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answers:

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I have a jar on the classpath which contains a hibernate.properties. This causes problems when my app starts because hibernate tries to use the settings from this file. Is there a way to explicitly specify the file that hibernate should look for, or tell it to ignore the properties file in the dependency jar?

A: 

Put the "right" hibernate.properties on the class path in front of the JAR containing the "unwanted" one.

Pascal Thivent
I'm not using hibernate.properties to configure my app so I don't have a "right" one to move up in the classpath. But, your suggestion got me thinking so I created an empty hibernate.properties that gets picked up first. Thanks for the reply.
Adam B