refactor: simplify toolkit service layer exports

Remove verbose `*Live` exports from toolkit services. Since Effect.Service
provides `.Default` automatically via class inheritance, we no longer need
separate exports like `ToolkitConfigLive` and `ToolkitLoggerLive`.

Changes:
- Remove `ToolkitConfigLive` export from config.ts
- Remove `ToolkitLoggerLive` export from logger.ts
- Update dependencies to use `.Default` directly instead of `*Live` exports
- Update Layer.provide() calls in database services to use `.Default`
- Apply changes consistently across mcp-server and toolkit packages

This simplification improves code consistency and reduces redundancy while
maintaining full backward compatibility for services that already use
`.Default` directly.