DOC: Update ReadtheDocs structure or theme

[nawtrey]

There are a few changes I wasn't able to implement in GH-100 that I would like to list here:

• For the API pages, change to use the page titles/headers instead of the module names (i.e. "Probability and Flux Calculations" instead of "kda.calculations". While the titles are annoying, it is also an issue because the 4th depth level is the KDA functions, which have tiny font and are basically unreadable. If we removed the 2nd depth level "kda.calculations", etc. it would look a lot better I think.
• Remove the redundant "Functions" and "Classes" at the bottom of each API page. I don't know why we would want a table of the functions listed at the bottom
• Add a "Home" link to the sidebar that links back to index.rst. I believe there is a simple way to do this where you make some other file (i.e. master.rst) the master file in the conf.py and then you add index.rst to the main toctree as Home <index> or something like that.