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?

Using the environment variable NPM_CONFIG_PREFIX does not work if ran inside a bash script via npm-script.

How can the CLI team reproduce the problem?

test.sh

#!/bin/bash
NPM_CONFIG_PREFIX=/tmp/test npm config get prefix
npm_config_prefix=/tmp/test npm config get prefix

package.json

{
  "name": "npm-config-test",
  "scripts": {
    "test": "./test.sh",
    "test2": "NPM_CONFIG_PREFIX=/tmp/test npm config get prefix && npm_config_prefix=/tmp/test npm config get prefix",
    "test3": "NPM_CONFIG_PREFIX=/tmp/test ./test.sh",
    "test4": "npm_config_prefix=/tmp/test ./test.sh"
  }
}

Running ./test.sh directly works

➜  npm-config-test ./test.sh
/tmp/test
/tmp/test

Running it through an npm script fails

➜  npm-config-test npm test

> npm-config-test@1.0.0 test /home/$USER/npm-config-test
> ./test.sh

/home/$USER/n
/tmp/test

Running directly in an npm script works

➜  npm-config-test npm run test2

> npm-config-test@1.0.0 test2 /home/$USER/npm-config-test
> NPM_CONFIG_PREFIX=/tmp/test npm config get prefix && npm_config_prefix=/tmp/test npm config get prefix

/tmp/test
/tmp/test

Setting the variable uppercase before the script execution fails

➜  npm-config-test npm run test3

> npm-config-test@1.0.0 test3 /home/$USER/npm-config-test
> NPM_CONFIG_PREFIX=/tmp/test ./test.sh

/home/$USER/n
/tmp/test

Setting the variable lowercase before the script execution works

➜  npm-config-test npm run test4

> npm-config-test@1.0.0 test4 /home/$USER/npm-config-test
> npm_config_prefix=/tmp/test ./test.sh

/tmp/test
/tmp/test

supporting information:

• npm -v prints: 3.10.8
• node -v prints: v7.0.0
• npm config get registry prints: https://registry.npmjs.org/
• Windows, OS X/macOS, or Linux?: Linux/Ubuntu
• Container:
  • I develop using Vagrant on Windows.
  • I develop using Vagrant on OS X or Linux.
  • I develop / deploy using Docker.
    • Issue originally happened in docker-node, but it also happens on the host
  • I deploy to a PaaS (Triton, Heroku).