The Steam Deck uses Discover to allow you to install different programs. Discover is an easy way to install and manage applications, tools, and add-ons. With Discover, you can install Flatpak apps on the Steam Deck in Desktop Mode.
So what are flatpak apps? Let’s start with some terminology
Flatpak: a system for building, distributing, and running sandboxed desktop applications on Linux
Sandbox: applications that are run with Flatpak have extremely limited access to the host environment. This keeps applications isolated from one another.
Flatpak application: these are the applications the user installs via command line or the Discover app.
Why does Steam OS 3 Holo use flatpak apps?
Stability: Issues with a single Flatpak app or runtime is contained to not interfere with the system altogether.
Rootless Install: Steam OS 3 ships as an immutable system, meaning that by default there is no root password and users don’t have access to read write privileges. Flatpak applications do not require elevated privileges to be installed.
Sandboxed applications: To increase security, applications that are run with Flatpak are isolated from one another and have limited access to the host environment.
You can also install applications without the use of Discover. One easy way is to browse flathub.
Problems with Flatpak
Many users run into issues using Flatpak apps, especially when trying to send or receive files. Because of the tight security and sandboxed environments, the application might not have permissions to access the folders you want it to.
One way to fix this is to install Flatseal. Flatseal is a graphical utility to review and modify permissions from your Flatpak applications.