[Plugin: WP JS] More Information?

I have the initial part of wp-js working which includes two javascript files in my theme directory being combined together and compressed for download. My question is how do I get files in directories outside my theme to work? For instance in wp-includes/js/ or in various plugin directories.

This plugin is awesome and will be really useful to a lot of people to assist with speed of their wordpress blog.

Any help is appreciated.