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Does this mean the following does the same? flatpak run --env=DISPLAY=$DISPLAY org.qgis.qgis?
It's weird because flatpak generally forwards all environment variables.
Also note --share=network is already enabled by default.
Now to your actual issue:
I fear we'll need to see a bit more where the blocking is. Can you make sure that the system is running xdg-desktop-portals and they're working properly? I'm not sure what the plan is for those on remote systems.
I have a flatpak installation of QGIS 3.14 on a CentOS 7 system. I launch QGIS from an xterm with the command line:
flatpak run --share=network --command=bash org.qgis.qgis -c "DISPLAY=$DISPLAY qgis $*"
When a Project Save is attempted the following messages are displayed in the terminal:
Warning: Failed enumerating UDisks2 objects:
"org.freedesktop.DBus.Error.Disconnected"
"Not connected to D-Bus server"
and then QGIS becomes unresponsive and has to be killed with CTRL-C.
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