Remove VCF Maker

(As part of my sweep of execute() calls I ran into the modules with OldPipeline in their name.)

The VCFMaker tools appear to mostly be build36-only and have not been used as long as the usage log database has been active.  

@chrisamiller, would you like to offer an opinion if they're still needed?  (If they are, maybe at least the "Old Pipeline" ones could be removed?)