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Currently only settings of plugins are saved which have been specified for the setting using storage: SettingStorage.File. As these are stored in the json and not in the DB. For all others there is currently no API from Joplin.
Ok, but unfortunately this is not a real solution. Because you need to know all the settings. Furthermore, there is no easy way to import back into Joplin.
Backup plugin settings
https://discourse.joplinapp.org/t/export-import-settings/14668
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