[BUG] "Don't Ask Again" Overwrites Entire Permissions Array

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?

It's the same as https://github.com/anthropics/claude-code/issues/5710, no need to put all the details again. Since there are several issues opened about it and closed because of the stale bot, and considering that this repo has 5k issues, should we extend the stale config to a longer number of days?

What Should Happen?

Please see the link attached, it's pretty annoying to file all this info if won't be looked at.

Error Messages/Logs

Steps to Reproduce

.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.50

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other

Additional Information

_No response_