How can I copy a folder that contains symlinks and retain the symlinks in the destination folder? I'm doing something like this with PHP/Bash: system(cp -r production-clone-target production-sites/{$instanceName});but the symlinks do not appear in the destination folder. 
Copy folder with symlinks
symlink
Try adding the --preserve=links switch to your cp command.From man cp:    --preserve[=ATTR_LIST]          preserve the specified attributes (default: mode,ownership,timestamps), if possible additional attributes: context, links,xattr, allEdit: If under OS X; use cp -a.