Clean up the docs folder

This is mostly just a clean-up of the docs directory.
* Removed the auto-generated rst files from the repository.
* Added a hook in the Makefile that calls `sphinx-apidoc` to generate the module rst files.
* Moved all images into an images folder.

To make the docs from scratch, you should now just do the following,

    $ cd docs
    $ make html

The HTML docs will be in `_build/html`. To view the docs,

    $ open _build/html/index.html