Mac OS X do not merge folder content when folder of same name is copied from one location to another.
The terminal command will overwrite the sub-folder content of the destination folder if there are sub-folder of the same file name. Sounds a bit confusing, but if you try copying folders with files & folder inside, you should get the idea.
mv /src_folder/ /destination_folder/
Unknowingly, Mac OS actually have a command for you to merge folder content.
ditto /src_folder/ /destination_folder/
Find out more about ditto from Mac OS X Reference Library
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