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Here is a temporary workaround* I found out:
- First, make sure all your Java EE eclipse projects match the proper Facets: if not, under Eclipse, right click on your project / properties / Project Facets: select the EJB for EJB modules, Web Application for WAR modules etc... ( note : if you don't have all the facets listed, you can still edit the Eclipse project file org.eclipse.wst.common.project.facet.core.xml located in +.settings+ folder of your project)
- Once the Facets are correct, right click on your EAR project / Properties / Deployment Assembly, and select the modules you want to integrate with your EAR.
- Now remotely deploy your ear: right click on your server / Add and Remove... / Select your ear and click ok.
Eclipse should now generate the EAR with a generated application.xml and deploy it properly.
Keep in mind this is a temporary solution, as the information of the modules embedded in the EAR are duplicate with the Maven pom.xml.
Still waiting for other users input.
You may also want to take a look at the Maven plug-in for Weblogic Server that supports deployment of applications to the server. The following links have more information: