A GOG download only places the files, so games that look up their own registry keys (Fallout: New Vegas reads HKLM\Software\Bethesda Softworks\FalloutNV "Installed Path") said they were not installed. Every GOG launch now reads the setRegistry actions of the game's goggame-<id>.script and imports them into the prefix's 32-bit view through Proton's reg.exe, once per change of the script, so games already downloaded are fixed on their next launch.
MaxsTechReview
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