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.

rector.php

@@ -30,6 +30,7 @@ return static function (RectorConfig $rectorConfig): void {
 
     // part of the symfony 54 rules
     $rectorConfig->rule(\Rector\Symfony\Symfony53\Rector\StaticPropertyFetch\KernelTestCaseContainerPropertyDeprecationRector::class);
+    $rectorConfig->rule(\Rector\Symfony\Symfony60\Rector\MethodCall\GetHelperControllerToServiceRector::class);
     $rectorConfig->disableParallel();
 
     //define sets of rules