I just remembered I left something out of the pdf document. The ignore list for each "Pack" above will ignore any file from the Basic Pack. But to be able to have Pathfinder load the 3PP Pack it requires the Basic Pack.
So TCArknight you should setup the Basic Pack repository into its own folder. Then do sync of the latest files. Then "Copy" the COM_ files from the Basic Pack folder over to the folder holding your 3PP Local Repository.
Its one extra step but really lets us reuse allot features in multiple Packs. In example when we start to do the Psionic Bestiary the GM Pack monster things that Frumple has created are going to be very useful. I have already moved his Disease helpers into the Basic Pack for this reason.
Hopefully this all makes sense.