To remove indentation to this part (making it more readable), I would suggest to do this:

```bash
for line in $(cat "$1");
do
    if [[ ${line} == "#"* ]] || [[ ${line} == ";"* ]] ; then
        continue
    fi

    if [ -d ${line} ]; then
        sudo cp -R ${line} "${2}${line}"
        RETURN_CODE="$?"

        if [ "$?" -ne "0" ]; then
            logError "Error copying ${line}!"
            return 1
        fi

    elif [ -f ${line} ]; then
        sudo cp ${line} "${2}${line}"
        RETURN_CODE="$?"

        if [ "$?" -ne "0" ]; then
            logError "Error copying ${line}!"
            return 1
        fi

    else
        logError "Missing file or directory: ${line}"
        return 2
    fi
done
```

Do you get the idea? What do you think?