Fix placeholder handler pattern in MCP registry

[todo-mdx]

ARCHITECTURE: Database and functions tools are registered with non-functional handlers that return { error: 'Use /mcp endpoint' }. This is an architectural smell.

Location: src/api.ts lines 82-85, 94-97

TDD Steps:

• RED: Write test that calls tool handler directly and verify it fails properly
• GREEN: Either provide real handlers that route to implementation, or mark tools as handlerType: 'route-only'
• REFACTOR: Consider unified pattern for auto-generated vs explicit tools