If you log into your web directory, you will see three folders. Your web pages are stored in "yourdomain.com" folder. The book is saying to keep those files outside "yourdomain.com" folder. The files can't be accessed by visitors but you can include the files.
For example, there is a file "example.php" file outside "yourdomain.com" folder. You can include the file like this require_once("../exmple.php")
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