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I'm updating my system through sudo dnf update command, but sometimes there is a notification that there are new updates available but I can see them only in software center neither sudo dnf update --refresh won't show any new updates. So I was just wondering what is the difference between that and what should I prefer?

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They both use the same back end dependency solver and pull from the same repositories, but due to different projects moving a different speeds, they don't pull from a unified local cache (including the metadata cache — the information about what updates are available and so on). And, because Fedora distributes content on a large volunteer mirror network, sometimes that's not all in sync — that's probably why dnf --refresh isn't doing any good.

The longer-term plan is for this to converge, avoiding the duplication.

As for which to prefer, the main difference is whether the updates are done online or offline — and offline requires a reboot. That's obviously usually less convenient, but it ensures that all security patches are actually in effect, and avoids glitches like Flash plugin up to date but Firefox keeps telling me that I have the old version (and potentially more serious problems with the system on disk being out of sync with what's running).

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