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But do real apps actually use them directly? Or only through the userland libraries?

Just FYI, the https://www.darlinghq.org project is doing MacOS app compat on Linux - i.e. building the userland libraries.

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Yes, real apps use Mach messaging directly. i.e.: https://source.chromium.org/chromium/chromium/src/+/main:ipc...
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Chrome is an outlier to how most apps will do things.
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The illustration that Chrome uses Mach ports is a counterexample to an (implied) insinuation that nothing in running in macOS user space uses Mach ports. Outlier or not, the fact there is at least one (albeit also very useful and very popular) application that uses them ties back to the conversation about how they're a kernel feature worth having for Mac compatibility.
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