Enhance MCP development features and introduce skills management

- Added configuration options for requiring human approval before applying LLM-generated MCP patches.
- Updated Docker setup to include skills directory.
- Integrated skills management into the backend, allowing for procedural guides and skill matching.
- Refactored database initialization to apply Alembic migrations.
- Enhanced task approval process to handle MCP patch applications with optional approval.
- Introduced new schemas for skills and updated existing APIs to support skills functionality.

This commit lays the groundwork for improved agent capabilities and better management of MCP development processes.

backend/app/database.py

@@ -1,13 +1,18 @@
-"""Async SQLAlchemy engine, session factory, and Base model."""
+"""Database schema migrations via Alembic."""
 from __future__ import annotations
 
+import asyncio
+import logging
 from collections.abc import AsyncGenerator
+from pathlib import Path
 
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
 from sqlalchemy.orm import DeclarativeBase
 
 from app.config import settings
 
+logger = logging.getLogger(__name__)
+
 engine = create_async_engine(settings.database_url, echo=False, pool_pre_ping=True)
 SessionLocal = async_sessionmaker(engine, class_=AsyncSession, expire_on_commit=False)
 
@@ -21,45 +26,19 @@ async def get_db() -> AsyncGenerator[AsyncSession, None]:
         yield session
 
 
-async def init_db() -> None:
-    """Create tables and apply lightweight dev migrations."""
-    from app import models  # noqa: F401
-    from sqlalchemy import text
+def _run_alembic_upgrade() -> None:
+    from alembic import command
+    from alembic.config import Config
 
-    async with engine.begin() as conn:
-        await conn.run_sync(Base.metadata.create_all)
-        # Dev migration: locations → vessels (rename legacy table/columns)
-        await conn.execute(
-            text(
-                """
-                DO $$
-                BEGIN
-                  IF EXISTS (SELECT 1 FROM information_schema.tables WHERE table_name = 'locations')
-                     AND NOT EXISTS (SELECT 1 FROM information_schema.tables WHERE table_name = 'vessels')
-                  THEN
-                    ALTER TABLE locations RENAME TO vessels;
-                  END IF;
-                  IF EXISTS (SELECT 1 FROM information_schema.columns WHERE table_name = 'devices' AND column_name = 'location_id')
-                  THEN
-                    ALTER TABLE devices RENAME COLUMN location_id TO vessel_id;
-                  END IF;
-                  IF EXISTS (SELECT 1 FROM information_schema.columns WHERE table_name = 'tasks' AND column_name = 'location_id')
-                  THEN
-                    ALTER TABLE tasks RENAME COLUMN location_id TO vessel_id;
-                  END IF;
-                  IF NOT EXISTS (SELECT 1 FROM information_schema.columns WHERE table_name = 'devices' AND column_name = 'catalog_key')
-                  THEN
-                    ALTER TABLE devices ADD COLUMN catalog_key VARCHAR(64);
-                  END IF;
-                END $$;
-                """
-            )
-        )
-        # Indexes for hot query paths (idempotent; covers pre-existing DBs).
-        for stmt in (
-            "CREATE INDEX IF NOT EXISTS ix_tasks_vessel_id ON tasks (vessel_id)",
-            "CREATE INDEX IF NOT EXISTS ix_task_events_task_id_id ON task_events (task_id, id)",
-            "CREATE INDEX IF NOT EXISTS ix_approval_requests_task_status "
-            "ON approval_requests (task_id, status)",
-        ):
-            await conn.execute(text(stmt))
+    ini = Path(__file__).resolve().parent.parent / "alembic.ini"
+    cfg = Config(str(ini))
+    command.upgrade(cfg, "head")
+
+
+async def init_db() -> None:
+    """Apply Alembic migrations to head."""
+    try:
+        await asyncio.to_thread(_run_alembic_upgrade)
+    except Exception as exc:  # noqa: BLE001
+        logger.exception("Database migration failed")
+        raise RuntimeError("Database migration failed") from exc