Zend Framework - Override module

Question

I'm working on multi-website CMS in Zend Framework.
I've came to a point where I need to override module from application/ folder in my website/application folder.
A bit better explanation of my issue:
Here's tree of my application (important part):

library/
application/
        module1/
            controllers/
            models/
            ....
        module2/
            controllers/
            models/
            ....
websites/
  website1.com/
       application/
            module1/
                controllers/
                models/
                ....

So what I need to do is that module1/ in websites/website1.com/application/ override module1/ in application, IF it exists. I want everything in module1/ in websites folder to override everything in main application folder.
I'd also like if there are 2 controllers in this module1 (for example IndexController and TestController) and if I put only TestController in websites folder under module1/controllers to override ONLY TestController from Application folder and to get IndexController from main folder.
Sorry if I failed to explain exactly what I'm trying to achieve. If there's something unclear, please ask.
Thank you.

Edit: Okey, first of all - thanks for your comments.
Reason for having websites/ folder is, mostly because of vhost as I prefer that all of my websites have separate (public?) folders, and reason for having one library with application folder is because, obviously, upgrade reasons (so when I, for example, upgrade Zend - I don't need to upgrade it for every website).
I'll most likely rarely use overriding option for controllers, and yes, I'd even prefer if I could, for example, extend main Controller (for example - IndexController) and override some functions, but I thought that's way harder then override whole class.
Here's full structure of my application:

 library/ - Library folder contains Zend and many other classes that I'll use in my application.
     Zend - Zend Framework
     MyCMS - Classes from my old CMS.
 sites/ - Folder that contains websties.
     website_1 - Website one.
         application/ - Application folder for website one. If I need to redefine module or something. So, if I need to override module: main_module, I'll  create folder main_module here with files that I want to override.
         config/ - Configuration for website_1 - if I need to override, for example, application.ini
         lang/ - Language files for this specific website.
         templates/ - Templates folder for website (layouts and templates). By the way, I'm using smarty.
             default/ - Main template.
                 layout/ - Layouts for Zend View.
                 css/
                 js/
                 images/
                 modules/
         files/ - Place to upload files in, for this website. This will contain user avatars and stuff.
         index.php - Main file that runs bootstrap and application.
         Bootstrap.php - Inherited bootstrap. In case I need to override some functions from default bootstrap.
 application/ - Main folder that contains application modules and stuff.
    main_module/
         configs/ - Module configuration.
             config.ini
         controllers/ - Controllers for this module.
         modules/ - Submodules. There are like boxes that I display on website. For example, if my main module is "news", here, I'll make new sub-module to display box with statistics.
             submodule/
                 services/ - XML/JSON/whatever service. If someone targets controller in services with specific parametars, it'll return response in requested format.
                     controllers/ - Services will only have controllers.
                 configs/ - Configuration for this submodule.
                 controllers/ - Controllers for this submodule.
                 models/ - Models for this submodule.
                 lang/ - Language files for this submodule.
                 template/ - Templates for this submodule.
                     helpers/
                     css/
                     js/
                     images/
                     index.html
         models/ - Models for main module.
         lang/
         services/  - Main module will also have services. See submodule services for explanation.
             controllers/
         template/
             helpers/
             css/
             js/
             images/
             index.html
     Bootstrap.php  - This is main bootstrap file that every website's bootstrap file will extend (and override some methods - if needed).

Answer 1

Update

Even though I highly discourage your directory structure, it's your application and you should structure it however you like.

To load multiple controllers, you should create a Front Controller Plugin to add paths to the controller directories stack

class My_Controller_Plugin_Paths extends Zend_Controller_Plugin_Abstract
{
    public function preDispatch()
    {
        // Something like this...
        // Would be best to load paths via config/database or somewhere
        $dispatcher = Zend_Controller_Front::getInstance()->getDispatcher();
        $dispatcher->addControllerDirectory('/path/to/website1.com/controllers')
                   ->addControllerDirectory('/path/to/website2.com/controllers');
    }
}

This is entirely untested, but you get the idea. Just make sure you register the plugin with the Front Controller in you bootstrap

---

I'd agree with @Laykes. This is a badly structured application.

I'm not sure of your exact requirements, but if it were my application, I would try to structure it like this:

/application
    /modules
        /default
            /controllers
                /IntexController.php      // Default_IndexController
                /Website1com
                    /IndexController.php  // Default_Website1com_IndexController (possibly extends Default_IndexController)

Here you can see a properly structured class inheritance without creating totally separate, and probably duplicate, application folder.

Autoloading anything like this though totally depends on you and your priorities. You could do a number of things, each with their own +ve's and -ve's.

• You could throw all paths into your include_paths in the order you want
• Check files exist and load from a front controller plugin

To name a couple.