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Speaking from personal experience, the patching process was done fairly quickly and no issues arose after testing the game on Project64 2.3.2 which is the latest public release for Windows to date.
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While Zelda: Master of Time’s release post is a bit scant on how to actually get the romhack up and running, a Reddit thread about it managed to clear up the questions that various people had.
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Once you manage to get your hands on Zelda: OOT 1.0, the patching process is pretty straightforward!
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