May only be Qubes 3.1. May only be Whonix and not all Debian templates.
Be ready with qvm-revert-template-changes. It can be used after reboot as long as the templateVM has not been started again.
My default NetVM is sys-whonix. On boot, sys-net hangs in yellow state, sys-whonix goes to green but is unable to run any processes. (Irrelevant) Checking kern.log via xl console, shows that mounting-dirs service is unable to start, resulting in no mounting of /home/user/ and a broken KDE.
[ 1.547644] systemd[1]: Cannot add dependency job for unit rinetd.service, ignoring: Unit rinetd.service failed to load: No such file or directory.
[ 1.547676] systemd[1]: Cannot add dependency job for unit rinetd.service, ignoring: Unit rinetd.service failed to load: No such file or directory.
[ 1.547772] systemd[1]: Found ordering cycle on local-fs.target/start
[ 1.547779] systemd[1]: Found dependency on qubes-mount-dirs.service/start
[ 1.547785] systemd[1]: Found dependency on qubes-sysinit.service/start
[ 1.547791] systemd[1]: Found dependency on qubes-db.service/start
[ 1.547796] systemd[1]: Found dependency on local-fs.target/start
[ 1.547802] systemd[1]: Breaking ordering cycle by deleting job qubes-mount-dirs.service/start
[ 1.547809] systemd[1]: Job qubes-mount-dirs.service/start deleted to break ordering cycle starting with local-fs.target/start
Missing libxen-4.6 update seems to be the cause, just uploaded the update. Also, enabling testing repository should be enough (the package was there, but I missed uploading it to stable).
So, to fix the issue - start the template, access its console (sudo xl console debian-8) and install updates (sudo apt-get update && sudo apt-get -V dist-upgrade).
These systemd dependency messages are unrelated. Discussed elsewhere already (would take me a while to figure out where). Should be fixed in Qubes R3.2 / Whonix 13.
[ Btw those systemd warnings are something to look out for when releasing new versions of Qubes / Whonix. Ideally there are none of them. ]