Access to PHP class files outside of DOCUMENT_ROOT

I am confused as to what constitutes “best practice” for the structure of the PHP web application. There are a number of suggestions to read this site. One of the commonly mentioned structures is "don't have any php files inside the root document." Although this sounds like good practice, I don’t see how it works - the web server does not recognize anything outside the root of the document. I assume that this document root is a public access directory, as shown below:

app-
  |
  - htdocs - document root
  | |
  | - index.php
  | - css/
  | - images/
  |
  - PHP classes in here/
  - Other PHP classes in here.../

Or is this “application” in the above example the root of the document, and dir htdocs is the public domain of the site structure?

, , htdocs, ?