Well here's a simple solution -- turn the notification off by default. That way people who don't want to upgrade don't feel like they're obliged to do so just because a new version came out. Those that do can go and turn on the update notifications.
Maybe add the ability to put a priority on releases. That is, if there's a major bug like a data loss issue, the fix for it should override anybody who turned off/left off update notifications and show them the update. For the rest of us who live on the edge, we want all update notifications without having to wait a week or two (contrary to popular belief, most of us don't check the calibre homepage daily looking for a new version).
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