`handle_request` already adds the `method` to the instrumentation data,
so there is no need to repeat this. Moreover, consumers can override
these anyway.
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.
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Co-Authored-By: Claude <noreply@anthropic.com>