Symptoms:
An internal error occurred during: "Updating classpath container: project name".
java.lang.NullPointerException at org.eclipse.wst.common.componentcore.internal.resources.VirtualResource.removeLink(VirtualResource.java:300)Solution is to edit .project file by hand and to include these natures in appropriate tag (you'll find it):
<nature>org.eclipse.wst.common.project.facet.core.nature</nature> <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>