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This term refers to your application's root folder.
Your application root will have always have a subfolder called WEB-INF.
Consider the following folder structure, which contains 3 applications.
webapps/ MyApp/ (this is the application root for the MyApp application) index.jsp WEB-INF/ web.xml jsp-examples/ (this is the application root for the jsp-examples application) index.jsp WEB-INF/ web.xml ROOT/ (this is the application root for the ROOT application) index.jsp info.jsp images/ logo.jpg photo1.gif WEB-INF/ web.xml
Note that the Application Root is different to the ROOT Application, which is the main application for your site. The ROOT Application, like all applications, has an Application Root as well. In this case <webapps>/ROOT/.