I don't understand why this is difficult?
You already know the root you are visiting from the getClassPath(),
so isn't it just a case of removing it.
Of course, some of the roots maybe nested inside the root you are visiting
(nested deployments), but it should be fairly easy to detect this and ignore
them since you will visit that specific root anyway?
i.e. in your example where you have
jms.rar/jms.jar/package/some.class
So the roots in the getClassPath() woud be
jms.rar
jms.rar/jms.jar
When visiting jms.rar you would ignore the jms.rar/jms.jar because that is in the
classpath.
When you visit jms.rar/jms.rar you simply remove the root from the path:
{jms.rar/jms.jar/}package/some.class
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