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I guess the simplest solution would be to revert the file, upgrade and modify the file. From memory, the only thing that has changed in that file for JDK 6 recently is the package.access property.
Apparently only documented in the java.security file itself is a system property ("java.security.properties") that allows the contents of the file to be overridden. Also mentioned in the Appendix C title of this document: [How to Implement a Provider in the Java Cryptography Architecture|http://java.sun.com/javase/6/docs/technotes/guides/security/crypto/HowToImplAProvider.html]