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Prepare output file improvements

Nico Harringer requested to merge prepare_output_file_improvements into master

To throttle Condor (in case of AFS problems or other file-system related issues) use the new max_materialize option. Note that for this option to work, the submission files and the .sh file has to be on AFS (see here for more information). So if on EOS, only use --max-materialize in conjunction with --condor-logs /afs/path/to/condor/log/folder.

To activate condor logfiles, use --make-condor-logs.

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