Rename callers

 * Rename "callers" package to "commands"
 * Rename individual callers to have more appropriate names. Closes #200.
 * Drop somatic threshold caller.
 * Move GenotypesEvaluator to Concordance, and make it no longer a Command.
 * Make conversion functions in AlleleConversions.scala not implicit.
could just call this `SomaticIndelCaller` if you like