[BUG] Background shell reminders persist for completed shells, cannot be cleared

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?

Description

Background Bash shells that have completed continue to generate <system-reminder> messages on every turn, consuming context rapidly.
The KillShell tool reports the shells as "completed" or "failed" but the reminders persist.

Expected Behavior

• Completed shells should not generate reminders
• OR KillShell should remove completed shells from tracking
• OR /clear should reset shell tracking state

Actual Behavior

• 50+ completed shells generate reminders every turn
• Each reminder consumes ~200 tokens
• Context fills rapidly (10k+ tokens/turn just from stale reminders)
• No way to clear them without starting a new session

Environment

• Claude Code CLI
• macOS Darwin 25.1.0
• Session resumed from previous conversation

Impact

Severe context bloat makes long sessions unusable. Users must start new sessions to escape accumulated shell reminders.

What Should Happen?

Expected Behavior

Option A (Preferred): Completed shells should automatically stop generating reminders. Once a shell exits (status: completed/failed), it should be removed from the reminder system.

Option B: KillShell should work on completed shells - not to kill the process, but to remove them from tracking. Currently it only operates on running processes.

Option C: Provide a /clear-shells command or have /clear also reset shell tracking state.

Why This Matters

Each reminder is ~200 tokens. With 52 stale shells, that's 10,400+ tokens per turn consumed by reminders for processes that finished long ago. This makes continued conversation impractical.

---
TL;DR for the issue: Shells should stop generating reminders after they complete, or users need a way to manually remove completed shells from tracking.

Error Messages/Logs

KillShell tool response (for all 52 shells):
  Shell 347829 is not running, so cannot be killed (status: completed)
  Shell 473051 is not running, so cannot be killed (status: completed)
  Shell 49fa25 is not running, so cannot be killed (status: failed)
  ... (52 similar responses)

  System reminder still showing (same turn, after KillShell):
  <system-reminder>
  Background Bash 347829 (command: ...) (status: running) Has new output available.
  </system-reminder>

  Key inconsistency: KillShell reports status: completed, but system-reminder shows status: running. The shell tracking state is
  inconsistent between these two systems.

  ---
  This shows the bug clearly: KillShell knows the shells are done, but the reminder system doesn't sync with that state.

Steps to Reproduce

Steps to Reproduce

1. Run multiple background commands over a session:

uv run python -m myapp 2>&1 &

1. Let the commands complete naturally
2. Observe system reminders continue appearing every turn:

<system-reminder>
Background Bash abc123 (command: ...) (status: running) Has new output available.
</system-reminder>

1. Attempt to kill shells with KillShell tool
2. KillShell reports: Shell abc123 is not running, so cannot be killed (status: completed)
3. Reminders continue appearing despite shell being completed

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.55 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Warp

Additional Information

_No response_