fix: SQLAlchemy PendingRollbackError + MCP support for Expand/Assistant

CUSTOM_UPDATES.md

@@ -8,7 +8,8 @@ This document tracks all customizations made to AutoCoder that deviate from the
 
 1. [UI Theme Customization](#1-ui-theme-customization)
 2. [Playwright Browser Configuration](#2-playwright-browser-configuration)
-3. [Update Checklist](#update-checklist)
+3. [SQLite Robust Connection Handling](#3-sqlite-robust-connection-handling)
+4. [Update Checklist](#4-update-checklist)
 
 ---
 
@@ -174,21 +175,115 @@ playwright_args = [
 
 ---
 
-## 3. Update Checklist
+## 3. SQLite Robust Connection Handling
+
+### Overview
+
+Added robust SQLite connection handling to prevent database corruption from concurrent access (MCP server, FastAPI server, progress tracking).
+
+**Features Added:**
+- WAL mode for better concurrency
+- Busy timeout (30 seconds)
+- Retry logic with exponential backoff
+- Database health check endpoint
+
+### Modified Files
+
+#### `api/database.py`
+
+**New functions added:**
+
+```python
+def get_robust_connection(db_path: str) -> sqlite3.Connection:
+    """
+    Create a SQLite connection with robust settings:
+    - WAL mode for concurrent access
+    - 30 second busy timeout
+    - Foreign keys enabled
+    """
+
+@contextmanager
+def robust_db_connection(db_path: str):
+    """Context manager for robust database connections."""
+
+def execute_with_retry(conn, sql, params=None, max_retries=3):
+    """Execute SQL with exponential backoff retry for transient errors."""
+
+def check_database_health(db_path: str) -> dict:
+    """
+    Check database integrity and return health status.
+    Returns: {healthy: bool, message: str, details: dict}
+    """
+```
+
+---
+
+#### `progress.py`
+
+**Changed from raw sqlite3 to robust connections:**
+
+```python
+# BEFORE:
+conn = sqlite3.connect(db_path)
+
+# AFTER:
+from api.database import robust_db_connection, execute_with_retry
+
+with robust_db_connection(db_path) as conn:
+    execute_with_retry(conn, sql, params)
+```
+
+---
+
+#### `server/routers/projects.py`
+
+**New endpoint added:**
+
+```python
+@router.get("/{project_name}/db-health")
+async def get_database_health(project_name: str) -> DatabaseHealth:
+    """
+    Check the health of the project's features database.
+    Useful for diagnosing corruption issues.
+    """
+```
+
+---
+
+#### `server/schemas.py`
+
+**New schema added:**
+
+```python
+class DatabaseHealth(BaseModel):
+    healthy: bool
+    message: str
+    details: dict = {}
+```
+
+---
+
+## 4. Update Checklist
 
 When updating AutoCoder from upstream, verify these items:
 
 ### UI Changes
 - [ ] `ui/src/styles/custom-theme.css` is preserved
 - [ ] `ui/src/components/KanbanColumn.tsx` changes are preserved
+- [ ] `ui/src/main.tsx` imports custom theme
 - [ ] Run `npm run build` in `ui/` directory
 - [ ] Test both light and dark modes
 
 ### Backend Changes
 - [ ] `client.py` - Playwright browser/headless defaults preserved
 - [ ] `.env.example` - Documentation updates preserved
+- [ ] `api/database.py` - Robust connection functions preserved
+- [ ] `progress.py` - Uses robust_db_connection
+- [ ] `server/routers/projects.py` - db-health endpoint preserved
+- [ ] `server/schemas.py` - DatabaseHealth schema preserved
 
 ### General
+- [ ] Test database operations under concurrent load
 - [ ] Verify Playwright uses Firefox by default
 - [ ] Check that browser runs headless by default
 
@@ -205,7 +300,8 @@ cd ui && npm run build
 
 ### Backend Only
 ```bash
-git checkout client.py .env.example
+git checkout client.py .env.example api/database.py progress.py
+git checkout server/routers/projects.py server/schemas.py
 ```
 
 ---
@@ -219,10 +315,17 @@ git checkout client.py .env.example
 | `ui/src/main.tsx` | UI | Imports custom theme |
 | `client.py` | Backend | Firefox + headless defaults |
 | `.env.example` | Config | Updated documentation |
+| `api/database.py` | Backend | Robust SQLite connections |
+| `progress.py` | Backend | Uses robust connections |
+| `server/routers/projects.py` | Backend | db-health endpoint |
+| `server/schemas.py` | Backend | DatabaseHealth schema |
 
 ---
 
 ## Last Updated
 
 **Date:** January 2026
+**Commits:**
+- `1910b96` - SQLite robust connection handling
+- `e014b04` - Custom theme override system
 **PR:** #93 - Twitter-style UI theme with custom theme override system