(not yet functional) Baum Welch estimate internal rather than stop transitions

This should actually work in principal, I think, unlike estimating
tau. But at the moment it fails in a flailing flurry of zeros and nans.
Merge branch 'two-state-casino' into single-random

Conflicts:
	examples/aligner/Makefile
	examples/aligner/main.cc
Fix problem with Baum Welch

The parameter outputTable was set to "no" in the backward algorithm
block that was doing baum welch estimation... but we needed the damn dp
table to be saved. Oddly enough, it was set to "no" in the original
hmmoc release, too. I'll need to investigate to figure out whether (if)
it was working then.