[BUG] Permissions prompt despite bypass

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?

I'm running Claude in bypass permissions mode. I expect all permissions prompts to be bypassed. Very recently, new permissions prompts started appearing. An example permissions prompt is

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 Bash command

   rm usr/lib/julia/basecompiler* usr/lib/julia/sys* 2>/dev/null; rm -rf usr/share/julia/compiled/v1.14/* 2>/dev/null; rm -rf
   /root/.julia/compiled/v1.14/* 2>/dev/null; true
   Clean artifacts

 Do you want to proceed?
 ❯ 1. Yes
   2. Yes, and don't ask again for similar commands in /workspace
   3. No

 Esc to cancel · Tab to amend · ctrl+e to explain

What Should Happen?

Permissions prompt should be bypassed

Error Messages/Logs

Steps to Reproduce

Unclear, triggered by some rm commands in tools, but not all.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.117

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

_No response_