Stochastic Viterbi added.
Added beginning of explicit duration code to viterbi
Started adding explicit duration.  Split explicit duration decoding algorithms
off to complex decoding algorithms that keep track of values for other calculations
Added checking of model Topology.
Fix Model finalize calling checks on NULL transitions
Add Continuous PDF emission for Real track
Remove CSV from SeqTracks and make Fasta Default format
Testing and updating development branch
Finish univariate PDF functions, Add initial default PDFs
Completed coding of the PDF functions and created default loading
of those function using void StateFuncs::loadUnivariatePdf()