Ditch all the {{site.url}}s from the <a href="">s to make life a bit easier

This was forcing me to add use the --url flag whenever I rebuilt the site and I
am the most impatient man in the world.
Make the vertical command documentation nav much more compact

As the number of commands grows, it's becoming increasingly ugly to give
individual commands so much vertical space in that nav list.
Fix the home link in the top left of the page