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claude-code - 💡(How to fix) Fix [BUG] .claude/skills/ not exempt from protected directory prompt on Windows (v2.1.94) [1 participants]

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anthropics/claude-code#45011•Fetched 2026-04-09 08:15:27
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Root Cause

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.

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Preflight Checklist

  • I have searched existing issues and found #37157 which describes the same problem — adding a Windows-specific reproduction
  • This is a single bug report (please file separate reports for different bugs)
  • 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.

extent analysis

TL;DR

The issue can be worked around by manually editing the SKILL.md files outside of Claude Code or by temporarily disabling the confirmation prompt through settings, although the root cause seems to be a discrepancy between the documented exemption for .claude/skills and the actual behavior.

Guidance

  • Review the permissions documentation to ensure that the exemption for .claude/skills is correctly understood and applied.
  • Verify that the dangerouslySkipPermissions: true setting is correctly configured and applied to the session.
  • Consider filing a bug report or feature request to address the discrepancy between the documented behavior and the actual behavior.
  • As a temporary workaround, edit the SKILL.md files manually using an external editor to avoid the confirmation prompt.

Example

No specific code snippet is applicable in this case, as the issue seems to be related to the configuration and behavior of Claude Code rather than a specific code error.

Notes

The issue persists across different versions (from 2.1.81 to 2.1.94) and operating systems (from macOS to Windows), suggesting a deeper issue with how permissions are handled for the .claude/skills directory.

Recommendation

Apply workaround: Given the persistence of the issue across versions and platforms, and the lack of a clear fix, applying a workaround such as manual editing of SKILL.md files or temporarily disabling the confirmation prompt seems to be the most practical approach until the root cause is addressed.

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claude-code - 💡(How to fix) Fix [BUG] .claude/skills/ not exempt from protected directory prompt on Windows (v2.1.94) [1 participants]