Repeated warnings about $USER being unset about yabai HOT 4 CLOSED

That is likely an error when trying to send a message, not from the running instance of yabai. See https://github.com/koekeishiya/yabai/blob/master/src/yabai.c#L53

Edit: Just re-read your post. Probably not related to what I said as you were running through brew services.

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For what it's worth, the message being printed is still prefixed with yabai: and not yabai-msg:. It also happens without any user interaction (no keypresses, no mouse movement, no applications open other than iTerm2 with tail -f /path/to/log), so I'm really unsure what's happening here.

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The message you get is only printed during startup of the actual persistent instance, so it would appear that something on your system tries to launch an instance of yabai at least.

_{Sent with GitHawk}

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The issue still occured after I ran brew services stop yabai, so you were definitely right about something on my system trying to launch yabai.

I think brew services or launchd went wrong somewhere and duplicated the launch services entry (or at least loaded it in a faulty state, which persisted reboots). Running sudo launchctl remove homebrew.mxcl.yabai fixed the issue for me.

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