Is there any php frameworks available that will support this “modular” approach out of the box ?

I was getting confused by the disparity between the recommended structures professed by coding frameworks, like Zend, and the strucutres adopted by real life, successful, CMS frameworks like WordPress and Drupal.

As you say “In theory, putting the models in the models/ directory, the controllers in the controllers/ directory and the views in the views/ directory makes perfect sense, but in practice, it doesn’t.”