[BUG] Bypass permissions

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?

Bypass permissions does not by-pass permissions on .claude/* file edits.
Please fix it. It's very annoying.

What Should Happen?

It asks approvals over and over again.

Error Messages/Logs

Steps to Reproduce

• Ask Claude Code to edit files under <project>/.claude folder.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.80 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_