deploy: Delete .updated file from /etc and /var on new deployments

deploy: Delete .updated file from /etc and /var on new deployments

Systemd units using ConditionNeedsUpdate run if the mtime of .updated in
the specified directory is newer than /usr. Since /usr has an mtime of
0, there's no way to have an older .updated file. Systemd units
typically specify ConditionNeedsUpdate=/etc or ConditionNeedsUpdate=/var
to support stateless systems like ostree.

Remove the file from the new deployment's /etc and the OS's /var
regardless of where they came from to ensure that these systemd units
run when booting new deployments. This will provide a method to run
services only on upgrade.

Closes: #1628
https://bugzilla.gnome.org/show_bug.cgi?id=752950

Closes: #1631
Approved by: cgwalters