cli: Output on the console even with --log-file

In 51f89902 (slapos/cli/entry.py, slapos/cli/format.py, slapos/format.py:
Do not double the log output when "slapos node boot" failed., 2017-05-11)
we fixed a problem that every failure during boot causing twice more output
(which filled up the disk very fast), but a side effect was that using
--log-file no longer cause messages to also go to the console.

The "Always send higher-level messages to the console via stderr" comment
in entry.py seems that this was always intentional to output messages on
the console.

Keep the same "don't configure again logging system when it's already
configured", but implemented in a slightly different way, because since
a FileHandler is a StreamHandler, the check of already having a
StreamHandler was true also for the case where --log-file added a
FileHander (a few lines above, also in configure_logging method)