File level clone of boot drive leaves extra folders, can I remove or hide?

I made a file level drive clone with DiskUtility and then again with Carbon Copy Cloner (to confirm behavior) in preparation to go from 10.5.1 to 10.5.2 and found extra folders on the new copy.
dev
home
net
These folders are in addition to the usual app, users, library etc. They appear to behave like /etc and /var in that there is not a folder for them on a non running OS boot drive. They claim to be empty. Can they be deleted, hidden, turned invisible? Advice?
Thanks.

Kostas is correct. These folders are used by the system, and will be hidden from the users when the disk is running as the current system.

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