The Pathfinder Society Guide to Organized Play is up to version 8.0 (August 4, 2016), and is currently named Pathfinder Society Roleplaying Guild Guide. There are updated rules and restrictions listed there that are not reflected in the Affected Version of PCGen. At least one difference I am aware of is in the Librarian (Dark Archive) trait, which is listed on page 28 of the current version.
N/A - Source Document/Data Issue
I plan on implementing this and version 7 similar to new sources. The ideas is that the multi-sets Core Assumption and Complete would always use the current version, but the user would be able to manually pick an earlier version. I have some thoughts on how I will do this, but they are not fully fleshed out since the implication (to be a consistent model) is that any Additional Resources versions (all the _pfs folders under each main source) going forward should also follow a similar model, linked to the version of the guide. Ultimately I may decide this idea (version selectable) is too much work. If that's the conclusion, I'll just implement the changes in 8 into the current model.
I will be finishing gtpsop as its final version, v6. That matches the official guide name and rules from Paizo. A new source for Pathfinder Society Guild Guide will be created for v8. I think I'm just going to skip v7, unless I see any significant differences between v7 and v8 that may warrant the need for a user to load a character using only the v7 rules.
I've submitted a PR. Waiting for Travis.