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Yuzu will lives under new name
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Why throw away the commit history?
One of the problems with Yuzu (to nintendo) was that it contained the encryption keys pulled off nintendo switches. By removing commit history you actually can permanently remove this part of the code. There might be a more clever way to do this. Thats my best guess.
I downloaded and set up Yuza the day before all this went down, and it did not include encryption keys. And trust me, I looked.