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I think the creator/maintainer for the databases is a user who goes bv "Chopswil" on the Paizo forums.
Separating by source is reasonable.
I would not want to exclude the Player Companion- or Campaign Setting- sourced items unless necessary. I believe all of the rules content is Open. Paizo generally only posts the content from the "Pathfinder Role Playing Game" book line on the PRD (the world-neutral main rule books line); with the exception of the Technology Guide, nothing from the Player Companion or Campaign Setting line has been posted to the PRD ... but that does not make the content Closed. These amount to a world-specific set of items that some GMs running that world would very much want.. while others may not. So separating by source would help them to make those decisions.
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