Significant Revision of Documentation

- Change theme of HTML output.
- Enable inter-sphinx documentation for pandas and music21.
- Revise formatting for many classes.
Added R Things to .gitignore

These files are automatically created when I run R to make a chart.
Write WorkflowController._two_part_modules() and Tests

I also modified a few other things in workflow.py, but it's no big.

And I revised some of the strings in the tests for _all_parts_modules(),
and to make sure that run() actually caches results from the most recent
experiment, which is required by export() and output().