@ghutchis
What do you think about pre-installing plugins for Flatpak? At least these default plugins, avogenerators, Molecules, and Crystals.
Plugin downloader does not place plugins in the correct directory. The correct directory is this.
/home/.local/share/flatpak/app/org.openchemistry.Avogadro2/current/active/files/share/OpenChemistry/Avogadro/