Remove obsolete MCP::Transports module

## Motivation and Context

`lib/mcp/transports/stdio.rb` was a deprecated shim that redirected users
from `MCP::Transports::StdioTransport` to `MCP::Server::Transports::StdioTransport`.
It has been 10 months since the migration path was introduced, providing sufficient time
for users to update their code.

## How Has This Been Tested?

All tests pass (`rake test`), and no code in the repository references `MCP::Transports`
or `mcp/transports/stdio`.

## Breaking Changes

`require "mcp/transports/stdio"` and `MCP::Transports::StdioTransport` are removed.
Use `require "mcp/server/transports/stdio_transport"` and `MCP::Server::Transports::StdioTransport` instead.

Author: koic