I am trying to remove a file from a dependency jar that I am including in my war file in maven. I am deploying the war to JBoss 5.1 and the jar in question contains a persis
You can achieve this with the TrueZIP Maven Plugin.
This should work for your use case:
org.codehaus.mojo truezip-maven-plugin 1.1 remove-a-file-in-sub-archive remove package target/my-webapp.war/WEB-INF/lib/dependency.jar/META-INF persistence.xml
Also see the examples.