JReFrameworker
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Investigate dealing with signed JARs
So far Oracle/OpenJDK haven't been signing rt.jar, but if they did or if the user was editing a signed JAR then it's probably best to unsign the JAR and then let the user decide how to resign it with a newly generated key or a store key.
Jars are automatically unsigned as of c1032b3f855b67d2192242ac6ca9a257ce5283c0 if they have changed since they would otherwise be identified as corrupted jars and fail to execute. A feature to resign and seal with a custom key store would be nice.