[BUG] VSCode extension requests permissions for commands already approved

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?

No matter how many times I click "Allow", whether it is for the project, globally, or just for me, these commands are _always_ flagged as needing permission. It ignores the Allow setting, and even creates duplicate permissions, as seen below from /permissions in the cli:

 10. Bash(gh api *)
 11. Bash(gh api *)
 12. Bash(gh pr *)
 13. Bash(gh run *)
 15. Bash(git diff *)
 16. Bash(git diff *)
 18. Bash(grep -n *)
 19. Bash(grep -nE *)
 20. Bash(grep *)

The 'grep' one is particularly egregious, but being asked to approve 'git diff' every time?

I also have every possible way you could refer to several scripts, e.g. scripts/run-tests.sh and ./scripts/run-tests.sh, and /User/full/path/to/scripts/run-tests.sh. With and without the asterisk. It doesn't matter, it asks every time.

I've tried deleting all permissions from all three settings files.

As another example, I'm digging through git history to see when something changed. It asks if it can run "git log [...]" and I say yes, always allow "git log *". Then not ten seconds later, it asks if it can run "git log [...]" about another file it is looking at.

What Should Happen?

Clicking 'allow' should mean the next time the exact same command is attempted, it doesn't ask again.

Error Messages/Logs

Steps to Reproduce

I have no idea. Some commands it remembers after the first "always allow". Some commands it never does.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.20

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

If there were a log file somewhere I'd provide it, but I don't see one in any of the expected locations. If there's instructions for running with logging enabled, I can't find it.