Isolation, while handy, is not infallible. Let's say that class A uses class B 
which in turn uses class C. Classes A and C are in your isolated EAR. Classes B 
and C are in the lib directory. You now have a problem because the "C" you are 
using is from the lib directory, not the EAR. The solution to this situation is 
to also package B within the EAR. In many cases this is possible, in some cases 
it is not, especially if the standard Java EE libraries are involved.

One way to resolve such situations is to set the -verbose:class JVM 
command-line option. This option causes the classloaders to print out each 
class loaded and the JAR file the class came from. This might help solve the 
isolation issue.

As far as the Maven transitive dependencies go, I cannot think of any way 
around it that would not be more painful. 

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