Vcf merge

Hi everyone,
This is some major surgery that I attempted on the set out outstanding changes to do variants with the new schema.  I'm open to suggestions on better ways to send it for review.  What I ended up doing was moving the new classes to new packages & directories so that the code could exist side by side until we commit it and remove the old code.  I think this is becoming unwieldy, so perhaps someone with better git-fu can advise on what the best way to get this reviewed might be.
Thanks in advance,
Neal