feat: Enhance MCP roots implementation and test coverage

- Add proper ListRootsResult wrapping in async client
- Implement paginated listRoots methods in server components
- Fix roots notification handling in async server
- Add roots integration tests
- Update architecture diagram and documentation layout

The changes improve the roots feature implementation with proper result
types,  and robust notification handling. Adds thorough
test coverage for roots functionality including async notifications and
root addition/removal scenarios.

Resolves #46