process_components_cif separate out functionality to split into individual cif

• from discussion with Sameer.
• for production want to be able to start processes that just depend on the split PDB-CCD mmcif as soon as possible
• so add command line options to process_components cif

option	what
--just_mmcif	does the split into individual mmcif files but no further processing. The --output_dir must be specified with this option.
--apart_from_mmcif	used after --just_mmcif to do the rest of the processing into coordinate files images chem.xml etc. The --output_dir option must be specified with this option. --clean must not be.
--clean	remove any existing output_dir completely

• not sure whether this is necessary need to sort out #29 #30 first.