How to remove classpath variables from WAS module

On our Dev box, our application module contains references to the `file:/apps/WebSphere61/systemApps/isclite.ear/` jar files and classpath entries. On our Prod box, however, it only contains the jar file containing all of our required classes. On Dev, this is causing a problem when using apache-commons-fileuploader as these classes are also references in the systemApps jar. How can we remove the systemApps library references from our application module's classpath? Websphere Application Server 6.1.0.17

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