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/tests/test_mcp_approvals.py

@@ -0,0 +1,106 @@
+"""Tests for MCP patch approval gating."""
+from __future__ import annotations
+
+import asyncio
+import os
+from unittest.mock import AsyncMock, MagicMock, patch
+
+import pytest
+
+os.environ.setdefault("SECRET_KEY", "test-secret-key-for-unit-tests-only")
+
+
+def test_repair_queues_apply_patch_when_approval_required(monkeypatch):
+    from app.config import get_settings, settings
+
+    get_settings.cache_clear()
+
+    proposal = {
+        "ok": True,
+        "summary": "Add missing tool",
+        "commit_message": "fix: add tool",
+        "files": [{"path": "server.py", "content": "# patched"}],
+    }
+
+    mock_db = MagicMock()
+    mock_db.commit = AsyncMock()
+    mock_session = MagicMock()
+    mock_session.__aenter__ = AsyncMock(return_value=mock_db)
+    mock_session.__aexit__ = AsyncMock(return_value=None)
+
+    async def _run():
+        with (
+            patch.object(settings, "mcp_dev_require_approval", True),
+            patch("app.agent.mcp_development.propose_mcp_patch", new=AsyncMock(return_value=proposal)),
+            patch(
+                "app.agent.mcp_development.backup_proposal_files",
+                new=AsyncMock(return_value={"server.py": "# old"}),
+            ),
+            patch("app.agent.mcp_development.execute_approved_patch", new=AsyncMock()) as mock_apply,
+            patch("app.database.SessionLocal", return_value=mock_session),
+        ):
+            from app.agent.mcp_development import attempt_mcp_repair
+
+            emit = AsyncMock()
+            result = await attempt_mcp_repair(
+                task_id=42,
+                server="pfsense-mcp",
+                tool="pfsense_list_rules",
+                args={"interface": "wan"},
+                issue="tool missing",
+                error="unknown tool",
+                output=None,
+                manager=AsyncMock(),
+                emit=emit,
+                device="pfsense",
+            )
+        return result, mock_apply, emit, mock_db
+
+    result, mock_apply, emit, mock_db = asyncio.run(_run())
+
+    assert result.get("pending_approval") is True
+    assert result.get("approval_type") == "mcp_apply_patch"
+    mock_apply.assert_not_called()
+    mock_db.add.assert_called_once()
+    mock_db.commit.assert_awaited_once()
+    assert any(c.args[1] == "approval" for c in emit.call_args_list)
+
+
+def test_repair_applies_immediately_when_approval_not_required(monkeypatch):
+    from app.config import get_settings, settings
+
+    get_settings.cache_clear()
+
+    proposal = {
+        "ok": True,
+        "summary": "Fix crash",
+        "files": [{"path": "server.py", "content": "# patched"}],
+    }
+
+    async def _run():
+        with (
+            patch.object(settings, "mcp_dev_require_approval", False),
+            patch("app.agent.mcp_development.propose_mcp_patch", new=AsyncMock(return_value=proposal)),
+            patch(
+                "app.agent.mcp_development.execute_approved_patch",
+                new=AsyncMock(return_value={"ok": True, "tools": ["a"]}),
+            ) as mock_apply,
+        ):
+            from app.agent.mcp_development import attempt_mcp_repair
+
+            return await attempt_mcp_repair(
+                task_id=1,
+                server="pfsense-mcp",
+                tool="t",
+                args={},
+                issue="x",
+                error="err",
+                output=None,
+                manager=AsyncMock(),
+                emit=AsyncMock(),
+            ), mock_apply
+
+    result, mock_apply = asyncio.run(_run())
+
+    assert result.get("ok") is True
+    mock_apply.assert_awaited_once()