There's not, at the present, a whole lot of Javascript used in this toolset. It's used
to provide the ASCIIMath support, and
on the mailbox/communications link at the bottom of the page (and the main reason it's used there is simply to encode the email address as it actually appears in the HTML to prevent spammers from harvesting your email address).
If you need to add new Javascript, then the rules are exactly the same as for the CSS files above. Just replace ".css" by ".js".