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/agent/__init__.py

@@ -1,3 +1,3 @@
-from app.agent.graph import run_task_agent
+"""Agent package — import submodules directly (e.g. app.agent.graph)."""
 
-__all__ = ["run_task_agent"]
+__all__: list[str] = []