The website is powered by Hakyll, with a few small extensions. The module CustomCompilers includes a Pandoc compiler with math extensions enabled, as well as a compiler that allows custom writers in Pandoc. I use a custom writer largely based on this example to add sidenotes to the HTML output.
Hakyll stores the compiled site in a folder called _site, which I don't track in this repository. The shell script publish.sh (which accepts a commit message as an argument) commits the contents of _site to https://github.com/wetmore/wetmore.github.com and pushes them to Github, which hosts the site.