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I will explain the context of ATG EAR file thought this concept is generic to any J2EE ear.
Any ATG EAR will have war files and atg_bootstrap_ejb.jar EJB jar.
In J2EE any class files or jars that is present in EJB will be available to all war files but the classes/jar which are in WAR file will be available only for that war file.
Other war files or ejb cannot access those classes present in other war files.
When jars added to build path, runAssembler will add those classes to atg_bootstrap_ejb.jar EJB which you can see it in atg_bootstrap_ejb.jar/META-INF/MANIFEST.MF file. Hence these jar or classes will be available to entire application.
If there are jars added in war/lib then those will not be available to other war or ejb files if present.
Refer below doc for more information on classpath