I have Ubuntu 16.04 and I’m trying to use the latest monodevelop installed via flatpak as my external script editor for Unity 5.6, but I can’t found the executable location, I tried .local/share/flatpak/app/com.xamarin.MonoDevelop/x86_64/stable/active/files/bin but nothing there is working for me.
Flatpack apps needs to be run using the ‘flatpack run’ command, so I don’t know if it will even work when you try to execute them directly.
What you can try is create a small bash script that executes the right flatpack command to run MonoDevelop. In Unity you browse to this script and set that as the external editor.