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Reason, because flatpak is part of Gnome. Are you using GNOME?... I recommend you to install XFCE and to change GDM to lightdm and test if you can remove flatpak without delete the access to your desktop...

Imagine flatpak is necessary for gnome-shell!

gnome-shell

xdg-desktop-portal-gtk

Reason, because flatpak is part of Gnome. Are you using GNOME?... I recommend you to install XFCE and to change GDM to lightdm and test if you can remove flatpak without delete the access to your desktop...

Imagine flatpak is necessary for gnome-shell!

gnome-shell

xdg-desktop-portal-gtk

Required By....

flatpak-builder
gnome-builder
discover 
gnome-software 
xdg-desktop-portal 
xdg-desktop-portal-gtk ....