conf: when looking for configurations look in /etc first, in /run second

After long consideration we came to the conclusion that user
configuration in /etc should always override the (generally computer
generated) configuration in /run. User configuration should always be
what matters over anything else. Hence rearrange the search orders
accordingly.

In general this should change very little as overriding like this is
seldomn done so far, and the order between /etc and /usr stays the same.