The SYSTEM.ADMIN.COMMAND.QUEUE is used to send administrative commands to Websphere MQ (display, stop, start, disable, etc.). This is probably used here to get a list of queue names and attributes. Normally application programs are not allowed to have access to this queue because of the increased rights.
Applications (userids ‘HCI’ or groups) can be granted granular, administrative access to specific queues without granting more broad rights.
Polling for messages is done on the individual queue level, as well as getting and putting messages.
I don’t know the internals of Cloverleaf as far as polling queues. MQ favors its own trigger monitor, where typically one process will poll all queues specified to be watched and then start the designated application that will work that queue.