One of the good things about working with Java is that there are an abundance of open source projects to help structure your application. These are valuable when your application starts to grow beyond a handful of pages. Although these can be a burden to learn they are an advantage when working in teams. Even though doing your own thing to organize a complex web application may appeal to you, whoever has to pick up and understand your work will appreciate the use of a framework that is already established and documented.
Two of the most popular web frameworks are Apache Struts54 and Spring Web Flow55. The emphasis of these projects is to organize the web application in a Model-View-Controller pattern.
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