[BUG] Cleaning up after switch to native Mac install could lead user to lose data

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?

Having migrated to the native Mac install, I now see:

Warning: Leftover npm global installation at /opt/homebrew/bin/claude
Fix: Run: npm -g uninstall @anthropic-ai/claude-code

My instinct is to do brew uninstall claude since I can see that it was installed via Homebrew. That looks like it would be bad because the claude-code formula wants to rmdir ~/.claude, so I'd lose data.

What Should Happen?

These instructions should be more specific about how to tell Homebrew to clean up without destroying data.

Error Messages/Logs

Steps to Reproduce

1. Install Claude Code with Homebrew.
2. Use for a long time.
3. Update to the native Mac install.
4. Notice dangerous instructions.

Claude Model

None

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.52

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_