Updates to epub build

Fixes the toc and various link errors resulting from the epub build (#1126). I also added a cover to the epub so it more closely resembles a book. Some other very minor edits.

The most significant change here is adding a separate toc file for epub builds (epub-contents.rst) and then updating the Makefile so that sphinx points to this new file instead of using the one declared in the config/all.py file. 

Running the resulting epub through a validator still results in about 170 warnings so it seems there's still quite a bit that needs attention.