fix: improve graceful shutdown handling for MCP server

[PhilipLudington]

• Add isShuttingDown flag to prevent double-shutdown race conditions
• Add SIGTERM and SIGHUP signal handlers in addition to SIGINT
• Add stdin close/end/error handlers for when MCP client disconnects
• Handle EPIPE/EOF errors gracefully as expected disconnection
• Call server.close() during shutdown for proper cleanup
• Exit with code 1 for actual errors vs code 0 for clean shutdown

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[CoderGamester]

Good improvement for a clean shutdown