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Might just be user error, but it seems that on close, sites for which I've enabled desktop notifications (like slack or gmail) forget that they're allowed to make desktop notifications: when I open back up and reopen those sites, they ask for notification permissions again.
There are various permission settings that take the values "true/false/ask". By default they are "ask". All of them support url patterns now so if you want to keep it at the default for all sites except a few which you want to allow or deny automatically you can do something like
The options that support an "ask" value are: