Retain all source IDs on VariantContext merge

[bbimber]

In GATK3, when merging variants, the IDs of all the source VCFs were retained. This code path seems like it intended that, since the variantSources set is generated, but it doesnt get used for anything. This PR will use that set to set the source of the resulting merged VC.

Note: i dont think I can kick off the test suite. It is possible this change would result in tests breaking, and those would need updates.