Disable copying of file

You can open Terminal and use one of the following (rsync would probably be the one for you if you want something that won't be completely lost if you halt the process):

The standard UNIX way

cp -R -v source/. destination

The geeky UNIX way (restartable)

rsync -vaEW source/ destination

The OSX "easy" way

ditto -V source destination

Source

I'm not sure about #2, but I suspect #1 is due to trailing slashes in the file path. cp -Rp /path/to/Application.app /path/to/destination will copy the entire package, while cp -Rp /path/to/Application.app/ /path/to/destination (note the trailing slash after the source) will copy just the contents.

BTW, you should use cp -R instead of cp -r -- in some implementations of cp they're the same, but in some versions the lowercase option has ... oddities. According to the man page on OS X:

COMPATIBILITY

Historic versions of the cp utility had a -r option. This implementation supports that option; however, its use is strongly discouraged, as it does not correctly copy special files, symbolic links, or fifo's.