It doesn't. Ninety-nine point five nines of software is architecture-independent, and if you're an App Store sharecropper you'll never notice. It's the users with paid-for x86 binaries who will be screwed, like they were when Apple removed the ability to run PowerPC binaries in OS X 10.7.
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They mentioned running Linux in a VM at least twice in the keynote. I'm not sure why, unless it's an acknowledgement that OS X is no longer a usable development environment.
Linux, like any OS written in the past 30 years, is substantially architecture-independent. My day job involves coding for several devices with Linux kernels on ARM (32bit) and Aarch64 and I have no idea which is which, nor any need to.
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(‘ARM’ has become meaningless marketing drivel; there are physically existing pairs of 32-bit ‘ARM’ processors that have exactly zero physically existing machine instructions in common.)
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[Dis]claimer: I have no long or short in AAPL. Anyone posting or voting in this thread should similarly disclose.