Adjust h5extract and km3modules' io

The by and cc are now stored in the w2list which is part of the event info. This is good news as we dont have to go over the user info of mc_tracks anymore. I have implemented a readout for the new productions. Old productions can still be processed with the h5extract option --mc-tracks-usr-data.

Therefore, I also propose to make that option non-default, as for all future productions there is no more info at all there, yet the objects do exist, so they just consume time.

While we are at it, I propose to make the option --with-calibration default, as in most use cases we want to use the correct calibration, right?

Please comment in the merge request.