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yeah, by now i have GOG editions installed in 3 (!) different folders, all by default. annoying, but i can live with it.
Interesting. I never realised there was this problem. From day one I just installed to my Games directory on a different partition no referencing gog.com or any other gog combination. I'm not discriminative on my games they all just get treated as games where ever I got them from :)
Just put all games in \Games\. Publisher-specific folder are an abomination.