How to copy .app or .prefPane (special) directory in OS X

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Whenever I copy via cp or rsync a .app or .prefPane (special) directory to another location in OS X, it only copies the Contents directory. How do you copy these from the CLI and preserve the directory "look" in the GUI?

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I found that if you copy the file to a directory with the same name it works correctly. If you don't specify a special directory destination it will NOT copy with the GUI preserved "look".

The command below does NOT work. It ONLY copies the Contents directory.

sudo rsync -a --progress Retrospect\ Client.prefPane/ ~/Desktop/

The command below works and copies correctly.

sudo rsync -a --progress Retrospect\ Client.prefPane/ ~/Desktop/Retrospect\ Client.prefPane

Leave it to Apple to screw up something so basic. I give thumbs down to Apple for this atrocious file naming convention. Awful.

I give another thumbs up to Debian and RHEL for keeping it simple.