Some factors like host environment setup, multiple projects for single/multiple clients, common helpers, cross-functionality between sites etc. determines how the folder architecture needs to be structured. Zend framework offers this flexibility.

Zend’s Default Directory Structure on installation
|– application
| |– Bootstrap.php
| |– configs
| | `– application.ini
| |– controllers
| | |– ErrorController.php
| | `– IndexController.php
| |– models
| `– views
| |– helpers
| `– scripts
| |– error
| | `– error.phtml
| `– index
| `– index.phtml
|– docs
|– library
|– public
| |– .htaccess
| `– index.php
`– tests
|– application
| `– bootstrap.php
|– library
| `– bootstrap.php
`– phpunit.xml

Below is a slight modification of the default architecture where by you can organize separate model-view-controllers for different projects. Other option is to organize project specific files under modules folder.

|– /sites
|–
`– Bootstrap.php
|– applicationONE
| | |– configs
| | `– application.ini
| |– controllers
| | `– ErrorController.php
| | `– IndexController.php
| |– modules (application specific modules)
| |– models
| `– views
| |– helpers
| `– scripts
| |– error
| |– index
|– library
| |– Zend
| |– Pear (Other libraries)
|– /var/www (public access directory – web root of the server will be set to this directory )
| `– .htaccess
| `– index.php
|– images
|– scripts
|– css

Refer to Zend’s Application Directory Layout for additional information

Zend: OLD Layout Architecture (Deprecated)

Zend: NEW Layout Architecture