS.high);
+    });
+
+    it('passes extended timeout for xhigh reasoning effort', async () => {
+      vi.mocked(spawnJSONLProcess).mockReturnValue((async function* () {})());
+
+      await collectAsyncGenerator(
+        provider.executeQuery({
+          prompt: 'Very complex reasoning task',
+          model: 'gpt-5.1-codex-max',
+          cwd: '/tmp',
+          reasoningEffort: 'xhigh',
+        })
+      );
+
+      const call = vi.mocked(spawnJSONLProcess).mock.calls[0][0];
+      // xhigh reasoning effort should have 4x the default timeout (120000ms)
+      expect(call.timeout).toBe(DEFAULT_TIMEOUT_MS * REASONING_TIMEOUT_MULTIPLIERS.xhigh);
+    });
+
+    it('uses default timeout when no reasoning effort is specified', async () => {
+      vi.mocked(spawnJSONLProcess).mockReturnValue((async function* () {})());
+
+      await collectAsyncGenerator(
+        provider.executeQuery({
+          prompt: 'Simple task',
+          model: 'gpt-5.2',
+          cwd: '/tmp',
+        })
+      );
+
+      const call = vi.mocked(spawnJSONLProcess).mock.calls[0][0];
+      // No reasoning effort should use the default timeout
+      expect(call.timeout).toBe(DEFAULT_TIMEOUT_MS);
+    });
+  });
+
+  describe('calculateReasoningTimeout', () => {
+    it('returns default timeout when no reasoning effort is specified', () => {
+      expect(calculateReasoningTimeout()).toBe(DEFAULT_TIMEOUT_MS);
+      expect(calculateReasoningTimeout(undefined)).toBe(DEFAULT_TIMEOUT_MS);
+    });
+
+    it('returns default timeout for none reasoning effort', () => {
+      expect(calculateReasoningTimeout('none')).toBe(DEFAULT_TIMEOUT_MS);
+    });
+
+    it('applies correct multiplier for minimal reasoning effort', () => {
+      const expected = Math.round(DEFAULT_TIMEOUT_MS * REASONING_TIMEOUT_MULTIPLIERS.minimal);
+      expect(calculateReasoningTimeout('minimal')).toBe(expected);
+    });
+
+    it('applies correct multiplier for low reasoning effort', () => {
+      const expected = Math.round(DEFAULT_TIMEOUT_MS * REASONING_TIMEOUT_MULTIPLIERS.low);
+      expect(calculateReasoningTimeout('low')).toBe(expected);
+    });
+
+    it('applies correct multiplier for medium reasoning effort', () => {
+      const expected = Math.round(DEFAULT_TIMEOUT_MS * REASONING_TIMEOUT_MULTIPLIERS.medium);
+      expect(calculateReasoningTimeout('medium')).toBe(expected);
+    });
+
+    it('applies correct multiplier for high reasoning effort', () => {
+      const expected = Math.round(DEFAULT_TIMEOUT_MS * REASONING_TIMEOUT_MULTIPLIERS.high);
+      expect(calculateReasoningTimeout('high')).toBe(expected);
+    });
+
+    it('applies correct multiplier for xhigh reasoning effort', () => {
+      const expected = Math.round(DEFAULT_TIMEOUT_MS * REASONING_TIMEOUT_MULTIPLIERS.xhigh);
+      expect(calculateReasoningTimeout('xhigh')).toBe(expected);
+    });
+
+    it('uses custom base timeout when provided', () => {
+      const customBase = 60000;
+      expect(calculateReasoningTimeout('high', customBase)).toBe(
+        Math.round(customBase * REASONING_TIMEOUT_MULTIPLIERS.high)
+      );
+    });
+
+    it('falls back to 1.0 multiplier for invalid reasoning effort', () => {
+      // Test that invalid values fallback gracefully to default multiplier
+      // This tests the defensive ?? 1.0 in calculateReasoningTimeout
+      const invalidEffort = 'invalid_effort' as never;
+      expect(calculateReasoningTimeout(invalidEffort)).toBe(DEFAULT_TIMEOUT_MS);
+    });
+
+    it('produces expected absolute timeout values', () => {
+      // Verify the actual timeout values that will be used:
+      // none: 30000ms (30s)
+      // minimal: 36000ms (36s)
+      // low: 45000ms (45s)
+      // medium: 60000ms (1m)
+      // high: 90000ms (1m 30s)
+      // xhigh: 120000ms (2m)
+      expect(calculateReasoningTimeout('none')).toBe(30000);
+      expect(calculateReasoningTimeout('minimal')).toBe(36000);
+      expect(calculateReasoningTimeout('low')).toBe(45000);
+      expect(calculateReasoningTimeout('medium')).toBe(60000);
+      expect(calculateReasoningTimeout('high')).toBe(90000);
+      expect(calculateReasoningTimeout('xhigh')).toBe(120000);
+    });
   });
 });

apps/server/tests/unit/providers/cursor-config-manager.test.ts

@@ -50,8 +50,8 @@ describe('cursor-config-manager.ts', () => {
       manager = new CursorConfigManager(testProjectPath);
 
       const config = manager.getConfig();
-      expect(config.defaultModel).toBe('auto');
-      expect(config.models).toContain('auto');
+      expect(config.defaultModel).toBe('cursor-auto');
+      expect(config.models).toContain('cursor-auto');
     });
 
     it('should use default config if file read fails', () => {
@@ -62,7 +62,7 @@ describe('cursor-config-manager.ts', () => {
 
       manager = new CursorConfigManager(testProjectPath);
 
-      expect(manager.getDefaultModel()).toBe('auto');
+      expect(manager.getDefaultModel()).toBe('cursor-auto');
     });
 
     it('should use default config if JSON parse fails', () => {
@@ -71,7 +71,7 @@ describe('cursor-config-manager.ts', () => {
 
       manager = new CursorConfigManager(testProjectPath);
 
-      expect(manager.getDefaultModel()).toBe('auto');
+      expect(manager.getDefaultModel()).toBe('cursor-auto');
     });
   });
 
@@ -93,7 +93,7 @@ describe('cursor-config-manager.ts', () => {
     });
 
     it('should return default model', () => {
-      expect(manager.getDefaultModel()).toBe('auto');
+      expect(manager.getDefaultModel()).toBe('cursor-auto');
     });
 
     it('should set and persist default model', () => {
@@ -103,13 +103,13 @@ describe('cursor-config-manager.ts', () => {
       expect(fs.writeFileSync).toHaveBeenCalled();
     });
 
-    it('should return auto if defaultModel is undefined', () => {
+    it('should return cursor-auto if defaultModel is undefined', () => {
       vi.mocked(fs.existsSync).mockReturnValue(true);
-      vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify({ models: ['auto'] }));
+      vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify({ models: ['cursor-auto'] }));
 
       manager = new CursorConfigManager(testProjectPath);
 
-      expect(manager.getDefaultModel()).toBe('auto');
+      expect(manager.getDefaultModel()).toBe('cursor-auto');
     });
   });
 
@@ -121,7 +121,7 @@ describe('cursor-config-manager.ts', () => {
     it('should return enabled models', () => {
       const models = manager.getEnabledModels();
       expect(Array.isArray(models)).toBe(true);
-      expect(models).toContain('auto');
+      expect(models).toContain('cursor-auto');
     });
 
     it('should set enabled models', () => {
@@ -131,13 +131,13 @@ describe('cursor-config-manager.ts', () => {
       expect(fs.writeFileSync).toHaveBeenCalled();
     });
 
-    it('should return [auto] if models is undefined', () => {
+    it('should return [cursor-auto] if models is undefined', () => {
       vi.mocked(fs.existsSync).mockReturnValue(true);
-      vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify({ defaultModel: 'auto' }));
+      vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify({ defaultModel: 'cursor-auto' }));
 
       manager = new CursorConfigManager(testProjectPath);
 
-      expect(manager.getEnabledModels()).toEqual(['auto']);
+      expect(manager.getEnabledModels()).toEqual(['cursor-auto']);
     });
   });
 
@@ -146,8 +146,8 @@ describe('cursor-config-manager.ts', () => {
       vi.mocked(fs.existsSync).mockReturnValue(true);
       vi.mocked(fs.readFileSync).mockReturnValue(
         JSON.stringify({
-          defaultModel: 'auto',
-          models: ['auto'],
+          defaultModel: 'cursor-auto',
+          models: ['cursor-auto'],
         })
       );
       manager = new CursorConfigManager(testProjectPath);
@@ -161,14 +161,14 @@ describe('cursor-config-manager.ts', () => {
     });
 
     it('should not add duplicate models', () => {
-      manager.addModel('auto');
+      manager.addModel('cursor-auto');
 
       // Should not save if model already exists
       expect(fs.writeFileSync).not.toHaveBeenCalled();
     });
 
     it('should initialize models array if undefined', () => {
-      vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify({ defaultModel: 'auto' }));
+      vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify({ defaultModel: 'cursor-auto' }));
       manager = new CursorConfigManager(testProjectPath);
 
       manager.addModel('claude-3-5-sonnet');
@@ -293,7 +293,7 @@ describe('cursor-config-manager.ts', () => {
     it('should reset to default values', () => {
       manager.reset();
 
-      expect(manager.getDefaultModel()).toBe('auto');
+      expect(manager.getDefaultModel()).toBe('cursor-auto');
       expect(manager.getMcpServers()).toEqual([]);
       expect(manager.getRules()).toEqual([]);
       expect(fs.writeFileSync).toHaveBeenCalled();

apps/server/tests/unit/services/auto-mode-service-planning.test.ts

@@ -202,8 +202,17 @@ describe('auto-mode-service.ts - Planning Mode', () => {
   });
 
   describe('buildFeaturePrompt', () => {
-    const buildFeaturePrompt = (svc: any, feature: any) => {
-      return svc.buildFeaturePrompt(feature);
+    const defaultTaskExecutionPrompts = {
+      implementationInstructions: 'Test implementation instructions',
+      playwrightVerificationInstructions: 'Test playwright instructions',
+    };
+
+    const buildFeaturePrompt = (
+      svc: any,
+      feature: any,
+      taskExecutionPrompts = defaultTaskExecutionPrompts
+    ) => {
+      return svc.buildFeaturePrompt(feature, taskExecutionPrompts);
     };
 
     it('should include feature ID and description', () => {
@@ -242,14 +251,15 @@ describe('auto-mode-service.ts - Planning Mode', () => {
       expect(result).toContain('/tmp/image2.jpg');
     });
 
-    it('should include summary tags instruction', () => {
+    it('should include implementation instructions', () => {
       const feature = {
         id: 'feat-123',
         description: 'Test feature',
       };
       const result = buildFeaturePrompt(service, feature);
-      expect(result).toContain('<summary>');
-      expect(result).toContain('</summary>');
+      // The prompt should include the implementation instructions passed to it
+      expect(result).toContain('Test implementation instructions');
+      expect(result).toContain('Test playwright instructions');
     });
   });
 

apps/server/tests/unit/services/claude-usage-service.test.ts

@@ -91,7 +91,7 @@ describe('claude-usage-service.ts', () => {
 
     it("should use 'where' command on Windows", async () => {
       vi.mocked(os.platform).mockReturnValue('win32');
-      const windowsService = new ClaudeUsageService(); // Create new service after platform mock
+      const ptyService = new ClaudeUsageService(); // Create new service after platform mock
 
       mockSpawnProcess.on.mockImplementation((event: string, callback: Function) => {
         if (event === 'close') {
@@ -100,7 +100,7 @@ describe('claude-usage-service.ts', () => {
         return mockSpawnProcess;
       });
 
-      await windowsService.isAvailable();
+      await ptyService.isAvailable();
 
       expect(spawn).toHaveBeenCalledWith('where', ['claude']);
     });
@@ -403,120 +403,22 @@ Resets Jan 15, 3pm
     });
   });
 
-  describe('executeClaudeUsageCommandMac', () => {
-    beforeEach(() => {
-      vi.mocked(os.platform).mockReturnValue('darwin');
-      vi.spyOn(process, 'env', 'get').mockReturnValue({ HOME: '/Users/testuser' });
-    });
-
-    it('should execute expect script and return output', async () => {
-      const mockOutput = `
-Current session
-65% left
-Resets in 2h
-`;
-
-      let stdoutCallback: Function;
-      let closeCallback: Function;
-
-      mockSpawnProcess.stdout = {
-        on: vi.fn((event: string, callback: Function) => {
-          if (event === 'data') {
-            stdoutCallback = callback;
-          }
-        }),
-      };
-      mockSpawnProcess.stderr = {
-        on: vi.fn(),
-      };
-      mockSpawnProcess.on = vi.fn((event: string, callback: Function) => {
-        if (event === 'close') {
-          closeCallback = callback;
-        }
-        return mockSpawnProcess;
-      });
-
-      const promise = service.fetchUsageData();
-
-      // Simulate stdout data
-      stdoutCallback!(Buffer.from(mockOutput));
-
-      // Simulate successful close
-      closeCallback!(0);
-
-      const result = await promise;
-
-      expect(result.sessionPercentage).toBe(35); // 100 - 65
-      expect(spawn).toHaveBeenCalledWith(
-        'expect',
-        expect.arrayContaining(['-c']),
-        expect.any(Object)
-      );
-    });
-
-    it('should handle authentication errors', async () => {
-      const mockOutput = 'token_expired';
-
-      let stdoutCallback: Function;
-      let closeCallback: Function;
-
-      mockSpawnProcess.stdout = {
-        on: vi.fn((event: string, callback: Function) => {
-          if (event === 'data') {
-            stdoutCallback = callback;
-          }
-        }),
-      };
-      mockSpawnProcess.stderr = {
-        on: vi.fn(),
-      };
-      mockSpawnProcess.on = vi.fn((event: string, callback: Function) => {
-        if (event === 'close') {
-          closeCallback = callback;
-        }
-        return mockSpawnProcess;
-      });
-
-      const promise = service.fetchUsageData();
-
-      stdoutCallback!(Buffer.from(mockOutput));
-      closeCallback!(1);
-
-      await expect(promise).rejects.toThrow('Authentication required');
-    });
-
-    it('should handle timeout with no data', async () => {
-      vi.useFakeTimers();
-
-      mockSpawnProcess.stdout = {
-        on: vi.fn(),
-      };
-      mockSpawnProcess.stderr = {
-        on: vi.fn(),
-      };
-      mockSpawnProcess.on = vi.fn(() => mockSpawnProcess);
-      mockSpawnProcess.kill = vi.fn();
-
-      const promise = service.fetchUsageData();
-
-      // Advance time past timeout (30 seconds)
-      vi.advanceTimersByTime(31000);
-
-      await expect(promise).rejects.toThrow('Command timed out');
-
-      vi.useRealTimers();
+  // Note: executeClaudeUsageCommandMac tests removed - the service now uses PTY for all platforms
+  // The executeClaudeUsageCommandMac method exists but is dead code (never called)
+  describe.skip('executeClaudeUsageCommandMac (deprecated - uses PTY now)', () => {
+    it('should be skipped - service now uses PTY for all platforms', () => {
+      expect(true).toBe(true);
     });
   });
 
-  describe('executeClaudeUsageCommandWindows', () => {
+  describe('executeClaudeUsageCommandPty', () => {
+    // Note: The service now uses PTY for all platforms, using process.cwd() as the working directory
     beforeEach(() => {
       vi.mocked(os.platform).mockReturnValue('win32');
-      vi.mocked(os.homedir).mockReturnValue('C:\\Users\\testuser');
-      vi.spyOn(process, 'env', 'get').mockReturnValue({ USERPROFILE: 'C:\\Users\\testuser' });
     });
 
-    it('should use node-pty on Windows and return output', async () => {
-      const windowsService = new ClaudeUsageService(); // Create new service for Windows platform
+    it('should use node-pty and return output', async () => {
+      const ptyService = new ClaudeUsageService();
       const mockOutput = `
 Current session
 65% left
@@ -538,7 +440,7 @@ Resets in 2h
       };
       vi.mocked(pty.spawn).mockReturnValue(mockPty as any);
 
-      const promise = windowsService.fetchUsageData();
+      const promise = ptyService.fetchUsageData();
 
       // Simulate data
       dataCallback!(mockOutput);
@@ -549,16 +451,19 @@ Resets in 2h
       const result = await promise;
 
       expect(result.sessionPercentage).toBe(35);
+      // Service uses process.cwd() for --add-dir
       expect(pty.spawn).toHaveBeenCalledWith(
         'cmd.exe',
-        ['/c', 'claude', '--add-dir', 'C:\\Users\\testuser'],
-        expect.any(Object)
+        ['/c', 'claude', '--add-dir', process.cwd()],
+        expect.objectContaining({
+          cwd: process.cwd(),
+        })
       );
     });
 
     it('should send escape key after seeing usage data', async () => {
       vi.useFakeTimers();
-      const windowsService = new ClaudeUsageService();
+      const ptyService = new ClaudeUsageService();
 
       const mockOutput = 'Current session\n65% left';
 
@@ -577,7 +482,7 @@ Resets in 2h
       };
       vi.mocked(pty.spawn).mockReturnValue(mockPty as any);
 
-      const promise = windowsService.fetchUsageData();
+      const promise = ptyService.fetchUsageData();
 
       // Simulate seeing usage data
       dataCallback!(mockOutput);
@@ -594,8 +499,8 @@ Resets in 2h
       vi.useRealTimers();
     });
 
-    it('should handle authentication errors on Windows', async () => {
-      const windowsService = new ClaudeUsageService();
+    it('should handle authentication errors', async () => {
+      const ptyService = new ClaudeUsageService();
       let dataCallback: Function | undefined;
       let exitCallback: Function | undefined;
 
@@ -611,18 +516,22 @@ Resets in 2h
       };
       vi.mocked(pty.spawn).mockReturnValue(mockPty as any);
 
-      const promise = windowsService.fetchUsageData();
+      const promise = ptyService.fetchUsageData();
 
-      dataCallback!('authentication_error');
+      // Send data containing the authentication error pattern the service looks for
+      dataCallback!('"type":"authentication_error"');
+
+      // Trigger the exit handler which checks for auth errors
+      exitCallback!({ exitCode: 1 });
 
       await expect(promise).rejects.toThrow(
         "Claude CLI authentication issue. Please run 'claude logout' and then 'claude login' in your terminal to refresh permissions."
       );
     });
 
-    it('should handle timeout with no data on Windows', async () => {
+    it('should handle timeout with no data', async () => {
       vi.useFakeTimers();
-      const windowsService = new ClaudeUsageService();
+      const ptyService = new ClaudeUsageService();
 
       const mockPty = {
         onData: vi.fn(),
@@ -633,7 +542,7 @@ Resets in 2h
       };
       vi.mocked(pty.spawn).mockReturnValue(mockPty as any);
 
-      const promise = windowsService.fetchUsageData();
+      const promise = ptyService.fetchUsageData();
 
       // Advance time past timeout (45 seconds)
       vi.advanceTimersByTime(46000);
@@ -648,7 +557,7 @@ Resets in 2h
 
     it('should return data on timeout if data was captured', async () => {
       vi.useFakeTimers();
-      const windowsService = new ClaudeUsageService();
+      const ptyService = new ClaudeUsageService();
 
       let dataCallback: Function | undefined;
 
@@ -663,7 +572,7 @@ Resets in 2h
       };
       vi.mocked(pty.spawn).mockReturnValue(mockPty as any);
 
-      const promise = windowsService.fetchUsageData();
+      const promise = ptyService.fetchUsageData();
 
       // Simulate receiving usage data
       dataCallback!('Current session\n65% left\nResets in 2h');
@@ -681,7 +590,9 @@ Resets in 2h
 
     it('should send SIGTERM after ESC if process does not exit', async () => {
       vi.useFakeTimers();
-      const windowsService = new ClaudeUsageService();
+      // Mock Unix platform to test SIGTERM behavior (Windows calls kill() without signal)
+      vi.mocked(os.platform).mockReturnValue('darwin');
+      const ptyService = new ClaudeUsageService();
 
       let dataCallback: Function | undefined;
 
@@ -696,7 +607,7 @@ Resets in 2h
       };
       vi.mocked(pty.spawn).mockReturnValue(mockPty as any);
 
-      windowsService.fetchUsageData();
+      ptyService.fetchUsageData();
 
       // Simulate seeing usage data
       dataCallback!('Current session\n65% left');

apps/server/tests/unit/services/feature-loader.test.ts

@@ -190,9 +190,10 @@ describe('feature-loader.ts', () => {
       const result = await loader.getAll(testProjectPath);
 
       expect(result).toEqual([]);
+      // With recovery-enabled reads, warnings come from AtomicWriter and FeatureLoader
       expect(consoleSpy).toHaveBeenCalledWith(
-        expect.stringMatching(/WARN.*\[FeatureLoader\]/),
-        expect.stringContaining('Failed to parse feature.json')
+        expect.stringMatching(/WARN.*\[AtomicWriter\]/),
+        expect.stringContaining('unavailable')
       );
 
       consoleSpy.mockRestore();
@@ -260,10 +261,13 @@ describe('feature-loader.ts', () => {
       expect(result).toBeNull();
     });
 
-    it('should throw on other errors', async () => {
+    it('should return null on other errors (with recovery attempt)', async () => {
+      // With recovery-enabled reads, get() returns null instead of throwing
+      // because it attempts to recover from backups before giving up
       vi.mocked(fs.readFile).mockRejectedValue(new Error('Permission denied'));
 
-      await expect(loader.get(testProjectPath, 'feature-123')).rejects.toThrow('Permission denied');
+      const result = await loader.get(testProjectPath, 'feature-123');
+      expect(result).toBeNull();
     });
   });
 
@@ -442,4 +446,471 @@ describe('feature-loader.ts', () => {
       );
     });
   });
+
+  describe('findByTitle', () => {
+    it('should find feature by exact title match (case-insensitive)', async () => {
+      vi.mocked(fs.access).mockResolvedValue(undefined);
+      vi.mocked(fs.readdir).mockResolvedValue([
+        { name: 'feature-1', isDirectory: () => true } as any,
+        { name: 'feature-2', isDirectory: () => true } as any,
+      ]);
+
+      vi.mocked(fs.readFile)
+        .mockResolvedValueOnce(
+          JSON.stringify({
+            id: 'feature-1000-abc',
+            title: 'Login Feature',
+            category: 'auth',
+            description: 'Login implementation',
+          })
+        )
+        .mockResolvedValueOnce(
+          JSON.stringify({
+            id: 'feature-2000-def',
+            title: 'Logout Feature',
+            category: 'auth',
+            description: 'Logout implementation',
+          })
+        );
+
+      const result = await loader.findByTitle(testProjectPath, 'LOGIN FEATURE');
+
+      expect(result).not.toBeNull();
+      expect(result?.id).toBe('feature-1000-abc');
+      expect(result?.title).toBe('Login Feature');
+    });
+
+    it('should return null when title is not found', async () => {
+      vi.mocked(fs.access).mockResolvedValue(undefined);
+      vi.mocked(fs.readdir).mockResolvedValue([
+        { name: 'feature-1', isDirectory: () => true } as any,
+      ]);
+
+      vi.mocked(fs.readFile).mockResolvedValueOnce(
+        JSON.stringify({
+          id: 'feature-1000-abc',
+          title: 'Login Feature',
+          category: 'auth',
+          description: 'Login implementation',
+        })
+      );
+
+      const result = await loader.findByTitle(testProjectPath, 'Nonexistent Feature');
+
+      expect(result).toBeNull();
+    });
+
+    it('should return null for empty or whitespace title', async () => {
+      const result1 = await loader.findByTitle(testProjectPath, '');
+      const result2 = await loader.findByTitle(testProjectPath, '   ');
+
+      expect(result1).toBeNull();
+      expect(result2).toBeNull();
+    });
+
+    it('should skip features without titles', async () => {
+      vi.mocked(fs.access).mockResolvedValue(undefined);
+      vi.mocked(fs.readdir).mockResolvedValue([
+        { name: 'feature-1', isDirectory: () => true } as any,
+        { name: 'feature-2', isDirectory: () => true } as any,
+      ]);
+
+      vi.mocked(fs.readFile)
+        .mockResolvedValueOnce(
+          JSON.stringify({
+            id: 'feature-1000-abc',
+            // no title
+            category: 'auth',
+            description: 'Login implementation',
+          })
+        )
+        .mockResolvedValueOnce(
+          JSON.stringify({
+            id: 'feature-2000-def',
+            title: 'Login Feature',
+            category: 'auth',
+            description: 'Another login',
+          })
+        );
+
+      const result = await loader.findByTitle(testProjectPath, 'Login Feature');
+
+      expect(result).not.toBeNull();
+      expect(result?.id).toBe('feature-2000-def');
+    });
+  });
+
+  describe('findDuplicateTitle', () => {
+    it('should find duplicate title', async () => {
+      vi.mocked(fs.access).mockResolvedValue(undefined);
+      vi.mocked(fs.readdir).mockResolvedValue([
+        { name: 'feature-1', isDirectory: () => true } as any,
+      ]);
+
+      vi.mocked(fs.readFile).mockResolvedValueOnce(
+        JSON.stringify({
+          id: 'feature-1000-abc',
+          title: 'My Feature',
+          category: 'ui',
+          description: 'Feature description',
+        })
+      );
+
+      const result = await loader.findDuplicateTitle(testProjectPath, 'my feature');
+
+      expect(result).not.toBeNull();
+      expect(result?.id).toBe('feature-1000-abc');
+    });
+
+    it('should exclude specified feature ID from duplicate check', async () => {
+      vi.mocked(fs.access).mockResolvedValue(undefined);
+      vi.mocked(fs.readdir).mockResolvedValue([
+        { name: 'feature-1', isDirectory: () => true } as any,
+        { name: 'feature-2', isDirectory: () => true } as any,
+      ]);
+
+      vi.mocked(fs.readFile)
+        .mockResolvedValueOnce(
+          JSON.stringify({
+            id: 'feature-1000-abc',
+            title: 'My Feature',
+            category: 'ui',
+            description: 'Feature 1',
+          })
+        )
+        .mockResolvedValueOnce(
+          JSON.stringify({
+            id: 'feature-2000-def',
+            title: 'Other Feature',
+            category: 'ui',
+            description: 'Feature 2',
+          })
+        );
+
+      // Should not find duplicate when excluding the feature that has the title
+      const result = await loader.findDuplicateTitle(
+        testProjectPath,
+        'My Feature',
+        'feature-1000-abc'
+      );
+
+      expect(result).toBeNull();
+    });
+
+    it('should find duplicate when title exists on different feature', async () => {
+      vi.mocked(fs.access).mockResolvedValue(undefined);
+      vi.mocked(fs.readdir).mockResolvedValue([
+        { name: 'feature-1', isDirectory: () => true } as any,
+        { name: 'feature-2', isDirectory: () => true } as any,
+      ]);
+
+      vi.mocked(fs.readFile)
+        .mockResolvedValueOnce(
+          JSON.stringify({
+            id: 'feature-1000-abc',
+            title: 'My Feature',
+            category: 'ui',
+            description: 'Feature 1',
+          })
+        )
+        .mockResolvedValueOnce(
+          JSON.stringify({
+            id: 'feature-2000-def',
+            title: 'Other Feature',
+            category: 'ui',
+            description: 'Feature 2',
+          })
+        );
+
+      // Should find duplicate because feature-1000-abc has the title and we're excluding feature-2000-def
+      const result = await loader.findDuplicateTitle(
+        testProjectPath,
+        'My Feature',
+        'feature-2000-def'
+      );
+
+      expect(result).not.toBeNull();
+      expect(result?.id).toBe('feature-1000-abc');
+    });
+
+    it('should return null for empty or whitespace title', async () => {
+      const result1 = await loader.findDuplicateTitle(testProjectPath, '');
+      const result2 = await loader.findDuplicateTitle(testProjectPath, '   ');
+
+      expect(result1).toBeNull();
+      expect(result2).toBeNull();
+    });
+
+    it('should handle titles with leading/trailing whitespace', async () => {
+      vi.mocked(fs.access).mockResolvedValue(undefined);
+      vi.mocked(fs.readdir).mockResolvedValue([
+        { name: 'feature-1', isDirectory: () => true } as any,
+      ]);
+
+      vi.mocked(fs.readFile).mockResolvedValueOnce(
+        JSON.stringify({
+          id: 'feature-1000-abc',
+          title: 'My Feature',
+          category: 'ui',
+          description: 'Feature description',
+        })
+      );
+
+      const result = await loader.findDuplicateTitle(testProjectPath, '  My Feature  ');
+
+      expect(result).not.toBeNull();
+      expect(result?.id).toBe('feature-1000-abc');
+    });
+  });
+
+  describe('syncFeatureToAppSpec', () => {
+    const sampleAppSpec = `<?xml version="1.0" encoding="UTF-8"?>
+<project_specification>
+  <project_name>Test Project</project_name>
+  <core_capabilities>
+    <capability>Testing</capability>
+  </core_capabilities>
+  <implemented_features>
+    <feature>
+      <name>Existing Feature</name>
+      <description>Already implemented</description>
+    </feature>
+  </implemented_features>
+</project_specification>`;
+
+    const appSpecWithoutFeatures = `<?xml version="1.0" encoding="UTF-8"?>
+<project_specification>
+  <project_name>Test Project</project_name>
+  <core_capabilities>
+    <capability>Testing</capability>
+  </core_capabilities>
+</project_specification>`;
+
+    it('should add feature to app_spec.txt', async () => {
+      vi.mocked(fs.readFile).mockResolvedValueOnce(sampleAppSpec);
+      vi.mocked(fs.writeFile).mockResolvedValue(undefined);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        title: 'New Feature',
+        category: 'ui',
+        description: 'A new feature description',
+      };
+
+      const result = await loader.syncFeatureToAppSpec(testProjectPath, feature);
+
+      expect(result).toBe(true);
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.stringContaining('app_spec.txt'),
+        expect.stringContaining('New Feature'),
+        'utf-8'
+      );
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('A new feature description'),
+        'utf-8'
+      );
+    });
+
+    it('should add feature with file locations', async () => {
+      vi.mocked(fs.readFile).mockResolvedValueOnce(sampleAppSpec);
+      vi.mocked(fs.writeFile).mockResolvedValue(undefined);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        title: 'Feature With Locations',
+        category: 'backend',
+        description: 'Feature with file locations',
+      };
+
+      const result = await loader.syncFeatureToAppSpec(testProjectPath, feature, [
+        'src/feature.ts',
+        'src/utils/helper.ts',
+      ]);
+
+      expect(result).toBe(true);
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('src/feature.ts'),
+        'utf-8'
+      );
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('src/utils/helper.ts'),
+        'utf-8'
+      );
+    });
+
+    it('should return false when app_spec.txt does not exist', async () => {
+      const error: any = new Error('File not found');
+      error.code = 'ENOENT';
+      vi.mocked(fs.readFile).mockRejectedValueOnce(error);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        title: 'New Feature',
+        category: 'ui',
+        description: 'A new feature description',
+      };
+
+      const result = await loader.syncFeatureToAppSpec(testProjectPath, feature);
+
+      expect(result).toBe(false);
+      expect(fs.writeFile).not.toHaveBeenCalled();
+    });
+
+    it('should return false when feature already exists (duplicate)', async () => {
+      vi.mocked(fs.readFile).mockResolvedValueOnce(sampleAppSpec);
+
+      const feature = {
+        id: 'feature-5678-xyz',
+        title: 'Existing Feature', // Same name as existing feature
+        category: 'ui',
+        description: 'Different description',
+      };
+
+      const result = await loader.syncFeatureToAppSpec(testProjectPath, feature);
+
+      expect(result).toBe(false);
+      expect(fs.writeFile).not.toHaveBeenCalled();
+    });
+
+    it('should use feature ID as fallback name when title is missing', async () => {
+      vi.mocked(fs.readFile).mockResolvedValueOnce(sampleAppSpec);
+      vi.mocked(fs.writeFile).mockResolvedValue(undefined);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        category: 'ui',
+        description: 'Feature without title',
+        // No title property
+      };
+
+      const result = await loader.syncFeatureToAppSpec(testProjectPath, feature);
+
+      expect(result).toBe(true);
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('Feature: feature-1234-abc'),
+        'utf-8'
+      );
+    });
+
+    it('should handle app_spec without implemented_features section', async () => {
+      vi.mocked(fs.readFile).mockResolvedValueOnce(appSpecWithoutFeatures);
+      vi.mocked(fs.writeFile).mockResolvedValue(undefined);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        title: 'First Feature',
+        category: 'ui',
+        description: 'First implemented feature',
+      };
+
+      const result = await loader.syncFeatureToAppSpec(testProjectPath, feature);
+
+      expect(result).toBe(true);
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('<implemented_features>'),
+        'utf-8'
+      );
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('First Feature'),
+        'utf-8'
+      );
+    });
+
+    it('should throw on non-ENOENT file read errors', async () => {
+      const error = new Error('Permission denied');
+      vi.mocked(fs.readFile).mockRejectedValueOnce(error);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        title: 'New Feature',
+        category: 'ui',
+        description: 'A new feature description',
+      };
+
+      await expect(loader.syncFeatureToAppSpec(testProjectPath, feature)).rejects.toThrow(
+        'Permission denied'
+      );
+    });
+
+    it('should preserve existing features when adding a new one', async () => {
+      vi.mocked(fs.readFile).mockResolvedValueOnce(sampleAppSpec);
+      vi.mocked(fs.writeFile).mockResolvedValue(undefined);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        title: 'New Feature',
+        category: 'ui',
+        description: 'A new feature',
+      };
+
+      await loader.syncFeatureToAppSpec(testProjectPath, feature);
+
+      // Verify both old and new features are in the output
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('Existing Feature'),
+        'utf-8'
+      );
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('New Feature'),
+        'utf-8'
+      );
+    });
+
+    it('should escape special characters in feature name and description', async () => {
+      vi.mocked(fs.readFile).mockResolvedValueOnce(sampleAppSpec);
+      vi.mocked(fs.writeFile).mockResolvedValue(undefined);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        title: 'Feature with <special> & "chars"',
+        category: 'ui',
+        description: 'Description with <tags> & "quotes"',
+      };
+
+      const result = await loader.syncFeatureToAppSpec(testProjectPath, feature);
+
+      expect(result).toBe(true);
+      // The XML should have escaped characters
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('&lt;special&gt;'),
+        'utf-8'
+      );
+      expect(fs.writeFile).toHaveBeenCalledWith(
+        expect.any(String),
+        expect.stringContaining('&amp;'),
+        'utf-8'
+      );
+    });
+
+    it('should not add empty file_locations array', async () => {
+      vi.mocked(fs.readFile).mockResolvedValueOnce(sampleAppSpec);
+      vi.mocked(fs.writeFile).mockResolvedValue(undefined);
+
+      const feature = {
+        id: 'feature-1234-abc',
+        title: 'Feature Without Locations',
+        category: 'ui',
+        description: 'No file locations',
+      };
+
+      await loader.syncFeatureToAppSpec(testProjectPath, feature, []);
+
+      // File locations should not be included when array is empty
+      const writeCall = vi.mocked(fs.writeFile).mock.calls[0];
+      const writtenContent = writeCall[1] as string;
+
+      // Count occurrences of file_locations - should only have the one from Existing Feature if any
+      // The new feature should not add file_locations
+      expect(writtenContent).toContain('Feature Without Locations');
+    });
+  });
 });

apps/server/tests/unit/services/settings-service.test.ts

@@ -647,9 +647,10 @@ describe('settings-service.ts', () => {
       const settings = await settingsService.getGlobalSettings();
 
       // Verify all phase models are now PhaseModelEntry objects
-      expect(settings.phaseModels.enhancementModel).toEqual({ model: 'sonnet' });
-      expect(settings.phaseModels.fileDescriptionModel).toEqual({ model: 'haiku' });
-      expect(settings.phaseModels.specGenerationModel).toEqual({ model: 'opus' });
+      // Legacy aliases are migrated to canonical IDs
+      expect(settings.phaseModels.enhancementModel).toEqual({ model: 'claude-sonnet' });
+      expect(settings.phaseModels.fileDescriptionModel).toEqual({ model: 'claude-haiku' });
+      expect(settings.phaseModels.specGenerationModel).toEqual({ model: 'claude-opus' });
       expect(settings.version).toBe(SETTINGS_VERSION);
     });
 
@@ -675,16 +676,17 @@ describe('settings-service.ts', () => {
       const settings = await settingsService.getGlobalSettings();
 
       // Verify PhaseModelEntry objects are preserved with thinkingLevel
+      // Legacy aliases are migrated to canonical IDs
       expect(settings.phaseModels.enhancementModel).toEqual({
-        model: 'sonnet',
+        model: 'claude-sonnet',
         thinkingLevel: 'high',
       });
       expect(settings.phaseModels.specGenerationModel).toEqual({
-        model: 'opus',
+        model: 'claude-opus',
         thinkingLevel: 'ultrathink',
       });
       expect(settings.phaseModels.backlogPlanningModel).toEqual({
-        model: 'sonnet',
+        model: 'claude-sonnet',
         thinkingLevel: 'medium',
       });
     });
@@ -710,15 +712,15 @@ describe('settings-service.ts', () => {
 
       const settings = await settingsService.getGlobalSettings();
 
-      // Strings should be converted to objects
-      expect(settings.phaseModels.enhancementModel).toEqual({ model: 'sonnet' });
-      expect(settings.phaseModels.imageDescriptionModel).toEqual({ model: 'haiku' });
-      // Objects should be preserved
+      // Strings should be converted to objects with canonical IDs
+      expect(settings.phaseModels.enhancementModel).toEqual({ model: 'claude-sonnet' });
+      expect(settings.phaseModels.imageDescriptionModel).toEqual({ model: 'claude-haiku' });
+      // Objects should be preserved with migrated IDs
       expect(settings.phaseModels.fileDescriptionModel).toEqual({
-        model: 'haiku',
+        model: 'claude-haiku',
         thinkingLevel: 'low',
       });
-      expect(settings.phaseModels.validationModel).toEqual({ model: 'opus' });
+      expect(settings.phaseModels.validationModel).toEqual({ model: 'claude-opus' });
     });
 
     it('should migrate legacy enhancementModel/validationModel fields', async () => {
@@ -735,11 +737,11 @@ describe('settings-service.ts', () => {
 
       const settings = await settingsService.getGlobalSettings();
 
-      // Legacy fields should be migrated to phaseModels
-      expect(settings.phaseModels.enhancementModel).toEqual({ model: 'haiku' });
-      expect(settings.phaseModels.validationModel).toEqual({ model: 'opus' });
-      // Other fields should use defaults
-      expect(settings.phaseModels.specGenerationModel).toEqual({ model: 'opus' });
+      // Legacy fields should be migrated to phaseModels with canonical IDs
+      expect(settings.phaseModels.enhancementModel).toEqual({ model: 'claude-haiku' });
+      expect(settings.phaseModels.validationModel).toEqual({ model: 'claude-opus' });
+      // Other fields should use defaults (canonical IDs)
+      expect(settings.phaseModels.specGenerationModel).toEqual({ model: 'claude-opus' });
     });
 
     it('should use default phase models when none are configured', async () => {
@@ -753,10 +755,10 @@ describe('settings-service.ts', () => {
 
       const settings = await settingsService.getGlobalSettings();
 
-      // Should use DEFAULT_PHASE_MODELS
-      expect(settings.phaseModels.enhancementModel).toEqual({ model: 'sonnet' });
-      expect(settings.phaseModels.fileDescriptionModel).toEqual({ model: 'haiku' });
-      expect(settings.phaseModels.specGenerationModel).toEqual({ model: 'opus' });
+      // Should use DEFAULT_PHASE_MODELS (with canonical IDs)
+      expect(settings.phaseModels.enhancementModel).toEqual({ model: 'claude-sonnet' });
+      expect(settings.phaseModels.fileDescriptionModel).toEqual({ model: 'claude-haiku' });
+      expect(settings.phaseModels.specGenerationModel).toEqual({ model: 'claude-opus' });
     });
 
     it('should deep merge phaseModels on update', async () => {
@@ -776,13 +778,13 @@ describe('settings-service.ts', () => {
 
       const settings = await settingsService.getGlobalSettings();
 
-      // Both should be preserved
+      // Both should be preserved (models migrated to canonical format)
       expect(settings.phaseModels.enhancementModel).toEqual({
-        model: 'sonnet',
+        model: 'claude-sonnet',
         thinkingLevel: 'high',
       });
       expect(settings.phaseModels.specGenerationModel).toEqual({
-        model: 'opus',
+        model: 'claude-opus',
         thinkingLevel: 'ultrathink',
       });
     });

apps/ui/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@automaker/ui",
-  "version": "0.11.0",
+  "version": "0.12.0",
   "description": "An autonomous AI development studio that helps you build software faster using AI-powered agents",
   "homepage": "https://github.com/AutoMaker-Org/automaker",
   "repository": {
@@ -40,6 +40,7 @@
   },
   "dependencies": {
     "@automaker/dependency-resolver": "1.0.0",
+    "@automaker/spec-parser": "1.0.0",
     "@automaker/types": "1.0.0",
     "@codemirror/lang-xml": "6.1.0",
     "@codemirror/language": "^6.12.1",
@@ -48,6 +49,22 @@
     "@dnd-kit/core": "6.3.1",
     "@dnd-kit/sortable": "10.0.0",
     "@dnd-kit/utilities": "3.2.2",
+    "@fontsource/cascadia-code": "^5.2.3",
+    "@fontsource/fira-code": "^5.2.7",
+    "@fontsource/ibm-plex-mono": "^5.2.7",
+    "@fontsource/inconsolata": "^5.2.8",
+    "@fontsource/inter": "^5.2.8",
+    "@fontsource/iosevka": "^5.2.5",
+    "@fontsource/jetbrains-mono": "^5.2.8",
+    "@fontsource/lato": "^5.2.7",
+    "@fontsource/montserrat": "^5.2.8",
+    "@fontsource/open-sans": "^5.2.7",
+    "@fontsource/poppins": "^5.2.7",
+    "@fontsource/raleway": "^5.2.8",
+    "@fontsource/roboto": "^5.2.9",
+    "@fontsource/source-code-pro": "^5.2.7",
+    "@fontsource/source-sans-3": "^5.2.9",
+    "@fontsource/work-sans": "^5.2.8",
     "@lezer/highlight": "1.2.3",
     "@radix-ui/react-checkbox": "1.3.3",
     "@radix-ui/react-collapsible": "1.1.12",
@@ -204,12 +221,34 @@
           "arch": [
             "x64"
           ]
+        },
+        {
+          "target": "rpm",
+          "arch": [
+            "x64"
+          ]
         }
       ],
       "category": "Development",
       "icon": "public/logo_larger.png",
       "maintainer": "webdevcody@gmail.com",
-      "executableName": "automaker"
+      "executableName": "automaker",
+      "description": "An autonomous AI development studio that helps you build software faster using AI-powered agents",
+      "synopsis": "AI-powered autonomous development studio"
+    },
+    "rpm": {
+      "depends": [
+        "gtk3",
+        "libnotify",
+        "nss",
+        "libXScrnSaver",
+        "libXtst",
+        "xdg-utils",
+        "at-spi2-core",
+        "libuuid"
+      ],
+      "compression": "xz",
+      "vendor": "AutoMaker Team"
     },
     "nsis": {
       "oneClick": false,

apps/ui/src/app.tsx

@@ -8,6 +8,7 @@ import { useCursorStatusInit } from './hooks/use-cursor-status-init';
 import { useProviderAuthInit } from './hooks/use-provider-auth-init';
 import './styles/global.css';
 import './styles/theme-imports';
+import './styles/font-imports';
 
 const logger = createLogger('App');
 

apps/ui/src/assets/fonts/zed/zed-fonts.css

@@ -0,0 +1,67 @@
+/* Zed Fonts - https://github.com/zed-industries/zed-fonts */
+
+/* Zed Sans - UI Font */
+@font-face {
+  font-family: 'Zed Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url('./zed-sans-extended.ttf') format('truetype');
+}
+
+@font-face {
+  font-family: 'Zed Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url('./zed-sans-extendeditalic.ttf') format('truetype');
+}
+
+@font-face {
+  font-family: 'Zed Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url('./zed-sans-extendedbold.ttf') format('truetype');
+}
+
+@font-face {
+  font-family: 'Zed Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-display: swap;
+  src: url('./zed-sans-extendedbolditalic.ttf') format('truetype');
+}
+
+/* Zed Mono - Code Font */
+@font-face {
+  font-family: 'Zed Mono';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url('./zed-mono-extended.ttf') format('truetype');
+}
+
+@font-face {
+  font-family: 'Zed Mono';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url('./zed-mono-extendeditalic.ttf') format('truetype');
+}
+
+@font-face {
+  font-family: 'Zed Mono';
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url('./zed-mono-extendedbold.ttf') format('truetype');
+}
+
+@font-face {
+  font-family: 'Zed Mono';
+  font-style: italic;
+  font-weight: 700;
+  font-display: swap;
+  src: url('./zed-mono-extendedbolditalic.ttf') format('truetype');
+}