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To get flatpak’s to honor your systems dark mode and not show you horrible white menubars, you can use this little snipplet:

First make sure that gtk-application-prefer-dark-theme is set to true in ~/.config/gtk-3.0/settings.ini. Install whatever flatpacks you want. Then run this:

for flatpak in $HOME/.var/app/*/
do
  confdir="${flatpak}config/gtk-3.0"

  mkdir -p $confdir
  cp $HOME/.config/gtk-3.0/settings.ini $confdir/settings.ini
done

Source: https://www.linuxuprising.com/2018/05/how-to-get-flatpak-apps-to-use-correct.html#comment-5174655826

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