Unbreak apps that reached a corrupted state due to #927

Previously to fixing #927, if you had a 'node_modules' directory
anywhere up the directory tree from your app and you had a package
in your app using NPM, all calls to 'npm' ran against the 'node_modules'
directory it found, so neither 'node_modules' nor 'npm-shrinkwrap.json'
would be created within your package's .npm directory.

The fix to #927 ensured that 'node_modules' was first created within
'.npm' but people who had already run 0.6.0 were still in a corrupted state.