SELF-SOLVED
The above codex guide you to keep WordPress in its own directory like whatever.com/wordpress and keep index.php at root directory like whatever.com/index.php. So you can power your domain name.
It works but the old visitors while they visit whatever.com/wordpress as usual, it will show page not found untill he is informed the new index.php being at whatever.com (root directory)
Since there is no response for this question, I set a redirection between old/new homepage.
