[BUG] Background process tracking shows false 'running' status for failed processes

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Bug Description

Dead processes continue showing as "running" with "new output available" status, even after they have failed or terminated.

Impact

• Blocks normal operation with constant false system reminders
• Users receive misleading feedback about process status
• Prevents proper workflow continuation

Evidence

• Process IDs 742928, eb6128 stuck in false "running" state for hours
• Processes show "new output available" despite being terminated
• Background process tracking system not properly detecting process termination

Expected Behavior

Failed or terminated processes should be marked as completed/failed, not running.

Actual Behavior

Dead processes remain in "running" status indefinitely with false "new output available" messages.

What Should Happen?

• Background processes should accurately reflect their actual status (running/completed/failed)
• When a process terminates or fails, it should immediately update to the correct status
• Dead processes should not continue showing "new output available"
• The system should clean up terminated process references automatically
• Users should only receive "new output available" notifications for genuinely active processes
• Process status should timeout and mark as failed if unresponsive for extended periods

Error Messages/Logs

Steps to Reproduce

Steps to Reproduce

1. Start a background process using the Bash tool with run_in_background: true
2. Let the process fail or terminate (either naturally or due to an error)
3. Use the BashOutput tool to check the process status
4. Observe that the process continues to show as "running"
5. Note that the system continues to show "new output available" messages
6. Wait several hours - the false "running" status persists
7. Try to continue normal workflow - constant system reminders about false "new output" block operation

Environment

• Platform: Windows (win32)
• Process IDs affected: 742928, eb6128
• Duration: Process stuck in false "running" state for multiple hours

Additional Context

• The issue prevents normal Claude Code operation due to persistent false notifications
• Multiple process IDs can be affected simultaneously
• No apparent way to manually clear the stuck process status

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

Sonnet 4 (claude-sonnet-4-20250514)

Platform

Other

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_