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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?