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~/. for Darwin, ~/Library/Application Support for macOS. That simple.

That sounds like a good distinction.

What are CLI tools that work under macOS but not under Darwin? Shortcuts like `code` or `pycharm` that open graphical apps? CLI tools that come bundled with macOS? Yeah these could use the latter.

Possibly anything that makes use of Cocoa (this need not imply that it's a GUI tool) or other system frameworks like IOKit, CoreBluetooth, or CoreAudio.

Darwin by itself also need not come with CoreFoundation & GCD (although I believe since these are open-sourced the only darwin distribution, PureDarwin does include it).

CLI shortcuts are bridges from Darwin to macOS. I agree, ~/Library/Application Support.

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