Create abf::setup_output() for consistency

[jhenin]

Partial response to #683

[jhenin]

@giacomofiorin Changes I have in progress are pinpointing a consistency issue: in NAMD, every time a simulation "run" is started, the output prefixes are updated from the NAMD parameters, which enables users to change them using NAMD scripts. However, this overrides any changes using the "cv" API. A possible way to deal with this is what I started doing: keeping track of any use of the cv API and then overriding changes in NAMD. Maybe a cleaner option would be the opposite: memorize the NAMD parameter values and only apply changes if they occur, not reset blindly to the NAMD values.