npm start fails after copying a generated project to a new directory

Created by: dceddia

Here is the failure:

$ npm start

> bug-test@0.0.1 start /Users/dceddia/Projects/pure-react/sandbox/bug-test-copy
> react-scripts start

module.js:339
    throw err;
    ^

Error: Cannot find module 'cross-spawn'
    at Function.Module._resolveFilename (module.js:337:15)
    at Function.Module._load (module.js:287:25)
    at Module.require (module.js:366:17)
    at require (module.js:385:17)
    at Object.<anonymous> (/Users/dceddia/Projects/pure-react/sandbox/bug-test-copy/node_modules/.bin/react-scripts:3:13)
    at Module._compile (module.js:425:26)
    at Object.Module._extensions..js (module.js:432:10)
    at Module.load (module.js:356:32)
    at Function.Module._load (module.js:311:12)
    at Function.Module.runMain (module.js:457:10)

npm ERR! Darwin 14.5.0
npm ERR! argv "/usr/local/Cellar/node/5.0.0/bin/node" "/Users/dceddia/.node/bin/npm" "start"
npm ERR! node v5.0.0
npm ERR! npm  v3.3.12
npm ERR! code ELIFECYCLE
npm ERR! bug-test@0.0.1 start: `react-scripts start`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the bug-test@0.0.1 start script 'react-scripts start'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the bug-test package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     react-scripts start
npm ERR! You can get their info via:
npm ERR!     npm owner ls bug-test
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR!     /Users/dceddia/Projects/pure-react/sandbox/bug-test-copy/npm-debug.log

To reproduce:

$ create-react-app bug-test
$ cp -r bug-test bug-test-copy
$ cd bug-test-copy
$ npm start

At first I thought it might have something to do with having run npm start from within bug-test before copying it, but skipping that step didn't have any effect.

Removing node_modules and reinstalling them fixes it:

$ cd bug-test-copy
$ rm -r node_modules
$ npm install
$ npm start   # works!

Using cp -a instead of cp -r does not cause the problem:

$ create-react-app bug-test
$ cp -a bug-test bug-test-copy
$ cd bug-test-copy
$ npm start   # works!

I'm running Node 5.0.0 and npm 3.3.12.

I tried (via nvm) with Node 6.3.1 and npm 3.10.3 and got the same behavior.

The cp -a vs cp -r makes me think this might be an npm bug.