When you use the maven.genapp.repackage.dir properties and set it to . , the files contained in the maven.genapp.repackage directory are not < moved > to the new package directory, but copied in it, and steel in the base directory. Here is the template.properties file : maven.genapp.repackage.dir= maven.genapp.repackage=main/src/java,test/src/unit maven.genapp.filter=project.xml maven.genapp.default.package=com.saint-gobain.sgsi.my_application maven.genapp.filter=project.xml,main/src/webapp/WEB-INF/web.xml The content of "main/src/java" are not moved in "main/src/java/com/saint-gobain/sgsi/my_application" but copyed in it and steel in the "main/src/java" directory. If I put the main and test directory in a "src" directory, and remove the "maven.genapp.repackage.dir" propertie, everything works fine. You can find in attachment the template