EISGIT for unrelated package

[haggholm]

I'm opening this issue because:

• npm is crashing.
• npm is producing an incorrect install.
• npm is doing something I don't understand.
• Other (see below for feature requests):

What's going wrong?

When installing a package, if a different package contains a .git directory, the install fails
with EISGIT. Note, there is as far as I can tell no need to do anything with the directory containing the .git directory; I do not know why it’s checked or touched at all. If there is some reason why it must be changed, EISGIT is a very confusing error message.

$ ls node_modules/@client/base/.git -ld
lrwxrwxrwx 1 petter petter 57 Jun 27 12:02 node_modules/@client/base/.git -> /mnt/scratch/shared/petter/witkit-devenv/client/base/.git
$ npm i fs-extra
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@^1.0.0 (node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.1.2: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

npm ERR! path /mnt/scratch/shared/petter/witkit-devenv/client/root/node_modules/@client/base
npm ERR! code EISGIT
npm ERR! git /mnt/scratch/shared/petter/witkit-devenv/client/root/node_modules/@client/base: Appears to be a git repo or submodule.
npm ERR! git     /mnt/scratch/shared/petter/witkit-devenv/client/root/node_modules/@client/base
npm ERR! git Refusing to remove it. Update manually,
npm ERR! git or move it out of the way first.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/petter/.npm/_logs/2017-06-27T19_09_33_849Z-debug.log

npm-debug.log.txt

Note: I had previously opened this as #10372 but had it closed by the bot. Others have reported the same issue in #10933, also closed by the bot. Both issues attracted comments, so there are clearly others who feel it’s a problem, even if the npm CLI team thus far has not.

How can the CLI team reproduce the problem?

Just add a .git directory inside any package in node_modules and try to install something unrelated.

supporting information:

• npm -v prints: 5.0.4
• node -v prints: v7.10.0
• npm config get registry prints: http://npm.dev.witkit.com/
• Windows, OS X/macOS, or Linux?: Linux
• Network issues:
  • Geographic location where npm was run:
  • I use a proxy to connect to the npm registry.
  • I use a proxy to connect to the web.
  • I use a proxy when downloading Git repos.
  • I access the npm registry via a VPN
  • I don't use a proxy, but have limited or unreliable internet access.
• Container:
  • I develop using Vagrant on Windows.
  • I develop using Vagrant on OS X or Linux.
  • I develop / deploy using Docker.
  • I deploy to a PaaS (Triton, Heroku).