3 Different methods for calculate StateLikelihood, [k][state] the orginal one, [state][k] reverse array, and [k*STATE_COUNT+state] using the offset method.
This commit keep all three setup, but going to refactor everything to the offset method
In the process of removing most double[][], replacing with double[offset]
Fixed bugs in likelihood calculation with offset
Setup for simulation run.
Tune proposal distribution a bit, still semi random. Generally it updates srp >> tree