Integrate ReshardVcf into ResolveComplexVariants

[mwalker174]

Adds a call to ReshardVcf at the end of ResolveComplexVariants. In addition, each of the BOTHSIDES_PASS and HIGH_SR_BACKGROUND contig-sharded variant tables is concatenated into a single genome-wide table prior to annotating records with these flags in CleanVcf. This has a slight cost in memory footprint in CleanVcf1a but ensures that shuffled records are properly annotated. Json templates and top-level workflows are also updated.

This branch was successfully tested on ResolveComplexVariants, GenotypeComplexVariants, and CleanVcf.