I had the devil of a time trying to get a custom website to show up on github pages. It was sphinx generated documentation and I had put it on the website under a directory called manual. It was all borked. Not only did the nice stylesheet not show up, none of the images showed up either. I tried a whole bunch of things, but finally, from a hint here, it turns out that you need to add an empty file named .nojeykll in the root directory, and that allows you to add your own custom projects.