When an early reboot is triggered because an upgrade script has disabled the
config mode, we need to explicitly call /etc/init.d/done, otherwise the overlay
will not be finalized after a firstboot and we get an endless reboot loop.

Since switching to Barrier Breaker/procd, we'd not notice if we were
upgrading from a version before renaming the config file to gluon-setup-mode
as the upgrade scripts run after the preinit.

Fix this by checking later during setup mode init again and rebooting into the
regular run mode if we detect this case.