You might have to install nautilus or another file manager in the debian-9
I didn't have files on qubes 3.2 debian8 to debian-9. Can't remember if
fresh install of 4.0 debian-9 template needs file manager installed too.
To sync new programs installed in template to the appvms desktop menu, start
the debian-9 template terminal, in it type qvm-sync-appmenus.
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