[BUG] "Yes, and always allow" never persists for edits inside `.claude/` directories

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 Claude Code prompts for permission to edit a file inside a .claude/ directory (project or global), choosing "Yes, and always allow" does not persist. The prompt re-appears for every subsequent edit to the same path/pattern within the same session and across sessions.
The choice is treated as a one-shot "yes" — no rule is written, and the next edit re-prompts.

What Should Happen?

Selecting "always allow" should add a matching Edit rule to ~/.claude/settings.json (or project .claude/settings.local.json) so future edits to the same path are auto-approved.

Error Messages/Logs

Steps to Reproduce

1. Trigger any edit under .claude/ (e.g. Edit ~/.claude/keybindings.json).
2. Choose "Yes, and always allow" at the permission prompt.
3. Trigger another edit to the same file → prompt re-appears.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.111

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

• Other Edit always-allow choices (outside .claude/) appear to persist correctly.
• Suspected cause: .claude/ paths may be filtered out of permission rule writes as a safety guard, but the UI still offers the option.