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/mcp_manager/commands.py

@@ -80,6 +80,10 @@ async def process_mcp_command(cmd: dict) -> dict:
             if not server:
                 raise ValueError("server name required")
             return await _execute_develop_command(cmd, manager)
+        elif action == "apply_patch":
+            if not server:
+                raise ValueError("server name required")
+            return await _execute_apply_patch_command(cmd, manager)
         else:
             raise ValueError(f"Unknown action: {action}")
         return {"ok": True, "action": action, "server": server}
@@ -139,6 +143,7 @@ async def _finalize_develop_task(task_id: int, result: dict, server: str) -> Non
                 "tools": result.get("tools"),
                 "push": result.get("push"),
                 "resolved": not has_pending,
+                "pending_approval": result.get("pending_approval"),
             }
             task.error = None
             task.status = TaskStatus.waiting_approval if has_pending else TaskStatus.succeeded
@@ -149,7 +154,9 @@ async def _finalize_develop_task(task_id: int, result: dict, server: str) -> Non
 
     if result.get("ok"):
         msg = result.get("summary") or f"MCP develop finished for {server}"
-        if has_pending:
+        if result.get("pending_approval"):
+            msg += " — approve MCP patch on this task."
+        elif has_pending:
             msg += " — approve git push on this task."
         await publish_event(task_id, "report", msg, {"kind": "mcp_develop", **result}, persist=True)
     else:
@@ -180,7 +187,7 @@ async def _develop_on_worker(cmd: dict, manager) -> dict:
         task_id=task_id,
         server=server,
         tool=cmd.get("tool") or "unknown",
-        args={},
+        args=cmd.get("args") or {},
         issue=cmd.get("issue") or "",
         error=cmd.get("error"),
         output=cmd.get("output"),
@@ -189,3 +196,22 @@ async def _develop_on_worker(cmd: dict, manager) -> dict:
         task_title=cmd.get("title") or f"MCP develop: {server}",
         push=cmd.get("push"),
     )
+
+
+async def _execute_apply_patch_command(cmd: dict, manager) -> dict:
+    from app.services.events import publish_event
+    from app.services.mcp_approvals import execute_approved_patch
+
+    task_id = int(cmd.get("task_id") or 0)
+    tool_args = cmd.get("tool_args") or {}
+
+    async def emit(tid: int, kind: str, message: str, payload: dict | None = None):
+        if tid:
+            await publish_event(tid, kind, message, payload)
+
+    return await execute_approved_patch(
+        task_id=task_id,
+        tool_args=tool_args,
+        manager=manager,
+        emit=emit,
+    )