Started big refactor.
More work on big refactor.
Getting Trajectory working without master.beast.
Might need a different way of handling ranges.
Removed range stuff from ReactionStringParser.
Steppers now use NewReaction objects.
Finished NewReaction draft.
Finished draft of Trajectory refactor.
Finished draft of Ensemble refactor.
Working on EnsembleSummary refactor.
Continued working on EnsembleSummary.
Still refactoring EnsembleSummary.
Forgot to add new MomentGroup class.
Main package now compiles.
Removed java interface examples.

I'm removing the interface entirely.  It's undocumented,
nobody uses it and it creates its own headaches.
Having to modify classpath in examples.

Will this be a problem?
StochasticLogistic.xml runs!

Need to fix "sim" component of JsonOutput - current method of
generation sucks and is broken.
JSON output working again.
Stochastic logistic example working.
StructuredSIR now working (Ensemble test)