Restructure setup and software guides

[agitter]

https://github.com/gitter-lab/ml-bio-workshop/blob/gh-pages/guide/software.md is now redundant with our https://github.com/gitter-lab/ml-bio-workshop/blob/gh-pages/_extras/about.md

We should also consider splitting the setup instructions so that only the literal steps to follow appear in that document. The update scripts, environment information, and troubleshooting should be moved.