[BUG] Can't figure out how to fix permission issues on Mac

Environment

• Platform (select one):
• [ X ] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 0.2.37
• Operating System: macOS 15.2
• Terminal: iTerm2

Bug Description

I've followed the instructions a few times: https://docs.anthropic.com/en/docs/agents-and-tools/claude-code/overview#recommended-create-a-new-user-writable-npm-prefix

But I can't get claude doctor to stop showing a permissions warning:

Enable automatic updates?

Claude Code can't update itself because it doesn't have sufficient permissions.

Please visit our troubleshooting guide...

And the warnings show inside claude code as well.

Here's what I'm running:

$ mkdir -p ~/.npm-global
$ npm config set prefix ~/.npm-global
$ npm install -g @anthropic-ai/claude-code

added 3 packages in 409ms

2 packages are looking for funding
  run `npm fund` for details
Reshimming mise lts...

$ which claude
/Users/ndbroadbent/.npm-global/bin/claude

$ claude doctor

Enable automatic updates?

Claude Code can't update itself because it doesn't have sufficient permissions.

...


$ ls -l /Users/ndbroadbent/.npm-global/bin/claude
lrwxr-xr-x  1 ndbroadbent  staff  52 Mar 12 10:28 /Users/ndbroadbent/.npm-global/bin/claude -> ../lib/node_modules/@anthropic-ai/claude-code/cli.js


$ ls -l /Users/ndbroadbent/.npm-global
total 0
drwxr-xr-x  3 ndbroadbent  staff  96 Mar 12 10:28 bin
drwxr-xr-x  3 ndbroadbent  staff  96 Mar 12 10:28 lib

$  which mise
/Users/ndbroadbent/.local/bin/mise

$ which npm
/Users/ndbroadbent/.local/share/mise/shims/npm

Note that it does work when I run sudo claude doctor:

sudo claude doctor
Password:

 ✓ npm permissions: OK

 Your installation is healthy and ready for auto-updates.

 Press Enter to continue…

$ ls -la ~/.claude.json
-rw-r--r--@ 1 ndbroadbent  staff  77516 Mar 12 10:36 /Users/ndbroadbent/.claude.json

$ ls -la ~/.claude/
total 0
drwxr-xr-x@   3 ndbroadbent  staff    96 Mar 12 10:19 .
drwxr-x---+ 133 ndbroadbent  staff  4256 Mar 12 10:29 ..
drwxr-xr-x@   4 ndbroadbent  staff   128 Mar 12 10:36 statsig

$ ls -la ~/.claude/statsig/
total 16
drwxr-xr-x@ 4 ndbroadbent  staff  128 Mar 12 10:36 .
drwxr-xr-x@ 3 ndbroadbent  staff   96 Mar 12 10:19 ..
-rw-r--r--@ 1 ndbroadbent  staff  105 Mar 12 10:36 statsig.session_id.2656274335
-rw-r--r--@ 1 ndbroadbent  staff   38 Mar  4 15:18 statsig.stable_id.2656274335

What permissions is it checking?

Steps to Reproduce

Not sure how to reproduce on other machines.

Expected Behavior

No permissions error. I'm running claude as my user, it has all the needed permissions.

Actual Behavior

Getting a permissions error

Additional Context

I'm using mise to manage my node and npm versions: https://github.com/jdx/mise
Could this be causing the issue?