Code highlighting doesn't seem to work. There are .highlight selector class in the accompanying CSS but the tags aren't generated in the page. It probably would work if highlight.js was added on the page.

Linking markdown files is also interesting. It rewrites the target url from .md to .html and also supports pointing to a clean path without the extension. Unfortunately it's not possible to follow the clean path when browsing the same file on github.

Still, overall it's a good improvement to github.