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claude-code - 💡(How to fix) Fix [BUG] bypassPermissions mode still prompts for .claude/skills edits despite documented exemption [1 comments, 2 participants]

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anthropics/claude-code#52531•Fetched 2026-04-24 06:04:41
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vincentthenguyenvincentthenguyen
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Error Message

Error Messages/Logs

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Preflight Checklist

  • I have searched existing issues and this hasn't been reported yet
  • 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?

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" />

extent analysis

TL;DR

The issue can likely be resolved by updating the configuration to correctly exempt the .claude/skills directory from permission prompts when defaultMode is set to bypassPermissions.

Guidance

  • Verify that the ~/.claude/settings.json file is correctly formatted and that the defaultMode is indeed set to bypassPermissions.
  • Check if there are any other configuration files or overrides that might be affecting the behavior of the .claude/skills directory.
  • Test editing files under .claude/skills with a different defaultMode setting to see if the issue is specific to bypassPermissions.
  • Review the documentation for any specific requirements or caveats for exempting directories from permission prompts.

Example

No code snippet is provided as the issue seems to be related to configuration rather than code.

Notes

The issue might be related to a misconfiguration or an override that is not immediately apparent. Further investigation into the configuration files and the documentation is necessary to resolve the issue.

Recommendation

Apply a workaround by double-checking the configuration files and overrides to ensure that the .claude/skills directory is correctly exempt from permission prompts when defaultMode is set to bypassPermissions, as the root cause is likely related to a configuration issue rather than a code bug.

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claude-code - 💡(How to fix) Fix [BUG] bypassPermissions mode still prompts for .claude/skills edits despite documented exemption [1 comments, 2 participants]