Flatpak is thought to have serious security concerns that should be considered before using Flatpak on secure systems.
Flatpak is a package management framework aiming to provide support for sandboxed, distro-agnostic binary packages for Linux desktop applications.
USE flags for sys-apps/flatpak Linux application sandboxing and distribution framework
||Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally|
||Add support for x11-libs/gtk+ (The GIMP Toolkit)|
||Add support for GObject based introspection|
||Add support for software made by KDE, a free software community|
||Enable PolicyKit (polkit) authentication support|
||Enable seccomp (secure computing mode) to perform system call filtering at runtime to increase security of programs|
||Enable use of systemd-specific libraries and features like socket activation or session tracking|
Chromium-based browsers suggest disabling suid USE-flag for sys-apps/bubblewrap for performance reasons.
Flatpak installation guide suggested to restart the system after installation. This might be no longer necessary.
emerge --ask sys-apps/flatpak
Add flathub repository
All operations with flatpak can be performed as user or as root, if performing as user --user flag can help if there are issues with permissions.
flatpak remote-add --user --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
- /var/lib/flatpak - global flatpak state (system-wide installed apps and repos)
- ~/.local/share/flatpak - per-user flatpak state (locally installed apps and repos)
- ~/.var/app/ - per application state (configuration files and cache)
To install an application, e.g. Thunderbird, run:
flatpak --user install org.mozilla.Thunderbird
To run the application use created .desktop file or run:
flatpak run org.mozilla.Thunderbird
To update installed applications and runtimes:
Flatpak documentiation offers a good guide about desktop integration and theming.
Flatpak applications don't follow the system's GTK theme by default. First find out what's the current GTK theme, e.g. Materia-dark-compact, and then install it for Flatpak applications to use. 
gsettings get org.gnome.desktop.interface gtk-theme
flatpak install flathub org.gtk.Gtk3theme.Materia-dark-compact
Fixing jagged fonts on Wayland
emerge --ask gnome-base/gnome-settings-daemon
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