Where are flatpaks actually stored?

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By default, flatpaks are stored in two (maybe three) different locations:

System-wide flatpak installations:

• apps are in /var/lib/flatpak/app/,

• runtimes are in /var/lib/flatpak/runtime

User files:

• User files are stored in ~/.var/app/

If you use the -–user option when installing a flatpak, it ends up in ~/.local/share/flatpak instead of /var/lib/flatpak/app/ (as mentioned above)

If wanted you can define a global install directory in /etc/flatpak/installations.d.