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Application plan.xml files not being picked up

We are running WL12214 and many of our applications are running successfully with plan.xml files. Recently 2 application deployments are failing because the plan.xml entries are not replacing the web.xml entries. I have tried clearing the cache and tmp folders for both the managed server and the admin console, but still the plan.xml file will not be picked up. I have tried using the upload facility as well as copying the files manually, still no joy. The stage mode settings are the default settings and the files are being copied around. Is there anywhere else that I can check?

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