Currently partial cleanup always removes the base files. It should not, to allow running cleanup again to remove even more components. This is mandatory for dwh/reports to be removed and is required for sane usage of the cleanup utility.
Alon, what is the status of this RFE?
It's partially implemented, missed 3.6, waiting to be re-considered for 4.0 planning.
Closing old RFEs. Please reopen if relevant.