GroupBySharedRegions updates:

for vcf-merge: allow entries with no alts to merge

 GroupBySharedRegions was relying on RawVariant to get the set of
 regions for a vcf entry. Entries with no alts don't generate
 RawVariants, so they'd never get a region and never merge. Now,
 we assign a region based on the reference allele to these.

for vcf-annotate:
 GroupBySharedRegions now reports groups ordered by the region of the
 first group member. Previously, the sort order was undefined.
bugfix: sort command for bed files was always using --unique