multiple_.htaccess

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteRule ^$ public/     [L]
    RewriteRule (.*) public/$1 [L]
</IfModule>

multiple_apps_backend_controllers_IndexController.php

<?php

namespace Multiple\Backend\Controllers;

use Phalcon\Mvc\Controller;

class IndexController extends Controller
{

	public function indexAction()
	{
		return $this->response->forward('login');
	}
}

multiple_apps_backend_controllers_LoginController.php

<?php

namespace Multiple\Backend\Controllers;

use Phalcon\Mvc\Controller;

class LoginController extends Controller
{

	public function indexAction()
	{
		$this->view->disable();
	}
}

multiple_apps_backend_controllers_ProductsController.php

<?php

namespace Multiple\Backend\Controllers;

use Phalcon\Mvc\Controller;
use Multiple\Backend\Models\Products as Products;

class ProductsController extends Controller
{

	public function indexAction()
	{
		$this->view->product = Products::findFirst();
	}
}

multiple_apps_backend_models_Products.php

<?php

namespace Multiple\Backend\Models;

use Phalcon\Mvc\Model;

class Products extends Model
{

}

multiple_apps_backend_Module.php

<?php

namespace Multiple\Backend;

use Phalcon\Loader;
use Phalcon\Mvc\View;
use Phalcon\Mvc\Dispatcher;
use Phalcon\DiInterface;
use Phalcon\Db\Adapter\Pdo\Mysql as Database;

class Module
{

	public function registerAutoloaders()
	{

		$loader = new Loader();

		$loader->registerNamespaces(array(
			'Multiple\Backend\Controllers' => '../apps/backend/controllers/',
			'Multiple\Backend\Models'      => '../apps/backend/models/',
			'Multiple\Backend\Plugins'     => '../apps/backend/plugins/',
		));

		$loader->register();
	}

	/**
	 * Register the services here to make them general or register in the ModuleDefinition to make them module-specific
	 */
	public function registerServices(DiInterface $di)
	{

		//Registering a dispatcher
		$di->set('dispatcher', function() {
			$dispatcher = new Dispatcher();
			$dispatcher->setDefaultNamespace("Multiple\Backend\Controllers\\");
			return $dispatcher;
		});

		//Registering the view component
		$di->set('view', function() {
			$view = new View();
			$view->setViewsDir('../apps/backend/views/');
			return $view;
		});

		//Set a different connection in each module
		$di->set('db', function() {
			return new Database(array(
				"host" => "localhost",
				"username" => "root",
				"password" => "secret",
				"dbname" => "invo"
			));
		});
	}
}

multiple_apps_backend_views_login_index.phtml

<h1>Welcome to Backend!</h1>

multiple_apps_backend_views_products_index.phtml

<h1>Welcome</h1>

<?php echo $product->name ?>

multiple_apps_frontend_controllers_IndexController.php

<?php

namespace Multiple\Frontend\Controllers;

use Phalcon\Exception;
use Phalcon\Mvc\Controller;

class IndexController extends Controller
{

	public function indexAction()
	{
        throw new Exception('test');
	}
}

multiple_apps_frontend_controllers_ProductsController.php

<?php

namespace Multiple\Frontend\Controllers;

use Phalcon\Mvc\Controller;

class ProductsController extends Controller
{

	public function indexAction()
	{
		return $this->response->redirect('login');
	}

    public function notFoundAction()
    {
        return $this->response->setContent('test');
    }
}

multiple_apps_frontend_controllers_UsersController.php

<?php

namespace Multiple\Frontend\Controllers;

use Phalcon\Mvc\Controller;

class UsersController extends Controller
{

	public function indexAction()
	{
		echo '<br>', __METHOD__;
	}
}

multiple_apps_frontend_models_Products.php

<?php

use Phalcon\Mvc\Model;

class Products extends Model
{

}

multiple_apps_frontend_Module.php

<?php

namespace Multiple\Frontend;

use Acl;
use Phalcon\Events\Manager;
use Phalcon\Loader;
use Phalcon\Mvc\Dispatcher;

class Module
{
    public function registerAutoloaders()
    {

        $loader = new Loader();

        $loader->registerNamespaces(
            [
                'Multiple\Frontend\Controllers' => '../apps/frontend/controllers/',
                'Multiple\Frontend\Models' => '../apps/frontend/models/',
            ]
        );

        $loader->register();
    }

    /**
     * Register the services here to make them general or register in the ModuleDefinition to make them module-specific
     */
    public function registerServices($di)
    {

        //Registering a dispatcher
        $di->set(
            'dispatcher',
            function () {
                $dispatcher = new Dispatcher();
                $dispatcher->setDefaultNamespace("Multiple\Frontend\Controllers\\");
                $eventsManager = new Manager();
                $eventsManager->attach(
                    'dispatch:beforeException',
                    function ($event, $dispatcher) {
                        $dispatcher->forward(
                            [
                                'controller' => 'products',
                                'action' => 'notFound',
                            ]
                        );
                        return false;
                    }
                );

                $dispatcher->setEventsManager($eventsManager);

                return $dispatcher;
            }
        );

        //Registering the view component
        $di->set(
            'view',
            function () {
                $view = new \Phalcon\Mvc\View();
                $view->setViewsDir('../apps/frontend/views/');

                return $view;
            }
        );

        $di->set(
            'db',
            function () {
                return new Database(
                    [
                        "host" => "localhost",
                        "username" => "root",
                        "password" => "secret",
                        "dbname" => "invo",
                    ]
                );
            }
        );
    }
}

multiple_apps_frontend_views_products_index.phtml

<h1>Welcome</h1>

<?php echo $product->name ?>

<?php echo $this->url(array('controller' => 'products', 'action' => 'algo')) ?>

multiple_public_.htaccess

AddDefaultCharset UTF-8

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteRule ^(.*)$ index.php?_url=/$1 [QSA,L]
</IfModule>

multiple_public_index.php

<?php

error_reporting(E_ALL);

use Phalcon\Loader;
use Phalcon\Mvc\Router;
use Phalcon\DI\FactoryDefault;
use Phalcon\Mvc\Application as BaseApplication;

class Application extends BaseApplication
{

	/**
	 * Register the services here to make them general or register in the ModuleDefinition to make them module-specific
	 */
	protected function registerServices()
	{

		$di = new FactoryDefault();

		$loader = new Loader();

		/**
		 * We're a registering a set of directories taken from the configuration file
		 */
		$loader->registerDirs(
			array(
				__DIR__ . '/../apps/library/'
			)
		)->register();

		//Registering a router
		$di->set('router', function(){

			$router = new Router();

			$router->setDefaultModule("frontend");

			$router->add('/:controller/:action', array(
				'module' => 'frontend',
				'controller' => 1,
				'action' => 2,
			));

			$router->add("/login", array(
				'module' => 'backend',
				'controller' => 'login',
				'action' => 'index',
			));

			$router->add("/admin/products/:action", array(
				'module' => 'backend',
				'controller' => 'products',
				'action' => 1,
			));

			$router->add("/products/:action", array(
				'module' => 'frontend',
				'controller' => 'products',
				'action' => 1,
			));

			return $router;

		});

		$this->setDI($di);
	}

	public function main()
	{

		$this->registerServices();

		//Register the installed modules
		$this->registerModules(array(
			'frontend' => array(
				'className' => 'Multiple\Frontend\Module',
				'path' => '../apps/frontend/Module.php'
			),
			'backend' => array(
				'className' => 'Multiple\Backend\Module',
				'path' => '../apps/backend/Module.php'
			)
		));

		echo $this->handle()->getContent();
	}

}

$application = new Application();
$application->main();