I have some experience writing web applications in Java for class projects. My first project used Servlets and my second, the Stripes framework.

However, I feel that I am missing the greater picture of Java web development. I don't really understand the web.xml and context.xml files. I'm not sure what constitutes a Java EE application as opposed to a generic Java web application. I can't figure out how a bean is different from an ordinary Java class (POJO?) and how that differs from an Enterprise Java Bean (EJB). These are just the first few questions I could think of, but there are many more.

What is a good way to learn how Java web applications function from the top down rather than simply how to develop an application with a specific framework? (Is there a book for this sort of thing?) Ultimately, I would like to understand Java web applications well enough to write my own framework.