Support clean server shutdown

Summary

Provide a reliable way to cleanly shut down a running MCP server, ensuring all resources are properly released.

Motivation

• Currently there's no clean way to stop a running server programmatically
• Resources (connections, tasks, file handles) may not be properly cleaned up on shutdown
• Important for testing, graceful restarts, and production deployments

Goal

• API for triggering graceful shutdown
• Proper cleanup of all active sessions and transports
• Configurable shutdown timeout / drain period

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