Strange, installing Flatpaks seems to work fine in 0.11.3-3 now (with
gnome-software 3.28.1-0ubuntu4.18.04.1 (the new version is a patch for
snaps from bionic-proposed, nothing to do with Flatpak I don't think)).
Glad that an Ubuntu dev is on it with keeping Flatpak up to date! :D

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https://bugs.launchpad.net/bugs/1716409

Title:
  Unable to install flatpakref on Ubuntu artful

Status in gnome-software package in Ubuntu:
  Fix Released
Status in gnome-software source package in Artful:
  Triaged

Bug description:
  I saw a news article with a link to install a flatpak.

  http://www.omgubuntu.co.uk/2017/09/download-pithos-pandora-app-1-4

  I clicked the link expecting to be able to install the flatpak, but
  the experience appears broken. I'm on an up to date Artful install

  What I did was:-

  Click on http://www.omgubuntu.co.uk/2017/09/download-pithos-pandora-app-1-4
  Click the flathub link:- 
https://flathub.org/repo/appstream/io.github.Pithos.flatpakref
  This downloaded the flatpakref file.
  I clicked the file in my browser, nothing happened

  I then tried finding the file in nautilus and double clicked it.
  GNOME Software launched and presented an error "Don't know how to handle 
'file:///home/alan/Downloads/io.github.Pithos.flatpakref' (see screenshot).

  If I search for pithos in GNOME Software I am able to find the older
  version from the deb repo, but not the newer version from flathub.

  Do we not support flatpak/flathub out of the box? Or is my system
  uniquely hosed?

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