Confirming this bug. More distressingly, after removing flatpak from my
system with apt, this change persisted; it left
/etc/profile.d/flatpak.sh on my system which would automatically run on
my main user, since it still had some leftover files in
.local/share/flatpak, and would crash the desktop session upon logging
in when it couldn't find relevant dependency.

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https://bugs.launchpad.net/bugs/1801814

Title:
  Environment overwrites XDG_DATA_DIRS

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