This commit moves the RPC message types from Mcp to a separate Mcp_message
module with a consistent structure:

1. Each message type (ResourcesList, ResourcesRead, etc.) has its own module
2. Each module contains Request, Response, and other relevant submodules
3. Each submodule has a single `type t` with JSON conversion functions
4. Each submodule includes the Json.Jsonable.S interface

This restructuring provides better type safety and a more consistent API
for handling JSON-RPC messages in the OCaml MCP implementation.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>