flatpak installs /etc/profile.d/flatpak.sh but it doesn't modify the environment.
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/etc/profile.d gets evaluated by bash but not simplelogin. David needs to look into this to get it working.
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Ideally SDDM should grow support for a wayland based greeter instead of a X11 greeter. This would involve looking at what XorgDisplayServer does and why the Greeter needs it.
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Turns out this is normally sourced by XSetup a bash script we run our X sessions through.
SDDM puts wayland sessions through a similar wayland-session script, can't remember what simple-login does.
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Simple Login does not evaluate it. It should, or we should use sddm on the phone too.