Tomcat application deployment

I was reading Tomcat application developer's guide:
http://tomcat.apache.org/tomcat-5.5-doc/appdev/deployment.html

Under the topic "Standard Directory Layout" it is said that:

When you install an application into Tomcat (or any other 2.2/2.3-compatible server), the classes in the WEB-INF/classes/ directory, as well as all classes in JAR files found in the WEB-INF/lib/ directory, are made visible to other classes within your particular web application. Thus, if you include all of the required library classes in one of these places (be sure to check licenses for redistribution rights for any third party libraries you utilize), you will simplify the installation of your web application -- no adjustment to the system class path (or installation of global library files in your server) will be necessary.

"are made visible to other classes within your particular web application".
What other classe are these, and where are they?
Dont the class files and the jar files make the application classes?

Yes, what it means is that you need to put them there, otherwise they are not visible.

Also don't forget that if you are using some framework there may be further directories etc.