Jake VDP wrote an astronomy paper (github source) that published to gh-pages (http://jakevdp.github.io/multiband_LS/) via gh-publisher. While each of those steps is a little clunky, one awesome feature of this page is that it has a "Send Feedback" button which then opens up a GitHub issue! This is a great way to create a dialogue with the manuscript authors and readers.

EDIT: Added link to gh-publisher