Fix mcp/shell stdin hang and robustness

[google-labs-jules]

Improved run-command tool implementation:

• Always close stdin to prevent processes (like grep or cat) from hanging when no input is provided.
• Added error handler to child.stdin to safely ignore EPIPE errors if the child process exits before input is fully written.

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PR created automatically by Jules for task 7433420889970538218 started by @ithinkihaveacat

[google-labs-jules]

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