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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