Cassie

One more candidate for "something else has the extensions", since it is invisible and increasingly common: Memory Integrity, under Core Isolation in Windows Security.

It uses virtualisation-based security, which means the hypervisor is running whether you asked for it or not. On a machine where somebody disabled Hyper-V to make VirtualBox work and it still failed, this is usually why.

Worth knowing before disabling it: it is a genuine security feature and turning it off to speed up a VM is a real trade, not a free win. Check whether VirtualBox on top of the hypervisor is fast enough first.

There is no application to look for because it is a system component, but it does leave something on disk. The check most people use:

/usr/bin/pgrep -q oahd && echo "installed" || echo "not installed"

oahd is the translation daemon, and it runs when Rosetta is present. The other common check is whether /Library/Apple/usr/share/rosetta exists.

To install it deliberately rather than through a prompt:

softwareupdate --install-rosetta --agree-to-license

Worth knowing that the click-through prompt and that command install exactly the same thing, so if you clicked the prompt, you have it. There is no partial state to worry about, which is the reassuring answer to what state your machine is in.

The Command Line Tools are a separate package with its own version, tied to the SDK it shipped with. A macOS update does not update them, because they are not part of the OS — they sit alongside it. So after a major update you have new system headers and an old toolchain that was built against the previous ones, and Homebrew, which compiles things, is the first thing to notice.

It keeps coming back because that is the shape of the problem, not a bug you can fix once.

The reliable repair is a clean reinstall rather than an update:

sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select --install

Removing first matters. Running the install over the top of a mismatched copy frequently reports success and leaves the old headers in place, which is why the fix sometimes appears not to work.

After that:

xcode-select -p
brew doctor