Refactor & clean

Cleaning around and converging aligner and casino to isolate the
difference between the two (these versions do the same thing now, but
aligner seems to have a memory leak).
Split HmmDriver into separate file

Note it needs to be in a header because it's templated
Move configuration to text file

GOD LOVES ME I refactored and moved the config to a text file and the
memory leak and shit disappeared.
Function baum welch estimation

WOOOOOOOOOOOOOOOOT