[BUG] .claude/skills/ not exempt from protected directory prompt on Windows (v2.1.94)

Preflight Checklist

• [x] I have searched existing issues and found #37157 which describes the same problem — adding a Windows-specific reproduction
• [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?

Editing files under .claude/skills/*/SKILL.md triggers the protected directory confirmation prompt:

"Do you want to make this edit to SKILL.md? Yes / Yes, and allow Claude to edit its own settings for this session / No"

This occurs even when running with dangerouslySkipPermissions: true in settings.

According to the permissions documentation:

Writes to .claude/commands, .claude/agents, and .claude/skills are exempt and do not prompt, because Claude routinely writes there when creating skills, subagents, and commands.

What Should Happen?

Files under .claude/skills/** should be editable without any confirmation prompt, regardless of permission mode — as documented.

Steps to Reproduce

1. Configure dangerouslySkipPermissions: true in settings
2. Create a skill at .claude/skills/my-skill/SKILL.md
3. Ask Claude to edit the SKILL.md file
4. Result: Confirmation prompt appears
5. Expected: Edit proceeds without prompt

Environment

• Claude Code version: 2.1.94
• OS: Windows 11 Enterprise (10.0.22631)
• Shell: Git Bash
• Permission mode: dangerouslySkipPermissions: true

Additional Context

This is a Windows reproduction of #37157. The original report was on macOS with v2.1.81. The issue persists on Windows with v2.1.94, suggesting it has not been fixed yet.

Affected paths in my project (all trigger the prompt):

• .claude/skills/resolve-issue/SKILL.md
• .claude/skills/review/SKILL.md
• .claude/skills/create-pr/SKILL.md
• etc.

This is particularly disruptive when using skills like /resolve-issue that invoke sub-skills (e.g., /review, /create-pr) which may edit their own SKILL.md — each edit pauses the automated workflow for manual confirmation.