- Replaces the Express-based HTTP transport with a more performant and modern implementation using Hono.
- Refactors the authentication layer into a modular, strategy-based system supporting both JWT and OAuth 2.1, configured via `MCP_AUTH_MODE`.
- Simplifies session management by removing transport-specific state in favor of a unified, session-scoped working directory.
- Introduces a centralized HTTP error handler for consistent JSON-RPC error responses.