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Yes, this is a known problem for the enterprise edition.
There seems to be two problems:
A - finding the transport.xml
B - finding the protocol implementation classes themselves
For A, it checks for current working directory. So one fix would be to copy transport.xml to the caller's working directory. For example, in this case it is called by the driver, you can try the web app home directory.
For B, it simply a matter of putting the oracle.edge.tools.transport implementation classes in your class path. Eith in the lib of the web-inf, or JVM lib, or add to the current paths.
Hope this helps.