Transition GitHub Pages site to a Jekyll based build

[matthewfeickert]

To be able to use a index.md Markdown file to generate an index.html page (so put all the information in the README.md and then cp README.md _site/index.md) Jekyll needs to be used with GitHub pages. At the moment the website is not Jekyll based (there is _site/.nojekyll) so to take advantage of this it will need to get changed to being Jekyll based.