Remove useless ModelContextProtocol::JsonRPC module

JSON-RPC is handled by https://github.com/Shopify/json-rpc-handler,
so `ModelContextProtocol::JsonRPC` module seems to have been
unintentionally left behind in the following commit:
c5591be

The files under `model_context_protocol/json_rpc/*.rb` have already been removed.

Author: koic