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For example, I installed the Flatpak for Audacity which currently ships version 2.1.3. How can I receive an update notification once version 2.2.0 is out?

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GNOME Software will notify you of available Flatpak and DPKG updates if you install the Flatpak backend (apt install gnome-software-plugin-flatpak). This is installed by default in most Linux distributions with GNOME Software; except Ubuntu since they want to promote Snap instead (gnome-software-plugin-snap).

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    As a remark, the gnome-software-plugin-* packages are available starting from Artful (Ubuntu 17.10). They're not available for the as-of-now latest LTS, Xenial (Ubuntu 16.04), or other versions before Artful. Apr 9, 2018 at 10:42

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