Improve module manager to accept instance

Hi,

For the performance and to make learning easier, we can accept modules instances :

Before :

```php
<?php
return array(
    'modules' => array(
        'Application',
        'Cron',
        'Administration',
        'Blog',
    ),
    'module_paths' => array(// my paths),
);
?>
```

Now, i do :

```php
<?php
return array(
    'modules' => array(
        'Application' => new Application\Module(),
        'Cron' => new Cron\Module(),
        'Administration' => new Administration\Module(),
        'Blog' => new Blog\Module(),
    ),
);
?>
```

There is no BC, more natural, and perf little better.