Public bug reported:

Software seems to be out-of-sync with command-line package changes like
"apt install, apt remove, apt upgrade, etc.)

What happens:
1. From a terminal, install an app. Let's use bijiben (GNOME Notes).
sudo apt install bijiben

2. After installation completes, open the Software app.

3. Search for bijiben.

4. The Notes app shows up with an Install button.

What should happen:
4. The Notes app shows up with a Remove button.

Although I'm reporting this bug from Ubuntu GNOME Yakkety, I confirm
that this bug also happens on a clean Ubuntu 16.04 LTS install.

Similarly, I'm getting prompts to install system updates that I've
installed hours before from the command line. (I can file a separate bug
for that although it feels like it might be the same issue.)

ProblemType: Bug
DistroRelease: Ubuntu 16.10
Package: gnome-software 3.20.1+git20160426.1.a976144-ubuntu-xenial-0ubuntu1
ProcVersionSignature: Ubuntu 4.4.0-22.39-generic 4.4.8
Uname: Linux 4.4.0-22-generic x86_64
ApportVersion: 2.20.1-0ubuntu4
Architecture: amd64
CurrentDesktop: GNOME
Date: Tue May 17 21:28:45 2016
EcryptfsInUse: Yes
InstallationDate: Installed on 2016-04-09 (38 days ago)
InstallationMedia: Ubuntu-GNOME 16.04 LTS "Xenial Xerus" - Beta amd64 (20160408)
SourcePackage: gnome-software
UpgradeStatus: No upgrade log present (probably fresh install)

** Affects: gnome-software (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-bug gnome3-ppa third-party-packages xenial yakkety

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https://bugs.launchpad.net/bugs/1582959

Title:
  Software app seems to be unaware of package changes from apt-get

Status in gnome-software package in Ubuntu:
  New

Bug description:
  Software seems to be out-of-sync with command-line package changes
  like "apt install, apt remove, apt upgrade, etc.)

  What happens:
  1. From a terminal, install an app. Let's use bijiben (GNOME Notes).
  sudo apt install bijiben

  2. After installation completes, open the Software app.

  3. Search for bijiben.

  4. The Notes app shows up with an Install button.

  What should happen:
  4. The Notes app shows up with a Remove button.

  Although I'm reporting this bug from Ubuntu GNOME Yakkety, I confirm
  that this bug also happens on a clean Ubuntu 16.04 LTS install.

  Similarly, I'm getting prompts to install system updates that I've
  installed hours before from the command line. (I can file a separate
  bug for that although it feels like it might be the same issue.)

  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: gnome-software 3.20.1+git20160426.1.a976144-ubuntu-xenial-0ubuntu1
  ProcVersionSignature: Ubuntu 4.4.0-22.39-generic 4.4.8
  Uname: Linux 4.4.0-22-generic x86_64
  ApportVersion: 2.20.1-0ubuntu4
  Architecture: amd64
  CurrentDesktop: GNOME
  Date: Tue May 17 21:28:45 2016
  EcryptfsInUse: Yes
  InstallationDate: Installed on 2016-04-09 (38 days ago)
  InstallationMedia: Ubuntu-GNOME 16.04 LTS "Xenial Xerus" - Beta amd64 
(20160408)
  SourcePackage: gnome-software
  UpgradeStatus: No upgrade log present (probably fresh install)

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