Josef,
the root of this issue is the following exception:
Code:
!ENTRY org.eclipse.core.jobs 4 2 2009-07-28 08:31:13.062
!MESSAGE An internal error occurred during: "Initializing Java Tooling".
!STACK 0
java.lang.ArrayIndexOutOfBoundsException: 2
at org.eclipse.emf.common.util.BasicEList.assign(BasicEList.java:124)
at org.eclipse.emf.common.util.BasicEList.addUnique(BasicEList.java:424)
at org.eclipse.emf.common.util.AbstractEList.add(AbstractEList.java:307)
at org.eclipse.emf.common.notify.impl.BasicNotifierImpl$EAdapterList.add(BasicNotifierImpl.java:142)
at org.eclipse.wst.common.componentcore.internal.StructureEdit.getEclipseResource(StructureEdit.java:251)
at org.eclipse.wst.common.componentcore.internal.impl.ResourceTreeNode.findMatchingVirtualPathsSet(ResourceTreeNode.java:195)
at org.eclipse.wst.common.componentcore.internal.impl.ResourceTreeNode.findModuleResourcesSet(ResourceTreeNode.java:178)
at org.eclipse.wst.common.componentcore.internal.impl.ResourceTreeNode.findModuleResources(ResourceTreeNode.java:143)
at org.eclipse.wst.common.componentcore.internal.resources.VirtualResource.getProjectRelativePaths(VirtualResource.java:132)
at org.eclipse.wst.common.componentcore.internal.resources.VirtualFile.getUnderlyingFiles(VirtualFile.java:104)
at org.eclipse.wst.common.componentcore.internal.resources.VirtualFile.getUnderlyingResources(VirtualFile.java:93)
at org.eclipse.wst.common.componentcore.internal.resources.VirtualResource.exists(VirtualResource.java:88)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.getManifestClasspath(J2EEModuleVirtualComponent.java:146)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.getManifestReferences(J2EEModuleVirtualComponent.java:291)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.getReferences(J2EEModuleVirtualComponent.java:103)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.update(J2EEComponentClasspathContainer.java:158)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.install(J2EEComponentClasspathContainer.java:297)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathInitializer.initialize(J2EEComponentClasspathInitializer.java:29)
at org.eclipse.jdt.internal.core.JavaModelManager.initializeContainer(JavaModelManager.java:2608)
at org.eclipse.jdt.internal.core.JavaModelManager$11.run(JavaModelManager.java:2514)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1800)
at org.eclipse.jdt.internal.core.JavaModelManager.initializeAllContainers(JavaModelManager.java:2554)
at org.eclipse.jdt.internal.core.JavaModelManager.getClasspathContainer(JavaModelManager.java:1773)
at org.eclipse.jdt.core.JavaCore.getClasspathContainer(JavaCore.java:2652)
at org.eclipse.jdt.internal.core.JavaProject.resolveClasspath(JavaProject.java:2561)
at org.eclipse.jdt.internal.core.JavaProject.resolveClasspath(JavaProject.java:2662)
at org.eclipse.jdt.internal.core.JavaProject.getResolvedClasspath(JavaProject.java:1861)
at org.eclipse.jdt.internal.core.JavaProject.buildStructure(JavaProject.java:424)
at org.eclipse.jdt.internal.core.Openable.generateInfos(Openable.java:258)
at org.eclipse.jdt.internal.core.JavaElement.openWhenClosed(JavaElement.java:515)
at org.eclipse.jdt.internal.core.JavaElement.getElementInfo(JavaElement.java:252)
at org.eclipse.jdt.internal.core.JavaElement.getElementInfo(JavaElement.java:238)
at org.eclipse.jdt.internal.core.JavaElement.getChildren(JavaElement.java:193)
at org.eclipse.jdt.internal.core.JavaProject.getPackageFragmentRoots(JavaProject.java:1756)
at org.eclipse.jst.j2ee.internal.project.J2EEProjectUtilities.getSourceContainers(J2EEProjectUtilities.java:858)
at org.eclipse.jst.j2ee.internal.project.J2EEProjectUtilities.getOutputContainers(J2EEProjectUtilities.java:895)
at org.eclipse.jst.j2ee.internal.project.J2EEProjectUtilities.getAllOutputContainers(J2EEProjectUtilities.java:931)
at org.eclipse.jst.j2ee.internal.classpathdep.ClasspathDependencyValidator$ClasspathDependencyValidatorData.<init>(ClasspathDependencyValidator.java:222)
at org.eclipse.jst.j2ee.classpathdep.ClasspathDependencyUtil.getComponentClasspathDependencies(ClasspathDependencyUtil.java:266)
at org.eclipse.jst.j2ee.classpathdep.ClasspathDependencyUtil.getComponentClasspathDependencies(ClasspathDependencyUtil.java:247)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.getJavaClasspathReferences(J2EEModuleVirtualComponent.java:199)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.getNonManifestReferences(J2EEModuleVirtualComponent.java:133)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.getReferences(J2EEModuleVirtualComponent.java:100)
at org.eclipse.jst.j2ee.componentcore.J2EEModuleVirtualComponent.getReferences(J2EEModuleVirtualComponent.java:96)
at org.eclipse.jst.common.jdt.internal.classpath.FlexibleProjectContainer.computeClasspathEntries(FlexibleProjectContainer.java:181)
at org.eclipse.jst.common.jdt.internal.classpath.FlexibleProjectContainer.<init>(FlexibleProjectContainer.java:122)
at org.eclipse.jst.j2ee.internal.web.classpath.WebAppLibrariesContainer.<init>(WebAppLibrariesContainer.java:48)
at org.eclipse.jst.j2ee.internal.web.classpath.WebAppLibrariesContainerInitializer.initialize(WebAppLibrariesContainerInitializer.java:34)
at org.eclipse.jdt.internal.core.JavaModelManager.initializeContainer(JavaModelManager.java:2608)
at org.eclipse.jdt.internal.core.JavaModelManager$11.run(JavaModelManager.java:2514)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1800)
at org.eclipse.jdt.internal.core.JavaModelManager.initializeAllContainers(JavaModelManager.java:2554)
at org.eclipse.jdt.internal.core.JavaModelManager.getClasspathContainer(JavaModelManager.java:1773)
at org.eclipse.jdt.core.JavaCore.initializeAfterLoad(JavaCore.java:3410)
at org.eclipse.jdt.internal.ui.InitializeAfterLoadJob$RealJob.run(InitializeAfterLoadJob.java:35)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
This exception is not related to STS. We'll need to investigate what is causing this.
Christian