How can I inject a bean into an ApplicationContext before it loads from a file?

As I had trouble solving this with an AnnotationConfigApplicationContext, I found the following alternative:

DefaultListableBeanFactory beanFactory = new DefaultListableBeanFactory();
beanFactory.registerSingleton("customBean", new CustomBean());
context = new AnnotationConfigApplicationContext(beanFactory);
context.register(ContextConfiguration.class);
context.refresh();

How about programmatically creating an empty parent context first, registering your object as a singleton with that context's BeanFactory using the fact that getBeanFactory returns an implementation of SingletonBeanRegistry.

parentContext = new ClassPathXmlApplicationContext();
parentContext.refresh(); //THIS IS REQUIRED
parentContext.getBeanFactory().registerSingleton("myBean", myBean)

Then specify this context as a parent to your "real" context The beans in the child context will then be able to refer to the bean in the parent.

String[] fs = new String[] { "/path/to/myfile.xml" } 
appContext = new FileSystemXmlApplicationContext(fs, parentContext);