[BUG] .git, .claude, and other protected directories aren't writable without a prompt even in bypassPermissions mode in 2.1.78+

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?

Claude code stops to prompt for permission to edit some files/folders, such as .git, .claude, and CLAUDE.md, even when I have allowed all tools and set skipDangerousModePermissionPrompt to true and am in bypassPermissions mode.

What Should Happen?

When I am in bypassPermissions mode and have allowed all tools and set skipDangerousModePermissionPrompt to true, I should not be prompted for edits. If I am still being prompted for permission, what is the purpose of these settings? I am a power user running claude code in a sandboxed environment and I understand the risk of setting those settings. If I then choose to _still_ set them, that should be my risk to take.

Error Messages/Logs

Steps to Reproduce

1. Allow everything in every setting you possibly can
2. Ask claude to make an edit to CLAUDE.md
3. Watch in horror as your settings are seemingly worthless

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.77

Claude Code Version

2.1.79

Platform

Anthropic API

Operating System

Other Linux

Terminal/Shell

Xterm

Additional Information

For reference: see the 2.1.78 changelog entry titled _Fixed .git, .claude, and other protected directories being writable without a prompt in bypassPermissions mode_