My files are organized that way:


If I configure my project to point on c:/top_level_dir/www/intranet, I don't have access to my MVC files other than by searching the classes, not practical.
All the exemples in the tutorial seems to make an assumption that the MVC files are below the web root, that is not the best practice as usually (and recommended by Zend and all independent authors) MVC files should be OUTSIDE the web root.

Any exemple to strictly follow best practices or structures like we can found in books such as "Zend Framework in Action"???

Zend Studio has a good Zend Framework Project template when you create a new project and everything is respecting the modular structure.
I prefer PHPEd over ZS but as most of my work is based on ZF, if I can't find good examples on how to configure ZF projects for debugging, I will drop PHPED.

Thanks.

Try PhpED's Project Settings Wizard and select project root directory above the web root, so it will include all the web files and out-of-the-web files.