I am looking for a way to copy a folder, with all the invisible and system files it contains in its "first level", but only some of the other visible, "normal" folders it contains? This is related to a "Time Machine" data transfer, from an old disk to a new one. But I think it is a question interesting in its own.
First create a new folder where you will copy the data to:
mkdir <dest_folder>. Then use:
# "First level" hidden files find <source_folder> -d 1 -name ".*" -print0 | xargs -0 -J % cp -R % <dest_folder> # Normal folders cp -R <source_folder>/<folder1> <source_folder>/<folder2> ... <dest_folder>