Firstly I must thank Philip Poots @pootsbook for informing me about github pages and Jekyll and giving me the nudge in the right direction that got me to stop playing starcraft 2 and doing something slightly more useful. I must also thank Philip for his own Jekyll based page which I forked to give myself an easier starting point.
As Jekyll has a lot of very useful plugins, several of which I thought would work well for me I went ahead and started using them.
After getting things just as I wanted them and the locally run code working well I realised that github pages do not allow for plugins.
Never fear, where there is a will there is usually a way and indeed I found it….. thanks to a multitude of blog posts on the subject scattered across the internet. It was a post by Aleksey V. Zapparov @zapparov that provided the necessary information I was missing, simply put I now have two branches, a source branch for the source and the master reserved for the compiled sources. I also have a nice rakefile so I no longer have to manually compile the source and push it to the repo.