Update documentation to reflect new repository structure and goals

[travs]

@gsarma Would be interested in doing this one perhaps first, since I need to get up to speed on those things anyway

[gsarma]

@travs let's talk about this. It might make more sense for me to do this since I was the one that overhauled the recent instantiation. But if you want to handle re-deploying the docs to readthedocs, that would be great.