But uh... fuck. This fucking sucks, Yuzu is basically dead now, they have to disband and take down their code.
If Yuzu lives it will only be pirate copies floating around, further development will... basically have to go underground more like game crackers, as this very settlement establishes that Nintendo will sue you into oblivion if you publicly work on this.
It has apparently been rehosted as 'Nuzu' on github... but I wouldn't be surprised if that or any similar instance just gets taken down once it gets reasonably popular.
MSFT sure as shit doesnt want to get sued by Nintendo.
Nowhere? They will be bankrupt and shutdown the LLC. Whatever their LLC accounts has will go to Nintendo, and any other asset the same. But I doubt they had pretty much anything, maybe the latest Patreon payment and maybe some extra money to pay websites and maybe any office or similar if they rented anything.