I don’t understand the sense for Github to have deep coupling with Jekyll. It makes no sense to have the Jekyll site compiled at the server side effectively coupling Jekyll with Github.
Had Github took the route to specify a build directory instead, many more static site generators would have had a fair fight.
I would love to know if there is any advantage in taking the additional load of compiling the files at the server side. Beyond the need to have Jekyll as a hard dependency, this makes no sense to me. This also limits the number of plugins that Github can safely run at the server side, complicating the process unnecessarily.