This adds @Han-Cao's merge_duplicates.py as a post-processing step after bcftools norm -f.

It merges together records at the same position that bcftools norm can create (see the original issue, #1493, for details).

Unfortunately, it seems like bcftools norm can shift together sites that can't be represented as one without allele conflicts. So the --keep first heuristic is used by default to choose one, but can be toggled in the mergeDuplicatesOptions field on the config XML.

As it stands bcftools norm -f and merge_duplicates.py are both on by default for vcfwave output. To apply it to the "Default" vcfs, then bcftoolsNorm="1" needs to be activated in the config.

Stacks on #1491