[BUG] rm -rf on single subdirectory deleted entire parent directory contents

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?

Summary

When executing rm -rf ~/claude-mcp/web-crawler-mcp to delete a single subdirectory, almost all contents of the parent directory ~/claude-mcp/ were deleted instead.

Environment

• Claude Code Version: 2.1.3
• Platform: macOS (Darwin 24.1.0)
• Date: 2026-01-27

Steps to Reproduce

1. User requested to delete only ~/claude-mcp/web-crawler-mcp folder
2. Claude executed: rm -rf ~/claude-mcp/web-crawler-mcp
3. Error appeared: rm: /Users/username/claude-mcp/: Permission denied
4. Result: Nearly all contents of ~/claude-mcp/ were deleted, not just the target subdirectory

Expected Behavior

Only web-crawler-mcp folder should be deleted.

Actual Behavior

• "Permission denied" error on parent directory
• Almost all folders inside ~/claude-mcp/ were deleted
• Only one unrelated folder remained

Impact

• 6 months of project files were lost
• Required full day of recovery work

Log Evidence

Session log shows the exact command was rm -rf ~/claude-mcp/web-crawler-mcp but the deletion affected the entire parent directory contents.

What Should Happen?

Only the specified subdirectory web-crawler-mcp should be deleted. Parent directory and sibling folders should remain intact.

Error Messages/Logs

rm: /Users/username/claude-mcp/: Permission denied

Steps to Reproduce

1. Have a directory ~/claude-mcp/ with multiple subdirectories
2. Request Claude to delete ONE specific subdirectory: rm -rf ~/claude-mcp/web-crawler-mcp
3. Claude executes the command
4. Result: Almost all contents of parent directory deleted, not just target folder

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.3

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

VS Code integrated terminal

Additional Information

Session ID: 997249f6-0edd-442c-a9ba-25d278244e7e
The command syntax was correct but execution affected wrong scope.