main: change check whether /etc is unpopulated to look for /etc/machine-id

main: change check whether /etc is unpopulated to look for /etc/machine-id

Previously, we checked whether /etc was completely empty. This makes it
difficult though for container managers such as nspawn to install a
small number of files (such as /etc/timezone), and have the system
otherwise populate its own tree.

Hence, change this by looking for /etc/machine-id, which should be a
good sign whether /etc is populated or not.