skip if something has already been done

[pilopilota]

we need to add controls on existing output files. something like "if trimmed file already exists, do not trim it again". otherwise when we stop at a given step (like tonight: stopped error at first realignment) we have to start again from the beginning.

[pilopilota]

idea: ExpFolder, SkipWhatsBeenDone and DeleteIntermediateSteps could be input arguments given by the user, so we don't have to change add commit push and pull every time.