fix(core): properly cleanup MCP server subprocesses on exit

[tt-a1i]

Summary

Fixes #1213

MCP server subprocesses were not being terminated when qwen-code exits, causing orphaned processes to accumulate. Each startup/exit cycle left behind zombie processes still holding WS ports.

Root cause: mcpClientManager.stop() was never called during the exit cleanup flow.

Changes:

• Add ToolRegistry.stop() to stop all MCP clients
• Add Config.shutdown() as a unified cleanup entry point (idempotent, handles uninitialized state)
• Register cleanup in gemini.tsx immediately after config creation

The cleanup now covers all execution modes (interactive, non-interactive, stream-json) since it's registered at the CLI entry point before any mode-specific branching.

Test

Added unit tests for:

• stop() disconnects all connected MCP clients
• stop() is idempotent (can be called multiple times safely)

[BlockHand]

Thank you for your contribution! I've already tested it and everything is fine. We will merge this PR.

[liqiongyu]

Thanks for the fix — wiring cleanup into the CLI exit flow via Config.shutdown looks solid.

One small potential gap: ToolRegistry.discoverToolsForServer() currently uses connectAndDiscover() (not McpClientManager/McpClient), so any client/transport started via that path won’t be tracked by mcpClientManager.stop() and thus won’t be closed by ToolRegistry.stop()/Config.shutdown. Today this path is used by /mcp auth and likely targets network servers, but if a command-based server ever goes through this flow it could still leave a subprocess around until process exit.

Might be worth a follow-up to route single-server re-discovery through McpClientManager (or otherwise track/stop those connections) so shutdown is comprehensive.

[DennisYu07]

I test this PR as well and it looks everything is fine. Thank you for your contribution.

[tt-a1i]

@liqiongyu good catch — I routed ToolRegistry.discoverToolsForServer() through McpClientManager (new discoverMcpToolsForServer()) so the connection is tracked and gets cleaned up on shutdown. added a few tests around the single-server rediscovery/replace path too. thanks!

[DennisYu07]

@tt-a1i I've rebased this PR and updated some unit tests. All tests are passing now. Could you please take another look when you have a moment? If everything looks good, we're ready to merge. Thank you!