Script Package Generator with v 5.0

I'd like to make the functions.js and plugin.js files smaller, and I found the JS Package Generator. But it doesn't appear to work with 5.0. Is there a way to get a customized package to reduce the JS sizes.

Ideally, I'd like a NPM or Bower package manager - but the package generator will be fine for the time being.
http://support.semicolonweb.com/js-package-generator/