I don't know enough about Glassfish to comment on using the classpath, but WARs are a standard zip format, you should be able to easily un-WAR all of the WARs, and if you know where it is looking for the files, you can put them in the correct path inside the WAR.
My first guess would be "/WEB-INF/classes/configuration/config.xml"
I believe Glassfish is able to deploy an exploded war (the unzipped directory structure, with a .war extension in the folder name) if it is on the same filesystem as the Glassfish server. You could test this configuration that way, and once it works, re-create the zipped WAR
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