[BUG] Claude Code writes broken Permission Syntax into settings.json

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?

Running claude doctor or the /doctor command inoide CC CLI, i see many reports like this:

 └ permissions
    └ allow
      ├ "Bash(git status*)": Use ":*" for prefix matching, not just "*". Change to "Bash(git status:*)" for prefix matching. Examples: Bash(npm run:*), Bash(git:*)
      ├ "Bash(git log*)": Use ":*" for prefix matching, not just "*". Change to "Bash(git log:*)" for prefix matching. Examples: Bash(npm run:*), Bash(git:*)
      ├ "Bash(git diff*)": Use ":*" for prefix matching, not just "*". Change to "Bash(git diff:*)" for prefix matching. Examples: Bash(npm run:*), Bash(git:*)
      ├ "Bash(git show*)": Use ":*" for prefix matching, not just "*". Change to "Bash(git show:*)" for prefix matching. Examples: Bash(npm run:*), Bash(git:*)

What Should Happen?

None of these settings have been added manually by myself. All settings have been written by Claude Code when asking for permission and using the option "Yes, for the whole session".

I see these settings in the .claude/settings.json on my home directory and also inside local project directories.

However, the settings seems to work accordingly as Claude Code is not asking for the respective permissions again. Only the doctor-command is providing bad feedback.

Nevertheless, this issue seems Claude to hold back from loading mcp-server configuration inside .mcp.json, as described here https://github.com/anthropics/claude-code/issues/5963#issuecomment-3243051224

Error Messages/Logs

Steps to Reproduce

Answering the permission-dialog inside claude code for certain actions to be taken with "yes for the whole session"

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.0.108 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_