implement graceful shutdown for Puma server#21441
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| @puma_log_io&.close | ||
| @puma_log_io = nil | ||
| @puma_launcher = nil |
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While working on #21297 I noticed that puma wasn't shutting down gracefully so I created this PR to address that issue separately
Refactors the way the MCP server starts and stops its HTTP transport by switching from using Rack's Puma handler to directly managing Puma via its server API. This allows for more graceful shutdowns and better control over the server lifecycle. The test suite is updated accordingly to mock and verify the new Puma integration and shutdown behavior.