Polypane stores all of its settings in the Application folder. This includes settings, cache, logs and more. Settings are stored as plain text json files and can be edited manually if needed, though they are only read on startup.
The folder location depends on your operating system:
If you delete files in this folder you will lose your settings, so beware. If you want to reset Polypane to its default settings, Go to the "help" menu and select "Delete settings and restart".
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