According to an official statement on Ryujinx's Discord server, developer gdkchan was contacted by Nintendo and they were offered an agreement to stop working on the emulator project, and while the agreement wasn't confirmed yet, the organization has been entirely removed.
Closed source "I swear this executable that will let you play all the games you want is legit" hosted on sourceforge or random websites that get hugged to death every day that ends in a y?
Also: it isn't like that would stop this kind of legal action. MS/Github are barely a factor. It is the devs themselves getting the "hey, stop it or we'll turn you into indentured servants" letters.