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Unfortunately you didn't miss anything, there's currently no way to switch it. You could try to rename or move your current directory and then it should ask you again. However, it's possible that it actually tolerates moves, in that case you'd have to make a .zip file and delete it.
You could also delete the app's sandbox container directory, which would wipe the preferences. For that, delete ~/Library/Containers/ch.entropy.ipython-notebook.
I'll keep this issue open to track adding such a feature in the future.
I've probably missed something obvious but how do you change the default document folder once it has been set during first run?
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