[Bug] Background Bash process notifications persist after output drained

Bug Description

Bug Report: Persistent Background Bash Notifications

Date: 2025-11-05

Summary

System reminders for background bash processes persist indefinitely even after processes complete and output is drained.

Steps to Reproduce

1. Run memory rebuild scripts in background (e.g., rebuild_jsonl_based_sqlite.sh, build_jsonl_based_leann_incremental_index.sh)
2. Wait for processes to complete
3. Use BashOutput tool to read all output from completed processes
4. Observe that system reminders continue appearing in subsequent messages

Expected Behavior

After using BashOutput to drain a process's output, the system reminder should disappear and not appear in future messages.

Actual Behavior

System reminders persist indefinitely with message "Background Bash {id} (command: {script}) (status: running) Has new output available."

Even after:

• Process completes (status shows "completed" or "failed" when checked)
• Output is drained via BashOutput tool
• Attempt to kill process confirms it's not running

Affected Process IDs

• b851f5, e1a199 (failed, from previous session)
• 3f47a4, ef6d52, 95f93b, e526d9 (completed, from previous session)
• cfed6d, d974e1 (completed, current session)

Impact

• Consumes message space with irrelevant notifications
• Creates confusion about process status
• Potentially wastes context tokens if user/AI attempts to re-drain already-drained output

Workaround

Restarting the embodiment (using /exit and reconnecting) clears all stale notifications.

Suggested Fix

System reminders for background bash processes should be cleared after:

1. Output is successfully read via BashOutput, OR
2. Process terminates and final output is drained

Environment Info

• Platform: darwin
• Terminal: tmux
• Version: 2.0.32
• Feedback ID: b114f8d1-8e4c-4658-9b9c-666d2f3ac391