Flatpak

Flatpak applications and runtimes installed system-wide or for the current user via the flatpak CLI.

[bootstrap.packages]
"flatpak:org.mozilla.firefox" = "latest"
"flatpak-user:org.gnome.Builder" = "latest"

Use the flatpak manager for the default system-wide installation and flatpak-user for the current user's installation. The scopes are separate, so a config can manage packages in either or both, including the same ID in both scopes. The package name is an application or runtime ID accepted by flatpak install and flatpak update.

mise does not install Flatpak or configure remotes implicitly. Install the flatpak CLI and add the required remote (commonly Flathub) before applying the config:

# Choose the scope you intend to manage:
flatpak remote-add --system --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
flatpak remote-add --user --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
mise bootstrap packages use flatpak:org.mozilla.firefox
mise bootstrap packages use flatpak-user:org.gnome.Builder

Check remote configuration in the same scope before installing:

flatpak remotes --system
flatpak remotes --user

Adding Flathub in user scope does not make it available to flatpak: system entries. When multiple remotes provide an ID, resolve the ambiguity in Flatpak's configuration; a mise declaration does not choose a remote by name.

Commands

mise bootstrap packages status
mise bootstrap packages apply --manager flatpak --dry-run
mise bootstrap packages apply --manager flatpak
mise bootstrap packages apply --manager flatpak-user
mise bootstrap packages upgrade --manager flatpak
mise bootstrap packages upgrade --manager flatpak-user

mise always passes an explicit scope to Flatpak so status, apply, and upgrade operate on the same installation. flatpak passes --system, while flatpak-user passes --user. Flatpak resolves the configured ID from the remotes configured for that scope.

Flatpak does not expose installation of arbitrary historical versions through these commands, so version pins are not supported. Use "latest" in config.

The manager is Linux-only and requires flatpak on PATH. On other platforms, or when the command is missing, shared configs list Flatpak entries as skipped. Installing an app does not create a mise shim; launch it through the desktop or flatpak run org.mozilla.firefox in the scope where it is installed.