Deleting files in /var/lib/cloudera-scm/commands manually will cause problems in Cloudera Manager because Cloudera Manager references these in the UI when a user clicks through to certain things such as commands in Cloudera Manager's history and BDR job history/logs.
By adjusting the command retention period, the volume of history kept on disk can be decreased and older data will be deleted. Adjust
Administration > Settings > Command Eviction Age
to a value appropriate for your system (which is a trade off between available disk space and the desired history retention). Please note that it will take some time for Cloudera Manager to action the changes and begin the deletion, and a restart of Cloudera Manager may be required in some instances