Normal "cp" command will exclude files/folders starting with ".". Below steps are needed to make sure everything is copied (essentially a backup) of a given folder.
1. Set shopt dotglob option to enable.
shopt -s dotglob
2. Copy hidden files and folder.
cp -pr sourceDir destDir
3. Set shopt dotglob option to disable.
shopt -u dotglob
Reference
Monday, March 15, 2010
Taking a backup of a folder in Fedora Linux
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