[BUG] worktrees in javascripts, defaulting to `.claude/<worktree>` clash with node's resolve, resulting incorrectly resolved dependencies, types, etc

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?

Described here: https://github.com/NullVoxPopuli/claude-worktrees-forgot-about-javascript

Copy-pasted here:

------------------------------------

Claude, by default, creates worktrees in a sub-folder of the main git root.

It's bad for JavaScript especially, because when node, bun, whatever using node's resolve algorithm searcehes for a bin or dependency, it searches _up_ the directory structure (yarn 1 relied on this to its detriment).

Example:

.                root
  ./index.js     main file    
  ./worktree-a   some worktree
      index.js   main file
````

If `index.js` has require/import:

- `./wortree-a/index.js` resolves the root's dependency if dependencies are not installed

This can be catestrophic in big repos where dependencies can move around or be upgraded frequently.

We can see how the mismatch manifests with this simple one liner:

```bash
# typescript is the only dependency in this repo
node -e "console.log(require.resolve('typescript'))"

[!NOTE] There is a script you can run ./do-it-for-me.sh that automates all this

1. at . of this repo,
2. pnpm install
3. node ./index.js or run the above, you'll get:

``bash
<repo>/node_modules/.pnpm/typescript@5.9.3/node_modules/typescript/lib/typescript.js
``

1. create a worktree -- if you don't have ignore-scripts=true set in youn ~/.npmrc, I did this for you.

(manually do: git worktree add ./some-sister-path

1. cd ./the-work-tree-path
2. run node './index.js or the above script, and you'll get:

``bash
<repo>/node_modules/.pnpm/typescript@5.9.3/node_modules/typescript/lib/typescript.js
``
This is bad because versions and the whole dep graph could be different between worktrees

1. run pnpm install
2. run node './index.js or the above script, and you'll get:

``bash
<repo>/the-work-tree-path/node_modules/.pnpm/typescript@5.9.3/node_modules/typescript/lib/typescript.js
``
this is the correct path, but there is no error when it doesn't exist

And with npm

1. at . of this repo,
2. npm install
3. node ./index.js or run the above, you'll get:

``bash
<repo>/node_modules/typescript/lib/typescript.js
``

1. create a worktree -- if you don't have ignore-scripts=true set in youn ~/.npmrc, I did this for you.

(manually do: git worktree add ./some-sister-path

1. cd ./the-work-tree-path
2. run node './index.js or the above script, and you'll get:

``bash
<repo>/node_modules/typescript/lib/typescript.js
``
This is bad because versions and the whole dep graph could be different between worktrees

1. run npm install
2. run node './index.js or the above script and you'll get:

``bash
<repo>/demo-a/node_modules/typescript/lib/typescript.js
``
this is the correct path, but there is no error when it doesn't exist

So what, the paths are different?

While this demonstration is simple, and doesn't show _what_ can go wrong, a common thing I've been seeing:

• TypeScript private brand types do not match (and they must match, else the private types are considered "different")
• Graphs of build dependencies need to be upgraded together, and resolve to incorrect versions (versions from other worktrees)
• Result in duplicate modules being bundled in vite apps (or any project that uses "bundling")

Solution?

Use Sister Worktrees, and don't ever nest worktrees.

e.g:

./repo
./repo-1
./repo-2

Also valid:

./repo
./repo-worktrees/
    ./repo-1
    ./repo-2

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

any that uses .claude/<worktree>

Platform

Other

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_