checkpoint, resolution of haplotype breakage issue (a->empty() errors)

There are still some outstanding concerns with this commit, but a checkpoint is
necessary as this code state has excellent performance against indels, another
1% better than the previous commit.
further improvements to indel (and SNP) detection

A further 1% improvement in AUC for indels, and .5% improvemint in AUC for
SNPs.  Changes in this commit are not yet well-optimized, and users should be
aware that runtime performance here will be slower than in previous commits.
(3x slower for 100 10X samples.)  Subsequent commits will focus on reducing
runtime.