Allow ensure-dirs to run partially and skip big file chunks

The startup of the daemons would take a lot of time otherwise,
also it's not needed to set the permissions of those file over
and over again, because if the daemons are once migrated to the
user they will keep creating the file for that user.

The full run is intended as initial upgrade

Signed-off-by: René Nussbaumer <rn@google.com>
Reviewed-by: Michael Hanselmann <hansmi@google.com>