Call setAllowBeanDefinitionOverriding before initializer

Update initialization order in `SpringApplication` to ensure
`setAllowBeanDefinitionOverriding` is called before initializiers.

This prevents an initializer from accidentially overriding a bean.

Closes gh-50264

Author: philwebb

core/spring-boot/src/main/java/org/springframework/boot/SpringApplication.java

@@ -383,6 +383,13 @@ private void prepareContext(DefaultBootstrapContext bootstrapContext, Configurab
 		context.setEnvironment(environment);
 		postProcessApplicationContext(context);
 		addAotGeneratedInitializerIfNecessary(this.initializers);
+		ConfigurableListableBeanFactory beanFactory = context.getBeanFactory();
+		if (beanFactory instanceof AbstractAutowireCapableBeanFactory autowireCapableBeanFactory) {
+			autowireCapableBeanFactory.setAllowCircularReferences(this.properties.isAllowCircularReferences());
+			if (beanFactory instanceof DefaultListableBeanFactory listableBeanFactory) {
+				listableBeanFactory.setAllowBeanDefinitionOverriding(this.properties.isAllowBeanDefinitionOverriding());
+			}
+		}
 		applyInitializers(context);
 		listeners.contextPrepared(context);
 		bootstrapContext.close(context);
@@ -391,17 +398,10 @@ private void prepareContext(DefaultBootstrapContext bootstrapContext, Configurab
 			logStartupProfileInfo(context);
 		}
 		// Add boot specific singleton beans
-		ConfigurableListableBeanFactory beanFactory = context.getBeanFactory();
 		beanFactory.registerSingleton("springApplicationArguments", applicationArguments);
 		if (printedBanner != null) {
 			beanFactory.registerSingleton("springBootBanner", printedBanner);
 		}
-		if (beanFactory instanceof AbstractAutowireCapableBeanFactory autowireCapableBeanFactory) {
-			autowireCapableBeanFactory.setAllowCircularReferences(this.properties.isAllowCircularReferences());
-			if (beanFactory instanceof DefaultListableBeanFactory listableBeanFactory) {
-				listableBeanFactory.setAllowBeanDefinitionOverriding(this.properties.isAllowBeanDefinitionOverriding());
-			}
-		}
 		if (this.properties.isLazyInitialization()) {
 			context.addBeanFactoryPostProcessor(new LazyInitializationBeanFactoryPostProcessor());
 		}

core/spring-boot/src/test/java/org/springframework/boot/SpringApplicationTests.java

@@ -49,6 +49,7 @@
 import org.springframework.beans.factory.BeanCreationException;
 import org.springframework.beans.factory.BeanCurrentlyInCreationException;
 import org.springframework.beans.factory.BeanDefinitionStoreException;
+import org.springframework.beans.factory.BeanRegistrar;
 import org.springframework.beans.factory.ObjectProvider;
 import org.springframework.beans.factory.UnsatisfiedDependencyException;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -100,6 +101,7 @@
 import org.springframework.context.event.SimpleApplicationEventMulticaster;
 import org.springframework.context.event.SmartApplicationListener;
 import org.springframework.context.support.AbstractApplicationContext;
+import org.springframework.context.support.GenericApplicationContext;
 import org.springframework.context.support.StaticApplicationContext;
 import org.springframework.core.Ordered;
 import org.springframework.core.annotation.Order;
@@ -1139,6 +1141,21 @@ void beanDefinitionOverridingIsDisabledByDefault() {
 			.isThrownBy(() -> new SpringApplication(ExampleConfig.class, OverrideConfig.class).run());
 	}
 
+	@Test
+	void beanDefinitionOverridingIsAppliedToInitializer() { // gh-50264
+		assertThatExceptionOfType(BeanDefinitionOverrideException.class).isThrownBy(() -> {
+			BeanRegistrar registrar = (registry, env) -> {
+				registry.registerBean("someBean", String.class);
+				registry.registerBean("someBean", String.class);
+			};
+			ApplicationContextInitializer<GenericApplicationContext> initializer = (context) -> context
+				.register(registrar);
+			SpringApplication application = new SpringApplication(Example.class);
+			application.setInitializers(List.of(initializer));
+			application.run();
+		});
+	}
+
 	@Test
 	void beanDefinitionOverridingCanBeEnabled() {
 		assertThat(new SpringApplication(ExampleConfig.class, OverrideConfig.class)