Can you elaborate more about your scenario? What do you mean by "This is a fully provisioned app, not icenium." ,
are you using Icenium or not?
What 3rd party plugins are you using?.
About the plugins in config.xml those are there for Cordova 2.* compatibility. Those are not respected for 3.*, because each plugin (selected from project properties) knows how to add its things to the final config.xml.
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