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Ok. I've found root of the problem and it's looks like bug to me. But not in weld
org.glassfish.weld.BeanDeploymentArchiveImpl contains set of uris for bean.xml file that discovered in currently deployed module (i.e. ejb or war of ear), this set always contain at most one value (even I have several modules which has beans.xml inside) and this value was pointing to wrong beans.xml file. Basically it took file from non-ejb jar that happen to contain it's own beans.xml. I have found issue that fix this problem https://java.net/jira/browse/GLASSFISH-19406 but unfortunately it is only resolved for glassfish 4.0.
In case of several "bean.xml" files found inside single ear - what should be correct behavior from weld side? Will it merge this files somehow. In which order?