I figured out how to turn the auto connect for main and in/outs, but how do I stop it from auto connecting auditioner and clicktrack?
You can't. Neither of these can be controlled from the Ardour GUI. They can disconnected using qjackctl or some other jack control/connection application. We consider it important that they are always connected in a new session. Once you save the session, it will retain your new connections (or disconnected state).
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