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/alembic/versions/001_initial_schema.py

@@ -0,0 +1,92 @@
+"""Initial schema + legacy location→vessel renames.
+
+Revision ID: 001_initial
+Revises:
+Create Date: 2026-06-14
+"""
+from __future__ import annotations
+
+from typing import Sequence, Union
+
+from alembic import op
+
+revision: str = "001_initial"
+down_revision: Union[str, None] = None
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # Legacy dev DBs may still use locations/location_id — rename before create_all.
+    op.execute(
+        """
+        DO $$
+        BEGIN
+          IF EXISTS (SELECT 1 FROM information_schema.tables WHERE table_name = 'locations')
+             AND NOT EXISTS (SELECT 1 FROM information_schema.tables WHERE table_name = 'vessels')
+          THEN
+            ALTER TABLE locations RENAME TO vessels;
+          END IF;
+          IF EXISTS (SELECT 1 FROM information_schema.columns WHERE table_name = 'devices' AND column_name = 'location_id')
+          THEN
+            ALTER TABLE devices RENAME COLUMN location_id TO vessel_id;
+          END IF;
+          IF EXISTS (SELECT 1 FROM information_schema.columns WHERE table_name = 'tasks' AND column_name = 'location_id')
+          THEN
+            ALTER TABLE tasks RENAME COLUMN location_id TO vessel_id;
+          END IF;
+        END $$;
+        """
+    )
+
+    from app import models  # noqa: F401
+    from app.database import Base
+
+    bind = op.get_bind()
+    Base.metadata.create_all(bind)
+
+    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)",
+    ):
+        op.execute(stmt)
+
+    # catalog_key added on older DBs that predate the column.
+    op.execute(
+        """
+        DO $$
+        BEGIN
+          IF NOT EXISTS (
+            SELECT 1 FROM information_schema.columns
+            WHERE table_name = 'devices' AND column_name = 'catalog_key'
+          ) THEN
+            ALTER TABLE devices ADD COLUMN catalog_key VARCHAR(64);
+          END IF;
+        END $$;
+        """
+    )
+
+
+def downgrade() -> None:
+    op.drop_index("ix_approval_requests_task_status", table_name="approval_requests")
+    op.drop_index("ix_task_events_task_id_id", table_name="task_events")
+    op.drop_index("ix_tasks_vessel_id", table_name="tasks")
+
+    for table in (
+        "approval_requests",
+        "task_events",
+        "tasks",
+        "devices",
+        "vessels",
+        "audit_logs",
+        "balance_snapshots",
+        "users",
+    ):
+        op.execute(f"DROP TABLE IF EXISTS {table} CASCADE")
+
+    op.execute("DROP TYPE IF EXISTS approvalstatus")
+    op.execute("DROP TYPE IF EXISTS taskstatus")
+    op.execute("DROP TYPE IF EXISTS devicetype")
+    op.execute("DROP TYPE IF EXISTS role")