Poorly-documented-but-complete release

Currently, this software is mostly used by one group of researchers at Penn State. For our purposes, it is (mostly) satisfactory. However, our intent is for this software to be useful to other researchers, and as such, we are working on establishing a stable API and complete documentation.

This release is a checkpoint where things "work" for us, but are still in the prototyping stage and generally poorly documented. Future releases will have a more stable API and an essentially complete documentation.