It would be great if it were possible the schedule a the clean up geoprocessing history in a project. For example, in the Geoprocessing Options I could set GP history older than 2 weeks to be deleted. If this is not possible then make the GP history accessible via arcpy which can then be cleaned programmatically. I understand that technically this can be done by manipulating the files that make up the APRX but I would prefer not to mess around with them that way to avoid breaking things.