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Problem is, Yuzu team were breaking other laws. They were tweaking their codebase based on leaks.
Do you know how much of society depends on GPL code? Every Android phone, every Chromebook, most servers and many billion dollar companies rely on GPL code. Nintendo attempting to un-GPL Yuzu will wake some sleeping giants, who will realise other people might attempt to do the same to the projects they rely upon. As a result the defence fund for anyone Nintendo goes after like this will end up VERY well funded. As in, make-Disney-shit-their-pants well-funded.
As for your point on Gary Bowser, you’re kinda leaving out that Nintendo had a MUCH stronger case against him. Unlike emulators, the development of piracy modchips is very much illegal.
What are the names of these “sleeping giants” you mention, out of pure curiosity?
Linux Foundation - Linux is GPL and would be massively, negatively affected by an ability to suddenly un-GPL code
Google - their consumer OSes (Android and ChromeOS) use Linux as their base, not to mention their servers are almost entirely Linux.
IBM/Red Hat - RedHat is a billion dollar company specialising in providing Linux OSes.
Microsoft - surprising I know, but a lot of their internal and cloud stuff uses GPL code, including Linux.
Oracle - they ship a lot of GPL code, including a Linux distro.
EFF - The ability to un-GPL code would have catastrophic consequences on the internet, and this will be an issue they will weigh in on.
Apple - their servers don’t run on macOS.
And just about any company you can think of with a Linux server.
I mention Linux a lot, but that is because it can’t be understated how important it is in our global infrastructure. Linux is as much GPL as Yuzu, so if code can be retroactively un-GPL’ed from Yuzu, it can be done with one of the most important software projects in the world.