Just on a formatting note, it would be great to have a static generator that takes markdown input and generates this kind of html book with footnotes and references. Similar to [spec-md](http://leebyron.com/spec-md/). Anyone know of interesting projects along those lines?
The only thing that comes to mind is Pandoc [0], [1]. It is worth adding that it was originally created by John MacFarlane, a philosophy professor at the University of California, Berkeley. It's written in Haskell.