generalize Alleles to contain refBases & altBases, take 2

PROBABLY DON'T MERGE: this depends on the MD-tag fix in ADAM `0.13.1-SNAPSHOT`, which Frank estimated will go out in a release later this week. In the meantime, no need to have `master` point at an ADAM snapshot.

this PR includes indel code and some refactorings of Pileups, GenotypeAlleles, and others to support a universal notion of an Allele that is determined by multiple reference bases and multiple sequence bases.

I back-ported existing callers to be more general of their handling of variants/alleles, accordingly.

This should let us reuse a lot of @arahuja's bayesian/log-odds variant-analysis/filtering code across callers more easily.
Yes that is a somatic variant - however rare enough that we chose to ignore it early on.  I think some version of this just compared most likely variant in tumor to most likely variant in normal and as long as they were different we called a variant.  One advantage here was that if tumor was not variant we didn't even bother looking at the normal sample, saving some unecessary comptuation on the most common case (tumor is not variant)