Replace deprecated UnitOfWork::clear($entityClassName) with a more granular refresh

We removed EntityManager::clear($entityClassName) already, but this one is deprecated
as well: 212edaa80b/lib/Doctrine/ORM/UnitOfWork.php (L2762)

[MAILPOET-5745]

mailpoet/tests/integration/Settings/SettingsRepositoryTest.php

@@ -0,0 +1,49 @@
+<?php declare(strict_types = 1);
+
+namespace MailPoet\Test\Settings;
+
+use MailPoet\Entities\SettingEntity;
+use MailPoet\Settings\SettingsRepository;
+use MailPoetTest;
+
+class SettingsRepositoryTest extends MailPoetTest {
+  public function testItFetchesAlwaysFreshData(): void {
+    $repository = $this->diContainer->get(SettingsRepository::class);
+
+    $setting = new SettingEntity();
+    $setting->setName('name');
+    $setting->setValue('value');
+    $this->entityManager->persist($setting);
+    $this->entityManager->flush();
+
+    $this->assertSame('value', $setting->getValue());
+    $this->entityManager->createQueryBuilder()
+      ->update(SettingEntity::class, 's')
+      ->set('s.value', ':value')
+      ->where('s.name = :name')
+      ->setParameter('value', 'new value')
+      ->setParameter('name', 'name')
+      ->getQuery()
+      ->execute();
+    $this->assertSame('value', $setting->getValue());
+
+    $newSetting = $repository->findOneByName('name');
+    $this->assertSame($setting, $newSetting);
+    $this->assertSame('new value', $setting->getValue());
+    $this->assertSame('new value', $newSetting->getValue());
+  }
+
+  public function testUpdateRefreshesExistingData(): void {
+    $repository = $this->diContainer->get(SettingsRepository::class);
+
+    $setting = new SettingEntity();
+    $setting->setName('name');
+    $setting->setValue('value');
+    $this->entityManager->persist($setting);
+    $this->entityManager->flush();
+
+    $this->assertSame('value', $setting->getValue());
+    $repository->createOrUpdateByName('name', 'new value');
+    $this->assertSame('new value', $setting->getValue());
+  }
+}