Zombie background shell reminders accumulate during long sessions

Description

During long Claude Code sessions that use background processes (run_in_background: true), "zombie" shell reminders accumulate and persist even after the actual processes have exited. These stale reminders clutter every subsequent message with notifications like:

<system-reminder>
Background Bash 3cd15a (command: ...) (status: running) Has new output available.
</system-reminder>

Steps to Reproduce

1. Start a long session that involves debugging/iterating on server code
2. Use run_in_background: true multiple times (e.g., starting servers that crash, restarting after fixes)
3. Continue the session until context summarization occurs
4. Observe that all background shell reminders persist, even for processes that:

• Crashed immediately with errors
• Were explicitly killed
• Completed successfully

Expected Behavior

• Shell reminders should only appear for actually running processes
• When a background process exits (success, failure, or killed), its reminder should be removed
• After context summarization, only truly running processes should have reminders

Actual Behavior

• All shell reminders persist indefinitely after context summarization
• Calling KillShell on zombie shells returns "Shell X is not running" but the reminder persists
• Each message includes 15+ stale reminders that cannot be cleared

Environment

• Claude Code CLI
• Long session with context summarization
• Multiple background process start/stop cycles

Impact

• Message clutter reduces readability
• Confusion about which processes are actually running
• No way to clear stale reminders

Possible Causes

1. Context summarization preserves shell metadata but doesn't sync with actual process state
2. No cleanup mechanism when background processes exit
3. Shell tracking state not updated when processes fail immediately after starting

🤖 Generated with Claude Code