With Muon, Sebastien actually meant Discover, which has the same
problems like GNOME Software.

GUI applications should still be visible, and the fact that some are not shown 
is a bug in the metadata generator or (more likely) the packaging or upstream 
software.
Not all of these issues were addressed before the release, due to not enough 
manpower and probably not enough people caring about it.
See http://mhall119.com/2016/03/help-make-gnome-software-beautiful/ for how to 
report issues and fix things properly.
This should be sorted out for Yakkety, and some issues can also be fixed by 
stable-release-updates, e.g. the Krita thing would be a pretty good candidate, 
since it is highly likely a packaging bug.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-software in Ubuntu.
https://bugs.launchpad.net/bugs/1579415

Title:
  Ubuntu Software Center does not display third party apps or all
  installed apps

Status in gnome-software package in Ubuntu:
  Opinion

Bug description:
  Description:  Ubuntu 16.04 LTS
  Release:      16.04

  gnome-software:
    Installed: 3.20.1+git20160426.1.a976144-ubuntu-xenial-0ubuntu1
    Candidate: 3.20.1+git20160426.1.a976144-ubuntu-xenial-0ubuntu1
    Version table:
   *** 3.20.1+git20160426.1.a976144-ubuntu-xenial-0ubuntu1 500
          500 http://gb.archive.ubuntu.com/ubuntu xenial-updates/main amd64 
Packages
          100 /var/lib/dpkg/status
       3.20.1+git20160420.1.ca63436.ubuntu-xenial-0ubuntu2 500
          500 http://gb.archive.ubuntu.com/ubuntu xenial/main amd64 Packages

  The new Ubuntu Software Center does not display all software. For
  example no third party repo applications are displayed.

  Search for example:

  Ubuntu-restricted-extras - no results
  muon - no results
  krita - no results
  samba - no results

  These do not show under installed either, though they are installed.

  However, all are shown in Synaptic Package Manager and MUON

  Additional:

  I have installed the old Ubuntu Software Center and can confirm that
  ALL applications are correctly listed.

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