[BUG] Claude Code runtime deletes project-level .claude/skills/ directory within seconds of file creation

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?

Claude Code's running process actively watches and deletes the entire .claude/skills/ directory within ~300ms of any file being created there, preventing project-level skills from being used. This contradicts the documented behaviour where project-level skills should coexist with plugin-provided skills.

The entire .claude/skills/ directory is deleted within ~300ms of any file appearing in it. This was confirmed by rapid polling:

mkdir -p .claude/skills/canary && echo "test" > .claude/skills/canary/SKILL.md
for i in $(seq 1 30); do
[ ! -f .claude/skills/canary/SKILL.md ] && echo "Deleted after ~$((i/10)).$((i%10))s" && break
sleep 0.1
done
# Output: Deleted after ~0.3s

What Should Happen?

Project-level skills in .claude/skills/ should persist on disk and be available as slash commands, as documented. Plugin skills use namespaced prefixes (e.g. /plugin-name:skill-name) and should not conflict with project-level skills.

Error Messages/Logs

Steps to Reproduce

Steps to Reproduce

1. Start a Claude Code session in a project directory
2. Create a project-level skill:

mkdir -p .claude/skills/test-skill
echo '---
name: test-skill
description: "A test skill"
---
Test content' > .claude/skills/test-skill/SKILL.md

1. Wait 1 second
2. Check if the file exists:

ls .claude/skills/test-skill/SKILL.md
# Result: No such file or directory — entire .claude/skills/ directory is gone

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Claude Code v2.1.76.

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Cursor

Additional Information

Investigation

• No hooks configured (.claude/settings.json only contains {"voiceEnabled": true})
• No .claude/settings.local.json or .claude/hooks.json exists
• No git hooks (all .sample files only)
• No npm lifecycle scripts that touch .claude/
• .claude/commands/ directory is not affected — only .claude/skills/ is wiped
• Other .claude/ subdirectories (e.g. .claude/my-skills/) are not affected — only the exact path .claude/skills/ is targeted
• The running claude CLI process is the only candidate; no other file-watching tools are active

Impact

• Project-level skills committed to git show as permanently deleted in git status, creating an unresolvable dirty working directory
• Teams cannot share project-specific skills via version control
• The only workaround is to use .claude/commands/ instead, which doesn't support multi-file skills with reference directories