It’s quite common when you first start using linux from the command line to get the error message:
cp: omitting directory
What this means is that linux cp or rm command doesn’t work on folders or directories as standard. There is a simple fix though just add the -r modifier.
To copy a directory
cp -r /var/www/source /var/www/destination
Removing a directory
rm -r /var/www/target
Obviously be very careful when using the recursive command with remove.