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There's a problem in 1.7.x (not in 1.6.x) that agent-jvm without classifier is actually the one with shaded libraries and it causes problems in Maven (has both shaded libraries and dependencies).
If you need agent - the library with proper manifest, you need org.jolokia:jolokia-agent-jvm library with javaagent Maven classifier:
This is from META-INF/MANIFEST.MF in jolokia-jvm-1.7.2 JAR
And this is from META-INF/MANIFEST.MF in jolokia-jvm-agent-2.0.2 JAR
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