Fix: Posterior decoding was excluding the first position.

The code of decoding posterior had incorrect for loop condition and stopped before evaluating zero position.
Changed to include zeroth iterator
Fix: Double sampling of stochastic sampling and 0-based hits table (comma-separated)

There was a second calling for traceback sampling in StochHMM.cpp.  Removed it.
Included -hits option in the usage statement
Updated print_hits to output tab separated file with 1-based coordinates
Updated model to reflect current format.
Previous model still works, but the current format doesn't require <MODEL STATES> section