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You could permissionwall that stuff, just like iOS asks for permissions to ask your location. If a random website wants to mess with Local Storage I know that I need to turn around.

... however i'm afraid that 99% of all users (the non-techies) would just be annoyed by the popup and click "OK"

Yes, that would have been a much better approach. It would hinder trackers, but not valid uses of localStorage.

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