What is WEB-INF used for in a Java EE web application?

The Servlet 2.4 specification says this about WEB-INF (page 70):

A special directory exists within the application hierarchy named WEB-INF. This directory contains all things related to the application that aren’t in the document root of the application. The WEB-INF node is not part of the public document tree of the application. No file contained in the WEB-INF directory may be served directly to a client by the container. However, the contents of the WEB-INF directory are visible to servlet code using the getResource and getResourceAsStream method calls on the ServletContext, and may be exposed using the RequestDispatcher calls.

This means that WEB-INF resources are accessible to the resource loader of your Web-Application and not directly visible for the public.

This is why a lot of projects put their resources like JSP files, JARs/libraries and their own class files or property files or any other sensitive information in the WEB-INF folder. Otherwise they would be accessible by using a simple static URL (usefull to load CSS or Javascript for instance).

Your JSP files can be anywhere though from a technical perspective. For instance in Spring you can configure them to be in WEB-INF explicitly:

<bean id="viewResolver" class="org.springframework.web.servlet.view.InternalResourceViewResolver"
    p:prefix="/WEB-INF/jsp/" 
    p:suffix=".jsp" >
</bean>

The WEB-INF/classes and WEB-INF/lib folders mentioned in Wikipedia’s WAR files article are examples of folders required by the Servlet specification at runtime.

It is important to make the difference between the structure of a project and the structure of the resulting WAR file.

The structure of the project will in some cases partially reflect the structure of the WAR file (for static resources such as JSP files or HTML and JavaScript files, but this is not always the case.

The transition from the project structure into the resulting WAR file is done by a build process.

While you are usually free to design your own build process, nowadays most people will use a standardized approach such as Apache Maven. Among other things Maven defines defaults for which resources in the project structure map to what resources in the resulting artifact (the resulting artifact is the WAR file in this case). In some cases the mapping consists of a plain copy process in other cases the mapping process includes a transformation, such as filtering or compiling and others.

One example: The WEB-INF/classes folder will later contain all compiled java classes and resources (src/main/java and src/main/resources) that need to be loaded by the Classloader to start the application.

Another example: The WEB-INF/lib folder will later contain all jar files needed by the application. In a maven project the dependencies are managed for you and maven automatically copies the needed jar files to the WEB-INF/lib folder for you. That explains why you don’t have a lib folder in a maven project.