Frustrating MacOS ENOTEMPTY rename issues on newer npm versions

[bailey-coding]

Describe the bug

I think Heroku CLI maybe doesn't face this because of using an older version of node, though I haven't double-checked with the versions of NPM used with it.

Sometimes updating one of my plugins causes a frustrating edge case causing the update to file, and requires additional steps to clean it up and solve.

To Reproduce
Steps to reproduce the behaviour are a little challenging, but might be possible creating a new CLI that bundles a modern version of npm.

❯ mycli update
Fetching information about CLI update [channel: alpha] [dist-tag: alpha-darwin-arm64]... done
Restarting CLI to update plugins with the new version
Updating CLI from 16.0.20-alpha-darwin-arm64.0 to 16.0.21-alpha-darwin-arm64.0... done
Fetching information about CLI update [channel: alpha] [dist-tag: alpha-darwin-arm64]... already up-to-date (16.0.21-alpha-darwin-arm64.0)

Updating 5 installed plugin(s)...
 ›   Notice: Do not forget to refresh your completion cache by restarting your shell or by running
 ›
 ›       $ source ~/.zshrc
 ›       # OR
 ›       $ source <(mycli completion zsh)
 ›
 ›    More info for setting up completion on other shells can be found by running `mycli completion --help`
 ›
npm error code ENOTEMPTY
npm error syscall rename
npm error path /Users/myuser/.local/share/@myorganisation/mycli/node_modules/@myorganisation/myplugin
npm error dest /Users/myuser/.local/share/@myorganisation/mycli/node_modules/@myorganisation/.myplugin-6EHKOOFt
npm error errno -66
npm error ENOTEMPTY: directory not empty, rename '/Users/myuser/.local/share/@myorganisation/mycli/node_modules/@myorganisation/myplugin' -> '/Users/myuser/.local/share/@myorganisation/mycli/node_modules/@myorganisation/.myplugin-6EHKOOFt'
npm error A complete log of this run can be found in: /Users/myuser/.npm/_logs/2026-03-20T12_50_38_218Z-debug-0.log
@myorganisation/mycli: Updating plugins... !

Expected behaviour

Plugins to happily successfully update

Screenshots
N/A

Environment (please complete the following information):

• OS & version: MacOS Tahoe 26.3.1
• Shell/terminal & version zsh 6.9
• Node: 24.11.1
• NPM: 10.9.6

Additional context

Some long-lived related NPM issues:

npm/cli#5825
npm/cli#6370

Claude + Amp related issues from it

anthropics/claude-code#7373
https://ampcode.com/threads/T-1c48ef54-b8b8-4d8a-aa20-33b7c897f9fe

[jfeingold35]

@bailey-coding , thanks for reporting this. We can put in some effort trying to figure out how to reproduce this, but if you can determine a reliable way to repro, that will be the best. In the meantime, thanks for your patience, as always.

[bailey-coding]

Yeah, sorry about it being a kind of vague annoying not easily reproducible bug, since it's only intermittently happening too.

It also could be somewhat exacerbated by specifically how we do rollup bundling and building/publishing plugins with Bazel too, where we could maybe get around the issue by just bundling all external dependencies with each plugin. 😅

I'll give setting up an example oclif project + plugin a try and see if I can somewhat easily reproduce it.

[github-actions]

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