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So there's this thing called systemd-sysext. It allows you to put "overlays" on your filesystem that cause additional files to appear alongside the regular ones, intermeshed with the regular file hierarchy. I was super happy when I learned about this! That is a neat and useful feature!

What I did not know is the moment you engage it, any "meshed" top-level directories are set readonly. So the sysext I installed put files in /usr/bin. This made /usr readonly. I did not notice this for two weeks.