My ear pom.xml contains this configuration: <build> <plugins> <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-ear-plugin</artifactId> <configuration> <modules> <!-- Internal dependencies --> <jarModule> <groupId>org.drools.solver.examples</groupId> <artifactId>examination-domain</artifactId> <bundleFileName>examination-domain.jar</bundleFileName> <includeInApplicationXml>true</includeInApplicationXml> </jarModule> <ejbModule> <groupId>org.drools.solver.examples</groupId> <artifactId>examination-business</artifactId> <bundleFileName>examination-business.jar</bundleFileName> </ejbModule> <webModule> <groupId>org.drools.solver.examples</groupId> <artifactId>examination-web</artifactId> <bundleFileName>examination-web.jar</bundleFileName> <contextRoot>/messor-web</contextRoot> </webModule> <!-- Global libs --> <jarModule> <groupId>org.jboss.seam</groupId> <artifactId>jboss-seam</artifactId> <bundleFileName>jboss-seam.jar</bundleFileName> <includeInApplicationXml>true</includeInApplicationXml> </jarModule> <jarModule> <groupId>org.jboss.el</groupId> <artifactId>jboss-el</artifactId> <bundleFileName>jboss-el.jar</bundleFileName> <includeInApplicationXml>true</includeInApplicationXml> </jarModule> </modules> </configuration> </plugin> </plugins> </build> Everytime I use the maven synchronization feature, IntelliJ ignores the above configuration and overwrites working iml's with not working iml's.