Applications not visible in Launcher

[serpro69]

(1) Issue/Bug Description:

After running dist-upgrade today, I've noticed that some apps have disappeared from the launcher (I can still see them in the applications menu Super +A

For example, I have obsidian installed via flatpak, and I also have 2 custom obsidian .desktop files that launch the application with extra arguments:

Since the upgrade, I can only see the last one in the launcher, whereas before all 3 would show up:

If I remove desktop file for the one that shows up, the other one appears in the launcher.

In addition to above, i have another app installed with flatpak, vlc, and no additional desktop files for it that I could find. It also does not show up in the launcher, but shows up in apps menu.
I have several apps installed via flatpak that also show up just fine, so this behavior seems a bit "random"

(2) Steps to reproduce (if you know):

(3) Expected behavior:

All apps should be visible in the launcher

(4) Distribution (run cat /etc/os-release):

NAME="Pop!_OS"
VERSION="22.04 LTS"
ID=pop
ID_LIKE="ubuntu debian"
PRETTY_NAME="Pop!_OS 22.04 LTS"
VERSION_ID="22.04"
HOME_URL="https://pop.system76.com"
SUPPORT_URL="https://support.system76.com"
BUG_REPORT_URL="https://github.com/pop-os/pop/issues"
PRIVACY_POLICY_URL="https://system76.com/privacy"
VERSION_CODENAME=jammy
UBUNTU_CODENAME=jammy
LOGO=distributor-logo-pop-os

(5) Gnome Shell version:

GNOME Shell 42.9

(6) Pop Shell version (run apt policy pop-shell or provide the latest commit if building locally):

pop-shell:
  Installed: 1.1.0~1702661180~22.04~8e176f1
  Candidate: 1.1.0~1702661180~22.04~8e176f1
  Version table:
 *** 1.1.0~1702661180~22.04~8e176f1 1001
       1001 http://apt.pop-os.org/release jammy/main amd64 Packages
       1001 http://apt.pop-os.org/release jammy/main i386 Packages
        100 /var/lib/dpkg/status

(7) Where was Pop Shell installed from:

(8) Monitor Setup (2 x 1080p, 4K, Primary(Horizontal), Secondary(Vertical), etc):

(9) Other Installed/Enabled Extensions:

(10) Other Notes:

Apt log entry:

Start-Date: 2024-10-18  08:09:28
Commandline: apt dist-upgrade
Requested-By: sergio (1000)
Upgrade: openvpn:amd64 (2.5.9-0ubuntu0.22.04.3, 2.5.11-0ubuntu0.22.04.1), cups-filters:amd64 (1.28.15-0ubuntu1pop1~1675905868~22.04~a59ec7b, 1.28.15-0ubuntu1.4), udev:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), libgsf-1-114:amd64 (1.14.47-1build2, 1.14.47-1ubuntu0.1), pop-launcher:amd64 (1.2.3~1723669139~22.04~6a1b8b9, 1.2.3~1727746060~22.04~476a8fb), libnss-myhostname:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), gjs:amd64 (1.72.4-0ubuntu0.22.04.3~really.is.1.72.2.0ubuntu2, 1.72.4-0ubuntu0.22.04.4), appstream-data-pop-icons:amd64 (0.0.3~1713548381~22.04~1074a51, 0.0.3~1727715771~22.04~23d51d3), gnome-control-center-faces:amd64 (1:41.4-1ubuntu12pop1~1701107237~22.04~eba04d3, 1:41.7-0ubuntu0.22.04.9pop0~1727959659~22.04~a1bcd6c), systemd-timesyncd:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), libgjs0g:amd64 (1.72.4-0ubuntu0.22.04.3~really.is.1.72.2.0ubuntu2, 1.72.4-0ubuntu0.22.04.4), xserver-xorg-video-amdgpu:amd64 (22.0.0-1ubuntu0.1pop1~1677198820~22.04~2e82f80, 22.0.0-1ubuntu0.2), libpam-systemd:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), appstream-data-pop:amd64 (0.0.3~1713548381~22.04~1074a51, 0.0.3~1727715771~22.04~23d51d3), libarchive13:amd64 (3.6.0-1ubuntu1.1, 3.6.0-1ubuntu1.2), gnome-shell-extension-system76-power:amd64 (2.0.6~1722536864~22.04~0b4304d, 2.0.7~1729110155~22.04~32de891), libgdm1:amd64 (42.0-1ubuntu7pop1~1675905960~22.04~7fd0bb0, 42.0-1ubuntu7.22.04.4pop0~1727959198~22.04~6fe7e40), bluez-cups:amd64 (5.64-0ubuntu1pop1~1674313994~22.04~579884f, 5.64-0ubuntu1.3), ubuntu-drivers-common:amd64 (1:0.9.6.1pop0~1652303087~22.04~1aab0f9, 1:0.9.6.2~0.22.04.7pop0~1727961281~22.04~a952724), libmutter-10-0:amd64 (42.9-0ubuntu4pop0~1694017775~22.04~f186280, 42.9-0ubuntu9pop0~1727960749~22.04~a024e16), bluez-obexd:amd64 (5.64-0ubuntu1pop1~1674313994~22.04~579884f, 5.64-0ubuntu1.3), element-desktop:amd64 (1.11.79, 1.11.81), libsystemd0:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), libfontembed1:amd64 (1.28.15-0ubuntu1pop1~1675905868~22.04~a59ec7b, 1.28.15-0ubuntu1.4), libnss-systemd:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), mutter-common:amd64 (42.9-0ubuntu4pop0~1694017775~22.04~f186280, 42.9-0ubuntu9pop0~1727960749~22.04~a024e16), fwupd-unsigned:amd64 (1:1.1-4pop0~1643174914~22.04~f30da97, 1:1.4-1pop0~1728056142~22.04~abf83a6), gnome-shell:amd64 (42.9-0ubuntu2.1pop0~1715266817~22.04~2c675c6, 42.9-0ubuntu2.2pop0~1727960056~22.04~84a3bea), systemd:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), libudev1:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), cups-filters-core-drivers:amd64 (1.28.15-0ubuntu1pop1~1675905868~22.04~a59ec7b, 1.28.15-0ubuntu1.4), firefox:amd64 (1:130.0.1~1726606343~22.04~44c3a30, 1:131.0.3~1728926590~22.04~7d07882), gdm3:amd64 (42.0-1ubuntu7pop1~1675905960~22.04~7fd0bb0, 42.0-1ubuntu7.22.04.4pop0~1727959198~22.04~6fe7e40), gir1.2-accountsservice-1.0:amd64 (22.07.5-2ubuntu1.3pop1~1675994188~22.04~45e75a8, 22.07.5-2ubuntu1.5pop0~1727958756~22.04~31bc419), fwupd-signed:amd64 (1:1.1-4pop0~1643174914~22.04~f30da97, 1:1.4-1pop0~1728056142~22.04~abf83a6), gir1.2-mutter-10:amd64 (42.9-0ubuntu4pop0~1694017775~22.04~f186280, 42.9-0ubuntu9pop0~1727960749~22.04~a024e16), update-manager-core:amd64 (1.0.0~1717459832~22.04~c3d9c72, 1.0.0~1729010520~22.04~6ecadbb), cups-browsed:amd64 (1.28.15-0ubuntu1pop1~1675905868~22.04~a59ec7b, 1.28.15-0ubuntu1.4), gnome-shell-common:amd64 (42.9-0ubuntu2.1pop0~1715266817~22.04~2c675c6, 42.9-0ubuntu2.2pop0~1727960056~22.04~84a3bea), gnome-control-center-data:amd64 (1:41.4-1ubuntu12pop1~1701107237~22.04~eba04d3, 1:41.7-0ubuntu0.22.04.9pop0~1727959659~22.04~a1bcd6c), gir1.2-gdm-1.0:amd64 (42.0-1ubuntu7pop1~1675905960~22.04~7fd0bb0, 42.0-1ubuntu7.22.04.4pop0~1727959198~22.04~6fe7e40), libbluetooth3:amd64 (5.64-0ubuntu1pop1~1674313994~22.04~579884f, 5.64-0ubuntu1.3), pop-icon-theme:amd64 (3.5.0~1687556040~22.04~3126c6a, 3.5.1~1727801177~22.04~1a575a8), nano:amd64 (6.2-1, 6.2-1ubuntu0.1), brave-browser:amd64 (1.70.123, 1.71.114), accountsservice:amd64 (22.07.5-2ubuntu1.3pop1~1675994188~22.04~45e75a8, 22.07.5-2ubuntu1.5pop0~1727958756~22.04~31bc419), gnome-control-center:amd64 (1:41.4-1ubuntu12pop1~1701107237~22.04~eba04d3, 1:41.7-0ubuntu0.22.04.9pop0~1727959659~22.04~a1bcd6c), systemd-sysv:amd64 (249.11-0ubuntu3.11pop0~1704473387~22.04~3ce38bf, 249.11-0ubuntu3.12pop0~1727961019~22.04~2b3beb7), bluez:amd64 (5.64-0ubuntu1pop1~1674313994~22.04~579884f, 5.64-0ubuntu1.3), ubuntu-release-upgrader-core:amd64 (1.0.0~1717459832~22.04~c3d9c72, 1.0.0~1729010520~22.04~6ecadbb), gnome-shell-extension-prefs:amd64 (42.9-0ubuntu2.1pop0~1715266817~22.04~2c675c6, 42.9-0ubuntu2.2pop0~1727960056~22.04~84a3bea), libaccountsservice0:amd64 (22.07.5-2ubuntu1.3pop1~1675994188~22.04~45e75a8, 22.07.5-2ubuntu1.5pop0~1727958756~22.04~31bc419), system76-dkms:amd64 (1.0.15~1723747371~22.04~341bcde, 1.0.16~1728590246~22.04~5c774d6), libcupsfilters1:amd64 (1.28.15-0ubuntu1pop1~1675905868~22.04~a59ec7b, 1.28.15-0ubuntu1.4), libgsf-1-common:amd64 (1.14.47-1build2, 1.14.47-1ubuntu0.1)
End-Date: 2024-10-18  08:10:53