I fixed this by just deleting the commons-codec-repackaged.jar library from the modules directory. Now mine builds fine with the correct library, but I am wondering if I should do it differently, in the case that I deploy to another glassfish server that I don't control. Is there a way of making this portable (eg. somehow adding modules to the default Glassfish that overrides the classes in the commons-codec-repackaged.jar.) I am not using the maven .pom structure. I am not really Glassfish savvy. I try to let Netbeans do all the connecting for me whenever I can.
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