Extract server capabilities into dedicated Capabilities class

Refactor capabilities handling into MCP::Server::Capabilities to improve
code organization and separation of concerns. This provides a cleaner API
for configuring server capabilities including prompts, resources, tools,
completions, logging, and experimental features.

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

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

lib/mcp/server.rb

@@ -3,6 +3,7 @@
 require "json_rpc_handler"
 require_relative "instrumentation"
 require_relative "methods"
+require_relative "server/capabilities"
 
 module MCP
   class Server