Difference between repo and jar version.

I got lumiere-2.4.8.jar and unpack it. I compared this version and version from github repo, that David produce us on the first place. I think this two versions is different and I do not know which one is better.

This Merge request contains difference between jar and repo.

I would like to add all difference that I found to this branch and then process xml files and check the difference.

Files for comparison:

• PiecewiseFitnessBirthDeathDistribution
• FitnessBirthDeathModel
• UnsortedAlignment
• MultiSiteScaledNumbers
• p0_ODE
• p0ge_InitialConditions
• p0ge_ODE
• p0ge_SiteConditions
• ScaledNumbers
• SmallNumber
• SmallNumberScaler
• EbolaExactP0FitnessModel
• EbolaGeoFitnessModel
• FluDeepMutScanFitnessModel
• FluGenotypeFitnessModel
• FluSiteSpecificFitnessModel
• FourGenotypeFitnessModel
• MultiSiteFitnessModel
• MutLoadFitnessModel
• NeutralFitnessModel
• SiteSpecificFitnessModel
• ExcludablePrior
• Utils