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Prior to ArcGIS Server 9.3.1, to use a Server Object Extension (SOE), since ArcGIS Server Java Edition does not support SOE natively, as a workaround, an SOE would have to be created in .NET, the .dll would have to be registered, and it would have to be used in Java by generating proxies using proxy-gen.
But at 9.3.1, if the same workflow as 9.2/9.3 is used and the SOE is called using IServerObjectExtensionManager.findExtensionByTypeName, an exception is thrown in the Java code.
This can be solved by following the instructions below.