First batch of doc revisions

Several changes go into this batch: I created a hierarchy around the API methods and reorganized a few methods to fit within that hierarchy (this makes it much easier to navigate when loaded into Flatdoc), I re-worded a few small things here and there, and I reformatted the commandline usage into a table for greater separation of syntax and descriptive text. Finally, I replaced the whiteboard photo of the process diagram with an SVG diagram showing basically the same thing.