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I'd hate to have a note taking PWA which data's get wiped every 7 days.

Solutions to this is to sync the data with a server, which then requires an account and user management, privacy considerations, keeping the server alive, backing up data, GDPR fun etc...

Any simple applications becomes a maintenance nightmare very quick.

They'd only be available with an explicit opt-in, so I don't see how. They'd probably only be available for webapps added to the homescreen too, so websites wouldn't even be able to spam the permissions request.

Positives like not having "save" ability on documents? Or not having push notifications so messaging applications, calendars and such is not possible? Both of these can be abused of course, but not having them forces many categories of apps to be native.

Users don't want notifications from random websites they browse to, but they need them for pwas they install to their home screen which are supposed to have parity with apps