So Flatpak install the apps into these location when install per-user basis.
Which the .var location persists over app upgrades according to this.
The plugin downloader right now put the plugins here,
Now, if the user decide to install system-wide, which need root permission.
The location will be here,
will still be create for system-wide installation as well.
Which I think is where it should be. So I think add “/home/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/other/” directory to plugin search path for Flatpak.
Not sure if it will work, will have to try it.
User can write to Flatpak, but if they install as system-wide, they will need root permission. It depends, but I encourage to install as user.
It is possible to install in external device like a USB storage. Using --installation flag. But I don’t think anyone really does it.