Updated Sphinx to the latest version

It wasn't clear from the existing documentation what version of Sphinx it was built with. Attempting to build the docs with the latest version (1.2.2) with `make html` caused build errors.

I simply ran `sphinx-quickstart` and let Sphinx rebuild `Makefile` and `conf.py` itself. I also added an entry to `.gitignore` to ignore the `docs/_build` directory, which is where Sphinx will now create the built documentation.

The additional commits are just cleanup: resolving build warnings, removing files that were from old documentation systems, etc.