In Eclipse, if you are using the Java Web Development view, you'll have configured:
- A Tomcat Server runtime that provides the servlet libraries
- A Java Runtime
- Other required libraries
The Web App Libraries that are in the project duplicate the first setting, so that you don't need a local Tomcat installed on the development box.
The rest sounds messy to me.
You have your src / JavaSource folder with the raw Java files in it. They shouldn't be in Web Content - that's for your HTML, images, JSPs, etc.
So a typical project setup:
Project Name/
JavaSource/ or src/ // holds all the Java Source Files, Servlets, Struts Actions
WebContent/ // Nice root folder to hold web content files
content files and folders
WEB-INF/ // Web App Config folder
lib/ // Libraries (but not tomcat ones)
web.xml
classes/ // Where your compiled Java goes, and configs (log4j.properties)
Some people put the JSP inside WEB-INF too, as it isn't required to be accessible in the JSP file state, only in the compiled state that Tomcat does itself.