Stop using /usr/etc, /usr/var, etc.
See https://gitlab.com/freedesktop-sdk/freedesktop-sdk/issues/439 for context.
This only affects Gnome runtimes based on Freedesktop.org 18.08.
Basically Gnome 3.30 (and higher) should use /etc and /var directly in project.conf and relocating data from /etc to /usr/etc and /var to /usr/var respectively when rolling the Flatpak images. Elements that are used to do this in FD.o can probably be reused.