Add cross-links and Table of Contents to the API section of the docs

[rpgoldman]

The API section of the existing docs is hard to navigate, because you get a reference to a class (e.g., ModuleDefinition) when you are reading about some other class, and there is no way to chase that reference, except through string search (Cmd-F or Ctrl-F), which often gives a ton of false positives in that page (e.g., "ModuleDefinition" is mentioned a lot).

If you are using Sphinx, I think it will do all this for you, if you ask it to.