You MUST shutdown the concurrent manager BEFORE you run cmclean.sql....WHY?

sqlplus apps/apps @cmclean

You MUST shutdown the concurrent manager BEFORE you run cmclean.sql
If you dont, what will happen is that currently running jobs will be marked as COMPLETED even though they are still running, and any dependent job will startup, possibly corrupting your data. Additionally, the internal manager might get confused as to how many jobs are running and might misallocate jobs to managers, basically a mess for job scheduling.
Once you shutdown the concurrent managers, cmclean.sql will mark all jobs that were in the running state as completed.
It is safe to do, since no jobs are running and they should be marked as completed.

Mohammed Riyaz Ahmed Khan
“The PATHAN Boy”