[BUG] npm install may conflict with native install

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?

If the npm install has the same prefix (~/.local) as the native install, then claude doctor thinks the former is the latter and that both are installed, and claude install doesn't uninstall the former and install the latter.

What Should Happen?

claude doctor should realize I'm running npm-global (not native) and that native isn't installed.

claude install should uninstall npm-global and install native.

Error Messages/Logs

$ claude doctor

 Diagnostics
 └ Currently running: native (1.0.115)
 └ Path: /usr/local/bin/node
 └ Invoked: ~/.local/bin/claude
 └ Config install method: unknown
 └ Auto-updates enabled: default (true)
 └ Search: OK (vendor)
 Warning: Multiple installations found
 └ npm-global at ~/.local/bin/claude
 └ native at ~/.local/bin/claude
 Warning: Running native installation but config install method is 'unknown'
 Fix: Run claude install to update configuration
 Warning: Leftover npm global installation at ~/.local/bin/claude
 Fix: Run: npm -g uninstall @anthropic-ai/claude-code

Steps to Reproduce

1. Run npm install -g --prefix ~/.local @anthropic-ai/claude-code
2. Run claude doctor
3. Run claude install

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.0.115 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Claude Docs: Set up Claude Code: Standard installation says: "Do NOT use sudo npm install -g", but on macOS, you need to use sudo to write to npm's default global prefix (/usr/local), so I ran npm config set prefix=~/.local before running npm install. But to simplify the "Steps to Reproduce" (above), I just added --prefix ~/.local to npm install (in step 1).