Have you tried/noticed different behavior between JTA and non-JTA entity managers.
If you are just after files system access you can configure it as an external jndi resource.
it is not really a no files rule, because you can access the file directly if you try, although there will be problems. As a architectural principle the application server provides resource management to the application. All of the applications resources should be provided by the application server, otherwise the server cannot guarantee the "cool stuff" thread management, network end points, portability , ha etc.
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