[BUG] bypassPermissions mode still prompts for .claude/skills edits despite documented exemption

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 defaultMode is set to bypassPermissions in ~/.claude/settings.json, editing files under .claude/skills/ still triggers a permission prompt. This contradicts the documented behavior which states .claude/skills is explicitly exempt from the .claude directory protection.

Notably, .claude/agents edits work correctly without prompting — only .claude/skills is affected.

What Should Happen?

File edits under .claude/skills/ should be auto-approved without a permission prompt when defaultMode is bypassPermissions, matching the behavior of .claude/agents.

Error Messages/Logs

Steps to Reproduce

1. Set defaultMode: "bypassPermissions" in ~/.claude/settings.json
2. Ask Claude to edit any file under ~/.claude/skills/ (e.g., a SKILL.md file)
3. A permission prompt appears instead of the edit being auto-approved

Note: The same edit to a file under ~/.claude/agents/ passes without prompting, confirming this is specific to .claude/skills.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.118

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

<img width="528" height="225" alt="Image" src="https://github.com/user-attachments/assets/28edb772-d915-4c09-9f64-e51832502ab7" />
<img width="506" height="104" alt="Image" src="https://github.com/user-attachments/assets/9648ae7c-d739-4eac-bb02-dbeea5bf830a" />