Flatpaks are duplicated after rebasing from Bluefin to Bazzite

Hi, I’m new here.

I had Bluefin installed and then made a switch to Bazzite with the officially provided command.

rpm-ostree rebase ostree-unverified-registry:ghcr.io/ublue-os/bazzite-gnome:stable

When I made the switch I had some flatpak apps installed manually in Bluefin.

At the first boot, in Bazzite’s Welcome window, I selected some of the apps that had been already installed, assuming it would be smart enough to skip already installed apps. But apparently, it has added duplicated entries. This is the output when I list all the flatpaks I have installed.

Could someone guide me on how to correct this?

Name                                                Application ID                                                    Version                        Branch                   Installation
Bitwarden                                           com.bitwarden.desktop                                             2024.5.0                       stable                   user
Brave Browser                                       com.brave.Browser                                                 1.66.118                       stable                   user
Discord                                             com.discordapp.Discord                                            0.0.54                         stable                   user
Flatseal                                            com.github.tchx84.Flatseal                                        2.2.0                          stable                   system
Google Chrome                                       com.google.Chrome                                                 125.0.6422.141-1               stable                   user
Extension Manager                                   com.mattjakeman.ExtensionManager                                  0.5.1                          stable                   system
Microsoft Edge                                      com.microsoft.Edge                                                125.0.2535.67-1                stable                   system
Microsoft Edge                                      com.microsoft.Edge                                                125.0.2535.67-1                stable                   user
OBS Studio                                          com.obsproject.Studio                                             30.1.2                         stable                   system
OBS Studio                                          com.obsproject.Studio                                             30.1.2                         stable                   user
Celluloid                                           io.github.celluloid_player.Celluloid                              0.26                           stable                   system
BoxBuddy                                            io.github.dvlv.boxbuddyrs                                         2.2.4                          stable                   system
Warehouse                                           io.github.flattool.Warehouse                                      1.6.2                          stable                   system
CPU-X                                               io.github.thetumultuousunicornofdarkness.cpu-x                    5.0.4                          stable                   system
Mission Center                                      io.missioncenter.MissionCenter                                    0.4.5                          stable                   system
mpv                                                 io.mpv.Mpv                                                        v0.38.0                        stable                   system
PCSX2                                               net.pcsx2.PCSX2                                                   v1.7.5861                      stable                   user
RPCS3                                               net.rpcs3.RPCS3                                                   0.0.32-1-e5ce88f0              stable                   user
Fedora Media Writer                                 org.fedoraproject.MediaWriter                                     5.1.1                          stable                   system
Freedesktop Platform                                org.freedesktop.Platform                                          22.08.24                       22.08                    user
Freedesktop Platform                                org.freedesktop.Platform                                          23.08.19                       23.08                    system
Mesa                                                org.freedesktop.Platform.GL.default                               24.0.4                         22.08                    user
Mesa (Extra)                                        org.freedesktop.Platform.GL.default                               24.0.4                         22.08-extra              user
Mesa                                                org.freedesktop.Platform.GL.default                               24.0.7                         23.08                    system
Mesa                                                org.freedesktop.Platform.GL.default                               24.0.7                         23.08                    user
Mesa (Extra)                                        org.freedesktop.Platform.GL.default                               24.0.7                         23.08-extra              system
Mesa (Extra)                                        org.freedesktop.Platform.GL.default                               24.0.7                         23.08-extra              user
ffmpeg-full                                         org.freedesktop.Platform.ffmpeg-full                                                             22.08                    user
openh264                                            org.freedesktop.Platform.openh264                                 2.1.0                          2.2.0                    system
openh264                                            org.freedesktop.Platform.openh264                                 2.1.0                          2.2.0                    user
openh264                                            org.freedesktop.Platform.openh264                                 2.4.1                          2.4.1                    system
GNU Image Manipulation Program                      org.gimp.GIMP                                                     2.10.38                        stable                   user
Calculator                                          org.gnome.Calculator                                              46.1                           stable                   system
Calendar                                            org.gnome.Calendar                                                46.0                           stable                   system
Characters                                          org.gnome.Characters                                              46.0                           stable                   system
Connections                                         org.gnome.Connections                                             46.0                           stable                   system
Contacts                                            org.gnome.Contacts                                                46.0                           stable                   system
Déjà Dup Backups                                    org.gnome.DejaDup                                                 45.2                           stable                   system
Déjà Dup Backups                                    org.gnome.DejaDup                                                 45.2                           stable                   user
Document Viewer                                     org.gnome.Evince                                                  46.2                           stable                   system
Logs                                                org.gnome.Logs                                                    45.0                           stable                   system
Image Viewer                                        org.gnome.Loupe                                                   46.2                           stable                   system
HEIC                                                org.gnome.Loupe.HEIC                                                                             stable                   system
Maps                                                org.gnome.Maps                                                    46.11                          stable                   system
Sushi                                               org.gnome.NautilusPreviewer                                       46.0                           stable                   system
GNOME Application Platform version 45               org.gnome.Platform                                                                               45                       system
GNOME Application Platform version 46               org.gnome.Platform                                                                               46                       system
Text Editor                                         org.gnome.TextEditor                                              46.1                           stable                   system
Weather                                             org.gnome.Weather                                                 46.0                           stable                   system
Pika Backup                                         org.gnome.World.PikaBackup                                        0.7.2                          stable                   system
Disk Usage Analyzer                                 org.gnome.baobab                                                  46.0                           stable                   system
Clocks                                              org.gnome.clocks                                                  46.0                           stable                   system
Fonts                                               org.gnome.font-viewer                                             46.0                           stable                   system
adw-gtk3-dark Gtk Theme                             org.gtk.Gtk3theme.adw-gtk3-dark                                                                  3.22                     system
adw-gtk3-dark Gtk Theme                             org.gtk.Gtk3theme.adw-gtk3-dark                                                                  3.22                     user
Adwaita theme                                       org.kde.KStyle.Adwaita                                                                           6.6                      system
KDE Application Platform                            org.kde.Platform                                                                                 5.15-23.08               user
KDE Application Platform                            org.kde.Platform                                                                                 6.6                      system
KDE Application Platform                            org.kde.Platform                                                                                 6.7                      user
QGnomePlatform                                      org.kde.PlatformTheme.QGnomePlatform                                                             5.15-23.08               user
QGnomePlatform                                      org.kde.PlatformTheme.QGnomePlatform                                                             6.6                      system
QAdwaitaDecorations                                 org.kde.WaylandDecoration.QAdwaitaDecorations                                                    5.15-23.08               user
QAdwaitaDecorations                                 org.kde.WaylandDecoration.QAdwaitaDecorations                                                    6.6                      system
QAdwaitaDecorations                                 org.kde.WaylandDecoration.QAdwaitaDecorations                                                    6.7                      user
QGnomePlatform-decoration                           org.kde.WaylandDecoration.QGnomePlatform-decoration                                              5.15-23.08               user
LibreOffice                                         org.libreoffice.LibreOffice                                       24.2.3.2                       stable                   user
Thunderbird                                         org.mozilla.Thunderbird                                           115.10.1                       stable                   system
Firefox                                             org.mozilla.firefox                                               126.0.1                        stable                   system
OpenRGB                                             org.openrgb.OpenRGB                                               0.9                            stable                   user
PPSSPP                                              org.ppsspp.PPSSPP                                                 1.17.1                         stable                   user
SuperTux                                            org.supertuxproject.SuperTux                                      0.6.3                          stable                   user
VLC                                                 org.videolan.VLC                                                  3.0.20                         stable                   user

You have some flatpaks installed as system and some as your user, you need to decided which one you want to keep:

Thanks, I think the ones I installed through the Software Centre are installed as “system”, while those I installed through Bazzite Portal are installed as “user”. I will gradually move them all to “system”. Maybe a potential improvement could have done to the Bazzite Portal to give the user an option to select. Thanks anyway for clarifying it.

The warehouse app might be useful for this: Install Warehouse on Linux | Flathub

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