The eclipse plugin automatically adds the java nature/builder as the first entry for each project. Anyway, sometime you will need to add more builders and in a different order. Specifying an addictional java builder in project properties, however, lead to a duplicate entries in .project. The problem is discussed at: http://www.eclipse.org/webtools/jst/components/j2ee/scenarios/MavenEclipseIntegration.html snippet: "Create a file project.properties under the csrweb folder, the folder where you will find project.xml. Now add the following in this file. maven.eclipse.projectnatures=org.eclipse.jst.j2ee.web.WebNature,org.eclipse.jdt.core.javanature,org.eclipse.wst.common.modulecore.ModuleCoreNature maven.eclipse.buildcommands=org.eclipse.wst.common.modulecore.DeployableModuleBuilder,org.eclipse.jdt.core.javabuilder,org.eclipse.jst.j2ee.web.LibDirBuilder,org.eclipse.wst.validation.validationbuilder,org.eclipse.jst.j2ee.LibCopyBuilder,org.eclipse.wst.common.modulecore.LocalDependencyResolver ... Open the .project and remove the first buildcommand javabuilder and the first nature org.eclipse.jdt.core.javanature. This is done to ensure that only one entry of javabuilder and org.eclipse.jdt.core.javanature exists. The correct order of builder and natures are needed to ensure proper functionality " This patch solves the problem avoiding addictional javabuilders and javanatures if they are already present in the list specified using project.properties. If maven.eclipse.projectnatures and maven.eclipse.buildcommands don't contain a such entry, everything works as before. The patch also contains a new specific plugin test.