[BUG] Permission preferences not persisting across sessions

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 clicking "Yes, and don't ask again" on permission prompts in
Claude Code, the preference is only saved for the current session.
After closing and reopening Claude Code, the same permission
prompts appear again instead of remembering the choice.

What Should Happen?

Permission preferences selected with "don't ask again" should be
persisted to disk and remembered across multiple Claude Code
sessions. Once a user approves a permission with "don't ask
again," that tool should work without prompting again in future
sessions.

Error Messages/Logs

Steps to Reproduce

1. Open Claude Code
2. Perform an action that triggers a permission prompt (e.g., running a Bash command or file operation)
3. Click "Yes, and don't ask again" button
4. Close Claude Code completely
5. Open Claude Code again
6. Perform the same action
7. Expected: Permission prompt does not appear
8. Actual: Permission prompt appears again

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.37 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other

Additional Information

Investigation found that there is no permissions.json or similar configuration file in ~/.claude/ that stores permission preferences. The ~/.claude/ directory is writable and accessible.
The absence of any persistent permission storage suggests permission choices are currently only maintained in memory during the session and are lost when the process closes.