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I have upgraded Fedora 23 to 24 through DNF (system-upgrade plugin), and now many packages installed by the primary repository are shown as installed from the command line, and DNF applies the label @@commandline instead of @fedora. If a package is updated, DNF apply the correct label @updates. Here an example: gnome-online-accounts.x86_64 3.20.3-1.fc24 @updates gnome-online-miners.x86_64 3.20.0-1.fc24 @fedora gnome-packagekit.x86_64 3.20.0-1.fc24 @@commandline gnome-packagekit-installer.x86_64 3.20.0-1.fc24 @@commandline gnome-packagekit-updater.x86_64 3.20.0-1.fc24 @fedora gnome-photos.x86_64 3.20.3-1.fc24 @updates gnome-power-manager.x86_64 3.20.0-1.fc24 @@commandline gnome-python2.x86_64 2.28.1-17.fc24 @@commandline gnome-python2-gconf.x86_64 2.28.1-17.fc24 @@commandline gnome-screenshot.x86_64 3.20.1-2.fc24 @updates gnome-session.x86_64 3.20.2-1.fc24 @updates gnome-session-wayland-session.x86_64 3.20.2-1.fc24 @updates gnome-session-xsession.x86_64 3.20.2-1.fc24 @updates gnome-settings-daemon.x86_64 3.20.1-3.fc24 @@commandline gnome-shell.x86_64 3.20.4-1.fc24 @updates gnome-shell-extension-common.noarch 3.20.1-1.fc24 @@commandline gnome-shell-extension-user-theme.noarch 3.20.1-1.fc24 @@commandline gnome-shell-extension-weather.noarch 0-0.14.git7587e23.fc22 @rpmfusion-free gnome-software.x86_64 3.20.4-1.fc24 @updates gnome-sound-recorder.noarch 3.20.2-1.fc24 @@commandline gnome-system-monitor.x86_64 3.20.1-1.fc24 @@commandline gnome-terminal.x86_64 3.20.2-2.fc24 @@commandline gnome-terminal-nautilus.x86_64 3.20.2-2.fc24 @@commandline gnome-themes-standard.x86_64 3.20.2-1.fc24 @@commandline gnome-todo.x86_64 3.20.2-1.fc24 @@commandline gnome-tweak-tool.noarch 3.20.1-1.fc24 @@commandline gnome-user-docs.noarch 3.20.2-1.fc24 @@commandline gnome-user-share.x86_64 3.18.1-1.fc24 @@commandline
I don't think we can do much about it.
Well, does the dnf API allow this to be set? If there's a call that system-upgrade can do to overwrite the provenience of packages it installs, the problem would be solved.
I forgot to write that i have the same bug on 2 pc, a desktop and a ultrabook, after upgrading from Fedora 23 to 24, and i think i'm not the only one to have this problem: https://ask.fedoraproject.org/en/question/85717/what-does-commandline-mean-dnf-list-installed/
*** This bug has been marked as a duplicate of bug 1324151 ***