[BUG]

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?

Since v2.1.78, .claude/ and .git/ directories now prompt for confirmation even in bypassPermissions mode. This was introduced as a "fix" but it's a regression in UX for users who explicitly chose bypass mode.

Environment:

• Claude Code v2.1.81
• Linux (Arch), Terminator

What Should Happen?

If I've set bypassPermissions, I've already accepted the risk. Being prompted once per session to write to .claude/ defeats the purpose. Either:

1. Respect bypass mode fully (preferred), or
2. Add a global toggle like protectDirectoriesInBypass: false to opt out

Error Messages/Logs

Steps to Reproduce

Ask claude code to edit a skill or a subagent in bypass perimssions mode.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.77

Claude Code Version

2.1.81

Platform

Anthropic API

Operating System

Other Linux

Terminal/Shell

Other

Additional Information

_No response_