Docs (Issue 3)

Updates to the readme for the Sphinx-based doc generation directory to help new users, and some clean-up of directory structure to remove non-source files. Fixes #3 

NB: atomic commits, so upstream can pick-and-choose. Commits to:
* fix the README: 92f8678, 75b7c53
* clean up docs/_build: b73f071, 83b9e5f
* clean up *.pyc in the src/ directory: 408ad48