Refactor code to directly use Doctrine's ManagerRegistry

Replaced most of the invocations of getDoctrine()->getManager() with ManagerRegistry->getManager(), and added ManagerRegistry injection to controllers where needed. This is part of an ongoing effort to improve code clarity, and avoid unnecessary method chaining in various parts of the codebase.

src/Bundle/ChillMainBundle/Controller/NotificationController.php

@@ -40,7 +40,7 @@ use function in_array;
  */
 class NotificationController extends AbstractController
 {
-    public function __construct(private readonly EntityManagerInterface $em, private readonly LoggerInterface $chillLogger, private readonly LoggerInterface $logger, private readonly ChillSecurity $security, private readonly NotificationRepository $notificationRepository, private readonly NotificationHandlerManager $notificationHandlerManager, private readonly PaginatorFactory $paginatorFactory, private readonly TranslatorInterface $translator, private readonly UserRepository $userRepository) {}
+    public function __construct(private readonly EntityManagerInterface $em, private readonly LoggerInterface $chillLogger, private readonly LoggerInterface $logger, private readonly ChillSecurity $security, private readonly NotificationRepository $notificationRepository, private readonly NotificationHandlerManager $notificationHandlerManager, private readonly PaginatorFactory $paginatorFactory, private readonly TranslatorInterface $translator, private readonly UserRepository $userRepository, private readonly \Doctrine\Persistence\ManagerRegistry $managerRegistry) {}
 
     /**
      * @Route("/create", name="chill_main_notification_create")
@@ -159,7 +159,7 @@ class NotificationController extends AbstractController
 
         $notification->addAddressee($this->security->getUser());
 
-        $this->getDoctrine()->getManager()->flush();
+        $this->managerRegistry->getManager()->flush();
 
         $logMsg = '[Notification] a user is granted access to notification trough an access key';
         $context = [