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It's a pretty minor issue, but I'm curious about why it is happening.

In GNOME Software, and in Notifications in GNOME Settings, some system applications appear twice. They don't appear twice in the application list.

For example, Archive Manager and Files are duplicated in Notifications in GNOME Settings. enter image description here

Where does GNOME get its application lists from here? Synaptic reports that only one package matching file-roller is installed.

Also, gnome-calendar is only installed once in Apt, but is duplicated in Software.

enter image description here

Can this be fixed?

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[...] duplicate entries come from multiple .desktop files in /usr/share/applications/

Issue is tracked here https://bugs.launchpad.net/ubuntu/+source/gnome-control-center/+bug/1562409 , it has more detailed information and possible workarounds (e.g. deleting duplicate .desktop files). Just be sure to read all comments thoroughly before deleting anything.

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