documentation updates

[samjtro]

Update documentation for all major packages. It has fallen far behind since v0.5.0 and it needs some major revisions.

[samjtro]

This will just be left continuously open. If anyone else would like to work on documentation, feel free to reply here.

[samjtro]

README is basically up to date at this point
Documentation has fallen behind, not too far as I've been adding some stuff, but far enough.