renaming package, moved from haplotype/spectrum.likelihood to likelihood.spectrum/halpotype
Refactoring, going to create the new Haplotype/HaplotypeModel data structure
OldHayplotyp MCMC can run again, might break a few things
A lot of refactoring, shoulde be multiple commit
Attempt to use spectrum code for haplotype calculation
Factor out abstract alignmentModel
minor bug fix
Refactoring data structure