This is a discussion topic for the following Common Issue:
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Does this (and the general experience) depend on how you upgrade? In particular, since dnf4 and dnf5 share only part of their information, does it make a difference which dnf is used to do an in-place upgrade to F41 (beta)? This may or may not affect which packages autoremove and the like (dnf5 after the upgrade) consider user-installed.
That’s a good question and I don’t know the answer (and I haven’t tested it). I’d expect that dnf4 and gnome-software/discover should yield the same result. Not sure about dnf5 (F40->F41). Perhaps @egoode can answer that.
The issue here is that dnf5-plugins is not automatically installed when dnf5 is installed.
I am in the process of releasing DNF 5.2.6.1 which has a conditional Recommends of dnf5-plugins if dnf-plugins-core is already installed. We’ll be able to get DNF 5.2.6.1 into F41 so that the F40 → F41 upgrade will automatically install the DNF 5 plugins if the user had already installed dnf-plugins-core (which would theoretically be all users, since the system-upgrade command needed to upgrade to F41 is a DNF 4 plugin). So this issue should be resolved before F41 is generally available.
does it make a difference which dnf is used to do an in-place upgrade to F41 (beta)?
It shouldn’t make a difference for this particular issue, but generally speaking, I recommend using DNF 4 to upgrade to F41. The version of DNF 5 in F40 repos is rather old and has a bug that prevents DNF 4 → DNF 5 history import from working correctly. Plus, the vast majority of users will be using DNF 4 to upgrade; the recommended upgrade path will be the same for F41 as in previous versions.