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 my 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.myapplication maven.genapp.filter=project.xml,main/src/webapp/WEB-INF/web.xml Here is my template directory tree : Main - conf - sql - src o java * coordination * model * service o resources o webapp Test - src o resources o unit Here is the result : Main - conf - sql - src o java * com * saint-gobain o sgsi * myapplication * coordination * model * service * coordination * model * service o resources o webapp Test - src o resources o unit When I put the main and test directory in a src directory, and remove the maven.genapp.repackage.dir, everything works fine.