So I have no idea what the problem is, but I can't save the game at all. I select a save file and the saving icon pops up, but the files all remain empty.
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Gald it's working ! Your second folder probably don't have sufficiant permission to read and/or write systems files. If a game need a specific DLL from windows to launch, it won't launch. The Pacifier Project is compiled as a standalone, thus is can launch from anywhere (in theory) but need access to write save files.