I have a simple test jekyll app like so:
index.html is:
There are plugins for HTML and CSS minification with Jekyll, but a search doesn't turn up anything obvious for JS.
However, the source for CSS one above is less than 100 lines and actually uses Juicer to do the minification, which can also do JS, so that plugin could easily be used as a template to implement your own JS minifier (it looks like even just s/css/js/g
would be close to working).