The documentation for Github pages is pretty good, but I ran into a couple of problems while setting up my project page. The first problem was with configuring my DNS server to use a CNAME that points back to the Github project page. This page has good information on adding the DNS records you'll need, but in this case I needed them to really spell it out for me and give me a sample BIND configuration.
Or maybe I'm just dense and it was after 10:00pm. My mind turns to crackers and jelly after 9:30. The table at the bottom of this page clued me into the problem. I didn't think that having a CNAME record with a "/" in it would workd, but when I ran named-checkzone on the config file it didn't give me any errors either. After carefully reading the page and the table information I realized that GIthub will setup the root of the site as /projectname and the domain name is determined by the CNAME file you configure in the respository.
I should just work on new things in the morning, cause once I had everything configured correctly it worked like a charm. Well almost...
The second problem had to do with Jekyll and SASS. For security reasons Github disables all Jekyll plugins which means that when they jekyll build your site some of the content may be off if you are relying on plugins. I didn't realize that I was relying on a plugin when I was locally using SASS as detailed in the Jekyll documentation. So I had a site on Github using a custom domain, but no stylesheets, doh.
I haven't solved the SASS, Jekyll, and Github issue in a cool and clever way, but I did compile the stylesheet using jekyll serve -w and manually copy the _site/css/style.css file into the css directory which then gets copied back when Github builds the site. Some extra hubabaloo, but things are now working and looking good.
Check out my new project site here. I'll be releasing the actual code soon. Just need to add a few last features.