[BUG] Claude Code ignores 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?

I have a file in ~/.claude/settings.json and [project]/.claude/settings.local.json.

I have authorized — manually modifying the file — mcp__serena__find_symbol in both of those files. When I launch claude, it asks for the permission again. If I select "Remember for this project", it completely overwrites the file and puts the exact same line which should have granted it permissions in the first place.

What Should Happen?

It should not ignore the permissions in my user or project directory.

Error Messages/Logs

Steps to Reproduce

Self-explanatory

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.13

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

IntelliJ IDEA terminal

Additional Information

_No response_