Develop Reference

Eclipse - an error as occurred see the log file

So I was using eclipse and all of a sudden it got stuck and when I tried reopening it this error popped up and eclipse won't open.
here the latest of the log file:
!SESSION 2016-10-18 21:53:30.325
----------------------------------------------- eclipse.buildId=4.6.0.I20160606-1100 java.version=1.8.0_101
java.vendor=Oracle Corporation BootLoader constants: OS=win32,
ARCH=x86_64, WS=win32, NL=en_US Framework arguments: -product
org.eclipse.epp.package.java.product Command-line arguments: -os
win32 -ws win32 -arch x86_64 -product
org.eclipse.epp.package.java.product
!ENTRY org.eclipse.osgi 4 0 2016-10-18 21:53:32.667 !MESSAGE An error
occurred while automatically activating bundle
org.eclipse.core.resources (85). !STACK 0
org.osgi.framework.BundleException: Exception in
org.eclipse.core.resources.ResourcesPlugin.start() of bundle
org.eclipse.core.resources. at
org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:795)
at
org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:724)
at
org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:932)
at
org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:309)
at org.eclipse.osgi.container.Module.doStart(Module.java:581) at
org.eclipse.osgi.container.Module.start(Module.java:449) at
org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:470)
at
org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
at
org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:529)
at
org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:325)
at
org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:334)
at
org.eclipse.osgi.internal.loader.sources.SingleSourcePackage.loadClass(SingleSourcePackage.java:36)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:407)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:361)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:353)
at
org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:161)
at java.lang.ClassLoader.loadClass(Unknown Source) at
org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:139)
at
org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at
org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at
org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at
sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at
java.lang.reflect.Method.invoke(Unknown Source) at
org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:673) at
org.eclipse.equinox.launcher.Main.basicRun(Main.java:610) at
org.eclipse.equinox.launcher.Main.run(Main.java:1519) Caused by:
org.eclipse.core.internal.resources.ResourceException: Incompatible
file format. Workspace was saved with an incompatible version: 0. at
org.eclipse.core.internal.resources.WorkspaceTreeReader.getReader(WorkspaceTreeReader.java:59)
at
org.eclipse.core.internal.resources.WorkspaceTreeReader.getReader(WorkspaceTreeReader.java:67)
at
org.eclipse.core.internal.resources.SaveManager.restoreTree(SaveManager.java:1056)
at
org.eclipse.core.internal.resources.SaveManager.restore(SaveManager.java:719)
at
org.eclipse.core.internal.resources.SaveManager.startup(SaveManager.java:1587)
at
org.eclipse.core.internal.resources.Workspace.startup(Workspace.java:2399)
at
org.eclipse.core.internal.resources.Workspace.open(Workspace.java:2156)
at
org.eclipse.core.resources.ResourcesPlugin.start(ResourcesPlugin.java:464)
at
org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:774)
at
org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method) at
org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:767)
... 29 more Root exception:
org.eclipse.core.internal.resources.ResourceException: Incompatible
file format. Workspace was saved with an incompatible version: 0. at
org.eclipse.core.internal.resources.WorkspaceTreeReader.getReader(WorkspaceTreeReader.java:59)
at
org.eclipse.core.internal.resources.WorkspaceTreeReader.getReader(WorkspaceTreeReader.java:67)
at
org.eclipse.core.internal.resources.SaveManager.restoreTree(SaveManager.java:1056)
at
org.eclipse.core.internal.resources.SaveManager.restore(SaveManager.java:719)
at
org.eclipse.core.internal.resources.SaveManager.startup(SaveManager.java:1587)
at
org.eclipse.core.internal.resources.Workspace.startup(Workspace.java:2399)
at
org.eclipse.core.internal.resources.Workspace.open(Workspace.java:2156)
at
org.eclipse.core.resources.ResourcesPlugin.start(ResourcesPlugin.java:464)
at
org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:774)
at
org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method) at
org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:767)
at
org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:724)
at
org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:932)
at
org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:309)
at org.eclipse.osgi.container.Module.doStart(Module.java:581) at
org.eclipse.osgi.container.Module.start(Module.java:449) at
org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:470)
at
org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
at
org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:529)
at
org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:325)
at
org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:334)
at
org.eclipse.osgi.internal.loader.sources.SingleSourcePackage.loadClass(SingleSourcePackage.java:36)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:407)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:361)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:353)
at
org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:161)
at java.lang.ClassLoader.loadClass(Unknown Source) at
org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:139)
at
org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at
org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at
org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at
sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at
java.lang.reflect.Method.invoke(Unknown Source) at
org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:673) at
org.eclipse.equinox.launcher.Main.basicRun(Main.java:610) at
org.eclipse.equinox.launcher.Main.run(Main.java:1519)
!ENTRY org.eclipse.osgi 4 0 2016-10-18 21:53:32.682 !MESSAGE
Application error !STACK 1 java.lang.NoClassDefFoundError:
org/eclipse/core/resources/IContainer at
org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:139)
at
org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at
org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at
org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at
sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at
java.lang.reflect.Method.invoke(Unknown Source) at
org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:673) at
org.eclipse.equinox.launcher.Main.basicRun(Main.java:610) at
org.eclipse.equinox.launcher.Main.run(Main.java:1519) Caused by:
java.lang.ClassNotFoundException: An error occurred while
automatically activating bundle org.eclipse.core.resources (85). at
org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:116)
at
org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:529)
at
org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:325)
at
org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:334)
at
org.eclipse.osgi.internal.loader.sources.SingleSourcePackage.loadClass(SingleSourcePackage.java:36)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:407)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:361)
at
org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:353)
at
org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:161)
at java.lang.ClassLoader.loadClass(Unknown Source) ... 13 more
Caused by: org.osgi.framework.BundleException: Exception in
org.eclipse.core.resources.ResourcesPlugin.start() of bundle
org.eclipse.core.resources. at
org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:795)
at
org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:724)
at
org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:932)
at
org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:309)
at org.eclipse.osgi.container.Module.doStart(Module.java:581) at
org.eclipse.osgi.container.Module.start(Module.java:449) at
org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:470)
at
org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
... 22 more Caused by:
org.eclipse.core.internal.resources.ResourceException: Incompatible
file format. Workspace was saved with an incompatible version: 0. at
org.eclipse.core.internal.resources.WorkspaceTreeReader.getReader(WorkspaceTreeReader.java:59)
at
org.eclipse.core.internal.resources.WorkspaceTreeReader.getReader(WorkspaceTreeReader.java:67)
at
org.eclipse.core.internal.resources.SaveManager.restoreTree(SaveManager.java:1056)
at
org.eclipse.core.internal.resources.SaveManager.restore(SaveManager.java:719)
at
org.eclipse.core.internal.resources.SaveManager.startup(SaveManager.java:1587)
at
org.eclipse.core.internal.resources.Workspace.startup(Workspace.java:2399)
at
org.eclipse.core.internal.resources.Workspace.open(Workspace.java:2156)
at
org.eclipse.core.resources.ResourcesPlugin.start(ResourcesPlugin.java:464)
at
org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:774)
at
org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method) at
org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:767)
... 29 more

java.lang.NullPointerException: Application ID must not be null

I just faced this bug during eclipse plugin-development.
The said NullPointerException with a stacktrace of ~90.000 lines popped up when testing the plugin via "Launch eclipse application", where the plugin worked like a charm 5 min before.
I did not find anything useful when searching the web for this Exception.
The stacktrace does not even show a file from my plugin, only eclipse-internal files are listed.
Here parts of the stacktrace (The whole trace is to big to add it here)
org.osgi.framework.BundleException: Error loading bundle activator.
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:711)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1582)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1562)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1533)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1476)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:340)
Caused by: java.lang.ClassNotFoundException: An error occurred while automatically activating bundle org.eclipse.core.runtime (119).
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:116)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:531)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:324)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:320)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:395)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:345)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:337)
at org.eclipse.osgi.internal.framework.BundleContextImpl.loadBundleActivator(BundleContextImpl.java:754)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:706)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:454)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:531)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:324)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:320)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:395)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:345)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:337)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:568)
at org.eclipse.equinox.internal.ds.model.ServiceComponent.createInstance(ServiceComponent.java:493)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.createInstance(ServiceComponentProp.java:270)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:331)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
at org.eclipse.equinox.internal.ds.Resolver.buildNewlySatisfied(Resolver.java:473)
at org.eclipse.equinox.internal.ds.Resolver.enableComponents(Resolver.java:217)
at org.eclipse.equinox.internal.ds.SCRManager.performWork(SCRManager.java:816)
at org.eclipse.equinox.internal.ds.SCRManager$QueuedJob.dispatch(SCRManager.java:783)
at org.eclipse.equinox.internal.ds.WorkThread.run(WorkThread.java:89)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.osgi.framework.BundleException: Exception in org.eclipse.core.internal.runtime.PlatformActivator.start() of bundle org.eclipse.core.runtime.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:792)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:721)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:454)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
... 34 more
Caused by: java.lang.NoClassDefFoundError: org/eclipse/equinox/internal/app/CommandLineArgs
at org.eclipse.core.internal.runtime.PlatformActivator.startAppContainer(PlatformActivator.java:47)
at org.eclipse.core.internal.runtime.PlatformActivator.start(PlatformActivator.java:33)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:771)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:764)
... 41 more
Caused by: java.lang.ClassNotFoundException: An error occurred while automatically activating bundle org.eclipse.equinox.app (173).
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:116)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:531)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:324)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:320)
at org.eclipse.osgi.internal.loader.sources.SingleSourcePackage.loadClass(SingleSourcePackage.java:36)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:391)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:345)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:337)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 47 more
Caused by: org.osgi.framework.BundleException: Exception in org.eclipse.equinox.internal.app.Activator.start() of bundle org.eclipse.equinox.app.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:792)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:721)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:454)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
... 56 more
Caused by: java.lang.NullPointerException: Application ID must not be null!
at org.osgi.service.application.ApplicationDescriptor.<init>(ApplicationDescriptor.java:128)
at org.eclipse.equinox.internal.app.EclipseAppDescriptor.<init>(EclipseAppDescriptor.java:52)
at org.eclipse.equinox.internal.app.EclipseAppContainer.createAppDescriptor(EclipseAppContainer.java:186)
at org.eclipse.equinox.internal.app.EclipseAppContainer.registerAppDescriptors(EclipseAppContainer.java:272)
at org.eclipse.equinox.internal.app.EclipseAppContainer.start(EclipseAppContainer.java:99)
at org.eclipse.equinox.internal.app.Activator.addingService(Activator.java:134)
at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:941)
at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:1)
at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256)
at org.osgi.util.tracker.AbstractTracked.trackInitial(AbstractTracked.java:183)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:318)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:261)
at org.eclipse.equinox.internal.app.Activator.start(Activator.java:56)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:771)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:764)
... 63 more
Root exception:
java.lang.ClassNotFoundException: An error occurred while automatically activating bundle org.eclipse.core.runtime (119).
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:116)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:531)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:324)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:320)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:395)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:345)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:337)
at org.eclipse.osgi.internal.framework.BundleContextImpl.loadBundleActivator(BundleContextImpl.java:754)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:706)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:454)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:531)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:324)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:320)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:395)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:345)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:337)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:568)
at org.eclipse.equinox.internal.ds.model.ServiceComponent.createInstance(ServiceComponent.java:493)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.createInstance(ServiceComponentProp.java:270)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:331)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
at org.eclipse.equinox.internal.ds.Resolver.buildNewlySatisfied(Resolver.java:473)
at org.eclipse.equinox.internal.ds.Resolver.enableComponents(Resolver.java:217)
at org.eclipse.equinox.internal.ds.SCRManager.performWork(SCRManager.java:816)
at org.eclipse.equinox.internal.ds.SCRManager$QueuedJob.dispatch(SCRManager.java:783)
at org.eclipse.equinox.internal.ds.WorkThread.run(WorkThread.java:89)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.osgi.framework.BundleException: Exception in org.eclipse.core.internal.runtime.PlatformActivator.start() of bundle org.eclipse.core.runtime.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:792)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:721)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:454)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
... 34 more
Caused by: java.lang.NoClassDefFoundError: org/eclipse/equinox/internal/app/CommandLineArgs
at org.eclipse.core.internal.runtime.PlatformActivator.startAppContainer(PlatformActivator.java:47)
at org.eclipse.core.internal.runtime.PlatformActivator.start(PlatformActivator.java:33)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:771)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:764)
... 41 more
Caused by: java.lang.ClassNotFoundException: An error occurred while automatically activating bundle org.eclipse.equinox.app (173).
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:116)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:531)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:324)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:320)
at org.eclipse.osgi.internal.loader.sources.SingleSourcePackage.loadClass(SingleSourcePackage.java:36)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:391)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:345)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:337)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 47 more
Caused by: org.osgi.framework.BundleException: Exception in org.eclipse.equinox.internal.app.Activator.start() of bundle org.eclipse.equinox.app.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:792)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:721)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:454)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
... 56 more
Caused by: java.lang.NullPointerException: Application ID must not be null!
at org.osgi.service.application.ApplicationDescriptor.<init>(ApplicationDescriptor.java:128)
at org.eclipse.equinox.internal.app.EclipseAppDescriptor.<init>(EclipseAppDescriptor.java:52)
at org.eclipse.equinox.internal.app.EclipseAppContainer.createAppDescriptor(EclipseAppContainer.java:186)
at org.eclipse.equinox.internal.app.EclipseAppContainer.registerAppDescriptors(EclipseAppContainer.java:272)
at org.eclipse.equinox.internal.app.EclipseAppContainer.start(EclipseAppContainer.java:99)
at org.eclipse.equinox.internal.app.Activator.addingService(Activator.java:134)
at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:941)
at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:1)
at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256)
at org.osgi.util.tracker.AbstractTracked.trackInitial(AbstractTracked.java:183)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:318)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:261)
at org.eclipse.equinox.internal.app.Activator.start(Activator.java:56)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:771)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:764)
... 63 more

It looks like I caused the trouble myself by deleting one single line at the top of the file "plugin.xml". Here the correct beginning of the file:
<?xml version="1.0" encoding="UTF-8"?>
<?eclipse version="3.4"?>
<plugin>
<extension
id="application"
point="org.eclipse.core.runtime.applications">
...
If id="application" is missing, the plugin will produce the described Exception.

Eclipse not starting up after reinstalling (log included)

I made a dumb mistake telling GWT to use my User Data Path as the place or my web archive, so GWT went ahead and cleared it. I restored most of the data and downloaded Eclipse again. Now when I try to start Eclipse, I am allowed to choose my workspace (I created a brand new one and tried to use it) but afterwards it just crashes and tells me to take a look at my error log. The log contains the following informations:
!SESSION 2015-08-13 11:58:43.076 -----------------------------------------------
eclipse.buildId=4.4.2.M20150204-1700
java.version=1.8.0_51
java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=de_DE
Framework arguments: -product org.eclipse.epp.package.java.product
Command-line arguments: -os win32 -ws win32 -arch x86_64 -product
org.eclipse.epp.package.java.product
!ENTRY org.eclipse.osgi 4 0 2015-08-13 11:59:26.157
!MESSAGE An error occurred while automatically activating bundle org.eclipse.core.net (75).
!STACK 0
org.osgi.framework.BundleException: Exception in org.eclipse.core.internal.net.Activator.start() of bundle org.eclipse.core.net.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:792)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:721)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:454)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:531)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:324)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:320)
at org.eclipse.osgi.internal.loader.sources.SingleSourcePackage.loadClass(SingleSourcePackage.java:36)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:391)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:345)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:337)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.activateProxyService(IDEWorkbenchAdvisor.java:291)
at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.postStartup(IDEWorkbenchAdvisor.java:271)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2922)
at org.eclipse.ui.internal.Workbench.access$8(Workbench.java:2797)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:633)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:579)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:135)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:380)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:235)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:648)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:603)
at org.eclipse.equinox.launcher.Main.run(Main.java:1465)
Caused by: java.lang.IllegalArgumentException: Node path "Êþº¾ 4 )com/camelup/client/view/signup/SignUpView java/lang/Object &com/google/gwt/user/client/ui/IsWidget getInput ()Ljava/util" is not valid.
at org.eclipse.equinox.internal.security.storage.SecurePreferences.validatePath(SecurePreferences.java:361)
at org.eclipse.equinox.internal.security.storage.SecurePreferences.node(SecurePreferences.java:95)
at org.eclipse.equinox.internal.security.storage.SecurePreferencesRoot.load(SecurePreferencesRoot.java:152)
at org.eclipse.equinox.internal.security.storage.SecurePreferencesRoot.<init>(SecurePreferencesRoot.java:84)
at org.eclipse.equinox.internal.security.storage.SecurePreferencesMapper.open(SecurePreferencesMapper.java:101)
at org.eclipse.equinox.internal.security.storage.SecurePreferencesMapper.getDefault(SecurePreferencesMapper.java:46)
at org.eclipse.equinox.security.storage.SecurePreferencesFactory.getDefault(SecurePreferencesFactory.java:49)
at org.eclipse.core.internal.net.ProxyType.getNode(ProxyType.java:523)
at org.eclipse.core.internal.net.ProxyType.loadProxyAuth(ProxyType.java:533)
at org.eclipse.core.internal.net.ProxyType.createProxyData(ProxyType.java:138)
at org.eclipse.core.internal.net.ProxyType.getProxyData(ProxyType.java:127)
at org.eclipse.core.internal.net.PreferenceManager.migrateInstanceScopePreferences(PreferenceManager.java:292)
at org.eclipse.core.internal.net.PreferenceManager.migrate(PreferenceManager.java:260)
at org.eclipse.core.internal.net.ProxyManager.checkMigrated(ProxyManager.java:404)
at org.eclipse.core.internal.net.ProxyManager.initialize(ProxyManager.java:269)
at org.eclipse.core.internal.net.Activator.start(Activator.java:181)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:771)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:764)
... 39 more
Root exception:
java.lang.IllegalArgumentException: Node path "Êþº¾ 4 )com/camelup/client/view/signup/SignUpView java/lang/Object &com/google/gwt/user/client/ui/IsWidget getInput ()Ljava/util" is not valid.
at org.eclipse.equinox.internal.security.storage.SecurePreferences.validatePath(SecurePreferences.java:361)
at org.eclipse.equinox.internal.security.storage.SecurePreferences.node(SecurePreferences.java:95)
at org.eclipse.equinox.internal.security.storage.SecurePreferencesRoot.load(SecurePreferencesRoot.java:152)
at org.eclipse.equinox.internal.security.storage.SecurePreferencesRoot.<init>(SecurePreferencesRoot.java:84)
at org.eclipse.equinox.internal.security.storage.SecurePreferencesMapper.open(SecurePreferencesMapper.java:101)
at org.eclipse.equinox.internal.security.storage.SecurePreferencesMapper.getDefault(SecurePreferencesMapper.java:46)
at org.eclipse.equinox.security.storage.SecurePreferencesFactory.getDefault(SecurePreferencesFactory.java:49)
at org.eclipse.core.internal.net.ProxyType.getNode(ProxyType.java:523)
at org.eclipse.core.internal.net.ProxyType.loadProxyAuth(ProxyType.java:533)
at org.eclipse.core.internal.net.ProxyType.createProxyData(ProxyType.java:138)
at org.eclipse.core.internal.net.ProxyType.getProxyData(ProxyType.java:127)
at org.eclipse.core.internal.net.PreferenceManager.migrateInstanceScopePreferences(PreferenceManager.java:292)
at org.eclipse.core.internal.net.PreferenceManager.migrate(PreferenceManager.java:260)
at org.eclipse.core.internal.net.ProxyManager.checkMigrated(ProxyManager.java:404)
at org.eclipse.core.internal.net.ProxyManager.initialize(ProxyManager.java:269)
at org.eclipse.core.internal.net.Activator.start(Activator.java:181)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:771)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:764)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:721)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:936)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:319)
at org.eclipse.osgi.container.Module.doStart(Module.java:571)
at org.eclipse.osgi.container.Module.start(Module.java:439)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:454)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:531)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:324)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:320)
at org.eclipse.osgi.internal.loader.sources.SingleSourcePackage.loadClass(SingleSourcePackage.java:36)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:391)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:345)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:337)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.activateProxyService(IDEWorkbenchAdvisor.java:291)
at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.postStartup(IDEWorkbenchAdvisor.java:271)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2922)
at org.eclipse.ui.internal.Workbench.access$8(Workbench.java:2797)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:633)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:579)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:135)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:380)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:235)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:648)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:603)
at org.eclipse.equinox.launcher.Main.run(Main.java:1465)
!ENTRY org.eclipse.osgi 4 0 2015-08-13 11:59:26.209
!MESSAGE Application error
!STACK 1
java.lang.NoClassDefFoundError: An error occurred while automatically activating bundle org.eclipse.core.net (75).
at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.activateProxyService(IDEWorkbenchAdvisor.java:291)
at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.postStartup(IDEWorkbenchAdvisor.java:271)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2922)
at org.eclipse.ui.internal.Workbench.access$8(Workbench.java:2797)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:633)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:579)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:135)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:380)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:235)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:648)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:603)
at org.eclipse.equinox.launcher.Main.run(Main.java:1465)
Thank you in advance for your help.
Edit: I did not add any Files to the new Workspace so far

It seems this is compatibility issue.
Please make sure you are using same bit version 64 bit or 32 bit type of jdk and eclipse.

So heres the answer:
I deleted the file inside of C:\Users\myUserName.eclipse\org.eclipse.equinox.security which was named something like secure_storage. That did the trick and I can start Eclipse again now :)

java.lang.NoClassDefFoundError: javax/persistence/EntityListeners

Does anyone know what this error?
java.lang.ExceptionInInitializerError
at presentation.utils.HibernateCommon.buildSessionFactory(HibernateCommon.java:39)
at presentation.utils.HibernateCommon.<clinit>(HibernateCommon.java:19)
at filter.HibernateSessionRequestFilter.init(HibernateSessionRequestFilter.java:28)
at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:275)
at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:397)
at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:108)
at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:3709)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4363)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:525)
at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:627)
at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:553)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:488)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1149)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:719)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
at org.apache.catalina.core.StandardService.start(StandardService.java:516)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
at org.apache.catalina.startup.Catalina.start(Catalina.java:578)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:288)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:413)
Caused by: java.lang.NoClassDefFoundError: javax/persistence/EntityListeners
at
org.hibernate.cfg.annotations.reflection.JPAMetadataProvider.getDefaults(JPAMetadataProvider.java:96)
at org.hibernate.annotations.common.reflection.java.JavaReflectionManager.getDefaults(JavaReflectionManager.java:226)
at org.hibernate.cfg.Configuration.secondPassCompile(Configuration.java:1358)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1829)
at presentation.utils.HibernateCommon.buildSessionFactory(HibernateCommon.java:35)
... 29 more
Caused by: java.lang.ClassNotFoundException: javax.persistence.EntityListeners
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1387)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1233)
... 34 more

You have to add the javax.persistence.jar to your classpath.

Click Here to download hibernate-jpa-2.0-api-1.0.1.Final.jar and put it into the project library, your application will work fine.

What is wrong with my GMF generated diagram code?

I have generated a non-RCP diagram editor with GMF. My Eclipse version is: Indigo Service Release 2. When I would like to Run as an Eclipse Application it fails and the following error log is generated:
!SESSION 2013-07-19 10:53:52.410 -----------------------------------------------
eclipse.buildId=M20120208-0800
java.version=1.7.0_25
java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=en_US
Framework arguments: -product org.eclipse.platform.ide
Command-line arguments: -product org.eclipse.platform.ide -data C:\Users\Peter\Coding\EclipseIndigo/../runtime-EclipseApplication -dev file:C:/Users/Peter/Coding/EclipseIndigo/.metadata/.plugins/org.eclipse.pde.core/QSTools plugin old/dev.properties -os win32 -ws win32 -arch x86_64 -consoleLog
!ENTRY org.eclipse.osgi 2 0 2013-07-19 10:53:55.250
!MESSAGE One or more bundles are not resolved because the following root constraints are not resolved:
!SUBENTRY 1 org.eclipse.osgi 2 0 2013-07-19 10:53:55.250
!MESSAGE Bundle reference:file:/C:/Users/Peter/Coding/EclipseIndigo/com.qs.qsmodel.diagram/ was not resolved.
!SUBENTRY 2 com.qs.qsmodel.diagram 2 0 2013-07-19 10:53:55.250
!MESSAGE Missing required bundle org.eclipse.gmf.tooling.runtime_0.0.0.
!ENTRY org.eclipse.osgi 2 0 2013-07-19 10:53:55.255
!MESSAGE The following is a complete list of bundles which are not resolved, see the prior log entry for the root cause if it exists:
!SUBENTRY 1 org.eclipse.osgi 2 0 2013-07-19 10:53:55.255
!MESSAGE Bundle com.qs.qsmodel.diagram_1.0.0.qualifier [488] was not resolved.
!SUBENTRY 2 com.qs.qsmodel.diagram 2 0 2013-07-19 10:53:55.255
!MESSAGE Missing required bundle org.eclipse.gmf.tooling.runtime_0.0.0.
!ENTRY org.eclipse.osgi 4 0 2013-07-19 10:53:55.269
!MESSAGE An error occurred while automatically activating bundle org.eclipse.ui.workbench (439).
!STACK 0
org.osgi.framework.BundleException: The activator org.eclipse.ui.internal.WorkbenchPlugin for bundle org.eclipse.ui.workbench is invalid
at org.eclipse.osgi.framework.internal.core.AbstractBundle.loadBundleActivator(AbstractBundle.java:171)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(BundleContextImpl.java:679)
at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(BundleHost.java:381)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(AbstractBundle.java:299)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:440)
at org.eclipse.osgi.internal.loader.BundleLoader.setLazyTrigger(BundleLoader.java:268)
at org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:463)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:400)
at org.eclipse.osgi.internal.loader.SingleSourcePackage.loadClass(SingleSourcePackage.java:35)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:473)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:429)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:417)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2483)
at java.lang.Class.getConstructor0(Class.java:2793)
at java.lang.Class.newInstance(Class.java:345)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:184)
at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:905)
at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:191)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
at org.eclipse.equinox.launcher.Main.main(Main.java:1386)
Caused by: java.lang.NoClassDefFoundError: org/eclipse/swt/SWTError
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2483)
at java.lang.Class.getConstructor0(Class.java:2793)
at java.lang.Class.newInstance(Class.java:345)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.loadBundleActivator(AbstractBundle.java:166)
... 36 more
Caused by: java.lang.ClassNotFoundException: org.eclipse.swt.SWTError
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:513)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:429)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:417)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 41 more
Root exception:
java.lang.NoClassDefFoundError: org/eclipse/swt/SWTError
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2483)
at java.lang.Class.getConstructor0(Class.java:2793)
at java.lang.Class.newInstance(Class.java:345)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.loadBundleActivator(AbstractBundle.java:166)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(BundleContextImpl.java:679)
at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(BundleHost.java:381)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(AbstractBundle.java:299)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:440)
at org.eclipse.osgi.internal.loader.BundleLoader.setLazyTrigger(BundleLoader.java:268)
at org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:463)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:400)
at org.eclipse.osgi.internal.loader.SingleSourcePackage.loadClass(SingleSourcePackage.java:35)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:473)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:429)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:417)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2483)
at java.lang.Class.getConstructor0(Class.java:2793)
at java.lang.Class.newInstance(Class.java:345)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:184)
at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:905)
at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:191)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
at org.eclipse.equinox.launcher.Main.main(Main.java:1386)
Caused by: java.lang.ClassNotFoundException: org.eclipse.swt.SWTError
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:513)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:429)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:417)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 41 more
!ENTRY org.eclipse.osgi 2 0 2013-07-19 10:53:55.291
!MESSAGE One or more bundles are not resolved because the following root constraints are not resolved:
!SUBENTRY 1 org.eclipse.osgi 2 0 2013-07-19 10:53:55.292
!MESSAGE Bundle reference:file:/C:/Users/Peter/Coding/EclipseIndigo/com.qs.qsmodel.diagram/ was not resolved.
!SUBENTRY 2 com.qs.qsmodel.diagram 2 0 2013-07-19 10:53:55.292
!MESSAGE Missing required bundle org.eclipse.gmf.tooling.runtime_0.0.0.
!ENTRY org.eclipse.osgi 2 0 2013-07-19 10:53:55.294
!MESSAGE The following is a complete list of bundles which are not resolved, see the prior log entry for the root cause if it exists:
!SUBENTRY 1 org.eclipse.osgi 2 0 2013-07-19 10:53:55.294
!MESSAGE Bundle com.qs.qsmodel.diagram_1.0.0.qualifier [488] was not resolved.
!SUBENTRY 2 com.qs.qsmodel.diagram 2 0 2013-07-19 10:53:55.294
!MESSAGE Missing required bundle org.eclipse.gmf.tooling.runtime_0.0.0.
!ENTRY org.eclipse.osgi 4 0 2013-07-19 10:53:55.298
!MESSAGE Application error
!STACK 1
org.eclipse.core.runtime.CoreException: Plug-in "org.eclipse.ui.ide.application" was unable to instantiate class "org.eclipse.ui.internal.ide.application.IDEApplication".
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException(RegistryStrategyOSGI.java:194)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:188)
at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:905)
at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:191)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
at org.eclipse.equinox.launcher.Main.main(Main.java:1386)
Caused by: java.lang.NoClassDefFoundError: org/eclipse/ui/application/WorkbenchAdvisor
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2483)
at java.lang.Class.getConstructor0(Class.java:2793)
at java.lang.Class.newInstance(Class.java:345)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:184)
... 16 more
Caused by: org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter$TerminatingClassNotFoundException: An error occurred while automatically activating bundle org.eclipse.ui.workbench (439).
at org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:122)
at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:463)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:400)
at org.eclipse.osgi.internal.loader.SingleSourcePackage.loadClass(SingleSourcePackage.java:35)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:473)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:429)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:417)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 21 more
Caused by: org.osgi.framework.BundleException: The activator org.eclipse.ui.internal.WorkbenchPlugin for bundle org.eclipse.ui.workbench is invalid
at org.eclipse.osgi.framework.internal.core.AbstractBundle.loadBundleActivator(AbstractBundle.java:171)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(BundleContextImpl.java:679)
at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(BundleHost.java:381)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(AbstractBundle.java:299)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:440)
at org.eclipse.osgi.internal.loader.BundleLoader.setLazyTrigger(BundleLoader.java:268)
at org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:107)
... 30 more
Caused by: java.lang.NoClassDefFoundError: org/eclipse/swt/SWTError
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2483)
at java.lang.Class.getConstructor0(Class.java:2793)
at java.lang.Class.newInstance(Class.java:345)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.loadBundleActivator(AbstractBundle.java:166)
... 36 more
Caused by: java.lang.ClassNotFoundException: org.eclipse.swt.SWTError
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:513)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:429)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:417)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 41 more

I have checked the org.eclipse.swt and the org.eclipse.core.net bundles at the Run as Eclipse application configurations and it works now.
Remark: it is worth enabling Validate plug-ins automatically prior to launching (Run configurations->Plug-ins>Validate plug-ins automatically prior to launching tick)