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Flatpak

Software & Apps 2026-04-01

Flatpak is the primary method for installing GUI applications on Shanios. Flathub is pre-configured and ready to use from first boot — no setup required. Flatpak app data lives in the @flatpak Btrfs subvolume, which is shared between both @blue and @green OS slots — your installed apps are available regardless of which slot you have booted, and survive every OS update and rollback untouched.

Pre-Installed Apps

Both editions ship with these apps pre-installed: Vivaldi Browser, OnlyOffice Desktop Editors, Warehouse (graphical Flatpak manager), Flatseal (sandbox permissions), Pods (Podman GUI), BoxBuddy (Distrobox GUI), and Gear Lever (AppImage manager).

The GNOME edition additionally includes GNOME's core productivity and utility apps. The KDE Plasma edition additionally includes the full gaming stack (Steam, Heroic, Lutris, RetroArch, Bottles, and more), KDE productivity apps, and virt-manager with QEMU extension.

Installing Apps

# Install from Flathub
flatpak install flathub org.videolan.VLC
flatpak install flathub com.spotify.Client
flatpak install flathub org.gimp.GIMP

# Search for an app
flatpak search gimp

# Install from GUI
# Open GNOME Software or KDE Discover — Flathub apps appear automatically

Managing Installed Apps

# List installed apps
flatpak list --app

# Update all apps
flatpak update

# Remove an app
flatpak uninstall org.videolan.VLC

# Remove an app and its data
flatpak uninstall --delete-data org.videolan.VLC

# Remove unused runtimes (free space)
flatpak uninstall --unused

Auto-Updates

Flatpak apps update automatically via a systemd timer running every 12 hours — one for system-wide installs, one for per-user:

# Check timer status
systemctl status flatpak-update-system.timer
systemctl --user status flatpak-update-user.timer

# Disable auto-updates (not recommended)
sudo systemctl disable flatpak-update-system.timer

Permissions & Sandboxing

Flatpak apps run in a sandbox. Use Flatseal (pre-installed) to manage permissions via GUI — it shows every permission for every installed app and lets you grant or revoke filesystem, network, device, and portal access per-app. Use the CLI for scripted overrides:

# View permissions for an app
flatpak info --show-permissions org.gimp.GIMP

# Grant filesystem access
flatpak override --user --filesystem=home org.gimp.GIMP

# Reset permissions to defaults
flatpak override --user --reset org.gimp.GIMP

App Data Location

| Type | Path | |------|------| | App data | ~/.var/app/<app-id>/ | | System runtime | /var/lib/flatpak/ (@flatpak subvolume — shared between @blue and @green) | | User runtime | ~/.local/share/flatpak/ |

The @flatpak subvolume is shared by both @blue and @green slots, so installed apps are available regardless of which slot you booted.

Running Apps from Terminal

# Run a Flatpak app
flatpak run org.videolan.VLC

# Run with extra permissions (temporary)
flatpak run --filesystem=home org.videolan.VLC

# Open a shell inside the Flatpak sandbox
flatpak run --command=sh org.videolan.VLC

Adding Other Remotes

# Add a remote (e.g., GNOME nightly)
flatpak remote-add --if-not-exists gnome-nightly \
  https://nightly.gnome.org/gnome-nightly.flatpakrepo

# List remotes
flatpak remotes

# Remove a remote
flatpak remote-delete gnome-nightly