Latest changes in advance of handing off the MDMC project

This version of MarkDuplicatesWithMateCigar passes unit tests
and runs through the torturous pericentromeric region of Chrm1
in the 6-wgs-bam extreme coverage test case. It has shown improved
performance against current MD in single-bam test cases.

These changes do not include a fix for the bug observed wherein
excess duplicates are marked for paired records with the same
chromosome, start position, and orientation.

I am hoping to implement these changes tonight (sunday) night, but
in the event that I dont or Nils wants to work this weekend, I push
these latest updates.