Updating and consolidating setup instructions

By popular request, I have brought the installation instructions in setup/index.html into line with what's currently in the 'boot-camps' repo, consolidated everything into one file, and included setup instructions for R (thanks, Jenny).  Please look it over and send corrections; in particular, I'd like a better list of what our Windows installer actually installs, and instructions for installing Make on top of Git Bash if people want to do it the hard way.