Why do you want to have a .java source code file in the classpath? Classpath is only used by the JVM to load compiled classes.
Compiled classes that are used in web application
servlets and
JSP must be stored according to the servlet API conventions.
Also, I think
Tomcat 3 and Tomcat 4 have different conventions about how Tomcat picks up classes that are available to the whole system.
Bill