Prevent initializers from being applied twice in AOT mode

Running the following application prints 2 times Foo constructor at startup while a single time as expected in regular mode.

@SpringBootApplication
public class CommandlinerunnerApplication {

	public static void main(String[] args) {
		SpringApplication app = new SpringApplication(CommandlinerunnerApplication.class);
		app.addInitializers((ApplicationContextInitializer<GenericApplicationContext>) context ->
				context.registerBean(Foo.class));
		app.run(args);
	}
}

public class Foo {

	public Foo() {
		System.out.println("Foo constructor");
	}
}

A look at the generated code shows that Foo__BeanDefinitions generated during AOT transformations based on the initializer is created as expected, but it seems the second invocation comes from the fact that SpringApplication#applyInitializers is still invoked at runtime.

Notice that on native, this second invocation fails with Runtime reflection is not supported for public com.example.commandlinerunner.Foo() because unlike the AOT generated one, it requires ExecutableMode#INVOKE reflection hints (not inferred because not needed by the AOT generated code which is fine with ExecutableMode#INTROSPECT).

Both issues should be solved by removing the second invocation of the initializers, but this need to be explored because it could involve unwanted side effects with some initializers.

Start at SpringApplication#applyInitializers and compare its runtime path with the AOT-generated Foo__BeanDefinitions path described in the report. Reproduce the application in regular and native modes, then trace why the initializer runs twice. Done means the duplicate construction and native reflection failure are addressed without unwanted initializer side effects.