Together with my then-colleague Kalev Lember, I recently added support for pre-installing Flatpak applications. It sounds fancy, but it is conceptually very simple: Flatpak reads configuration files from several directories to determine which applications should be pre-installed. It then installs any missing applications and removes any that are no longer supposed to be pre-installed (with some small caveats). For example, the following configuration tells Flatpak that the devel branch of the app org.test.Foo from remotes which serve the collection org.test.Collection, and the app org.test.Bar from any remote should be installed: