Merge work from Latent model

[jtmccr1]

This PR adds the code used in our exploration of latency in the Ebola reservoir.

Changes of note

• Most of the changes are in the latentStateBranchRate package and should not affect the rest of the code base.
• I have made some changes in TwoStateSericolaSeriesMarkovReward.java that limit the calculations done in loops. We get some speed up from this.
• I have added an IndicatorProductParameter for sampling parameters on [0,1). (Although it doesn't seem to affect the results, I think this approach could lead to inconsistencies, and have removed it in favor of the below changes.)
• We sample the proportion of time spent latent for each branch. I have made the indicator and the proportion (0,1) TreeParamterModels watched by the model. This set up allowed me to set the value of a parameter after a tree move without having to make changes to other parts of the code base ( I think initially - years ago - we had to make changes to TreeParameterModel).