pre-cell typing

I am creating this release to reference it elsewhere at this step. It is not ready for production use out of the box, though it could be helpful to others as-is with modifications.

This has a functioning pipeline for the steps before merging, the RNA and ATAC processing after merging, a parameter sweep to determine what to use for settings, and the harmony steps that yield the happy graphs in the end (assuming correct parameters). Next version will fix a couple bugs I know about (jackstraw not recording, general messiness, etc) and add cell typing as a step in the parameter sweep, as a parameter validation metric to add to jackstraw/variance/etc.