Ubuntu – How to exclude directories when listing files

It isn't your shell that determines whether output of ls is colorized. You must run ls --color=auto (either as an alias, or explicitly) in order to get colorised ls output. I suspect that your bash configuration included that alisa by default, but zsh doesn't for some reason. Seems odd that Ubuntu would have crippled their zsh installation in such a fashion, but I've given up trying to work out what they're up to.

If you are not sure, check that you are not running cp as an alias (from your shell type "alias cp"), if you don't have additional parameters (specially -n) cp -R will overwrite the files in desti_dir unless you have an issue with permissions.

But if you need to be sure, you can run diff to compare both directories

diff source_dir/ dest_dir/