[BUG] "Yes, and don't ask again" permission option doesn't persist to 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?

When selecting option 2 ("Yes, and don't ask again for [command] in [directory]") from the permission prompt, the permission is not persisted to ~/.claude/settings.json. The permissions.allow array remains empty, and the same permission prompt appears again on subsequent commands in the same session and in new sessions.

What Should Happen?

After selecting "Yes, and don't ask again", the permission should be written to ~/.claude/settings.json in the permissions.allow array, and subsequent commands matching that pattern should not prompt for permission.

Workaround
Manually editing ~/.claude/settings.json to add permissions works correctly:
"permissions": {
"allow": [
"Bash(cd:/path/to/directory/*)"
],
"deny": []
}

Environment

• OS: macOS (Darwin 24.6.0)
• Claude Code version: 2.0.69
• Model: claude-opus-4-5-20251101 (via Bedrock)

Error Messages/Logs

Steps to Reproduce

1. Run a command that requires permission (e.g., cd /path/to/directory && python3 script.py)
2. When prompted, select option 2: "Yes, and don't ask again for cd commands in /path/to/directory"
3. Run another command with cd to the same directory
4. The permission prompt appears again
5. Check ~/.claude/settings.json - the permissions.allow array is still empty: "allow": []

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.69 (Claude Code)

Platform

AWS Bedrock

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_