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I have an idea, suggestion or even just seeing what the feasibility is. I am not sure how many resources in the resource pack are shared between PureBDCraft and Vanilla. I prefer Vanilla, but some of the addons for PureBDCraft are pretty cool. I am not sure if it is feasible that in the future to split the core of BDCraft into a separate package that has all the shared assets and have the addons work on those. And then any differences would then have sperate resource packs for your flavor of BDCraft. It may be more difficult for users to manage the resource packs, but long term Minecraft doesn't change or remove too much so for updates unless it is a new mob or something would all have all the base models and wouldn't need updated as much. This may also allow for faster turn around for each flavor since there would be less models.
The other option is to go the other way and merge the two and use the picker to allow us to pick which flavor we want. Since the framework is there, but this would allow everyone to use the addons for their pack since there would only be one pack.
Again this may be a stupid idea and I apologize if this has already been discussed, suggested, or is not worth the time and effort.