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The exclude and the include is applied separately and the results of each are combined together to create the list of paths OpenEJB will scrape for annotations.
Note by default these settings will only affect which jars OpenEJB will scan for annotated components when no descriptor is found. If you would like to use these settings to also filter out jars to do contain descriptors, set the openejb.deployments.classpath.filter.descriptors property to true. The default is false.