Eclipse RCP application - cant build project - eclipse

Question

My Eclipse RCP project stopped running and i havent changed anything. I have two run configurations, one is .product and another one is application (both had run before problem occured).
When i try to run .product configuration, build is terminated without any log in console (i tried to run debugger but it is terminated somewhere inside native code).
When i try to run .application configuration, there is a lot of errors in console:
!ENTRY org.eclipse.ui.workbench 4 2 2015-12-30 08:00:41.367
!MESSAGE Problems occurred when invoking code from plug-in: "org.eclipse.ui.workbench".
!STACK 1
org.eclipse.core.runtime.CoreException: Plug-in "org.eclipse.swtbot.eclipse.ui" was unable to instantiate class "org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer".
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException(RegistryStrategyOSGI.java:194)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:186)
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.ui.internal.WorkbenchPlugin$1.run(WorkbenchPlugin.java:293)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at org.eclipse.ui.internal.WorkbenchPlugin.createExtension(WorkbenchPlugin.java:288)
at org.eclipse.ui.internal.EarlyStartupRunnable.getExecutableExtension(EarlyStartupRunnable.java:120)
at org.eclipse.ui.internal.EarlyStartupRunnable.run(EarlyStartupRunnable.java:68)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.ui.internal.Workbench$56.run(Workbench.java:2812)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Caused by: java.lang.NullPointerException
at org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer.<init>(PreferenceInitializer.java:46)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:184)
... 11 more
!SUBENTRY 1 org.eclipse.equinox.registry 4 1 2015-12-30 08:00:41.368
!MESSAGE Plug-in "org.eclipse.swtbot.eclipse.ui" was unable to instantiate class "org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer".
!STACK 0
java.lang.NullPointerException
at org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer.<init>(PreferenceInitializer.java:46)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
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.ui.internal.WorkbenchPlugin$1.run(WorkbenchPlugin.java:293)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at org.eclipse.ui.internal.WorkbenchPlugin.createExtension(WorkbenchPlugin.java:288)
at org.eclipse.ui.internal.EarlyStartupRunnable.getExecutableExtension(EarlyStartupRunnable.java:120)
at org.eclipse.ui.internal.EarlyStartupRunnable.run(EarlyStartupRunnable.java:68)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.ui.internal.Workbench$56.run(Workbench.java:2812)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
!SUBENTRY 1 org.eclipse.equinox.registry 4 1 2015-12-30 08:00:41.368
!MESSAGE Plug-in "org.eclipse.swtbot.eclipse.ui" was unable to instantiate class "org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer".
!STACK 0
java.lang.NullPointerException
at org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer.<init>(PreferenceInitializer.java:46)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
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.ui.internal.WorkbenchPlugin$1.run(WorkbenchPlugin.java:293)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at org.eclipse.ui.internal.WorkbenchPlugin.createExtension(WorkbenchPlugin.java:288)
at org.eclipse.ui.internal.EarlyStartupRunnable.getExecutableExtension(EarlyStartupRunnable.java:120)
at org.eclipse.ui.internal.EarlyStartupRunnable.run(EarlyStartupRunnable.java:68)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.ui.internal.Workbench$56.run(Workbench.java:2812)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
!ENTRY org.eclipse.ui 4 4 2015-12-30 08:00:41.370
!MESSAGE Unhandled Exception
!ENTRY org.eclipse.swtbot.eclipse.ui 4 0 2015-12-30 08:00:41.371
!MESSAGE Unable to execute early startup code for an extension
!STACK 1
org.eclipse.core.runtime.CoreException: Plug-in "org.eclipse.swtbot.eclipse.ui" was unable to instantiate class "org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer".
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException(RegistryStrategyOSGI.java:194)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:186)
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.ui.internal.WorkbenchPlugin$1.run(WorkbenchPlugin.java:293)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at org.eclipse.ui.internal.WorkbenchPlugin.createExtension(WorkbenchPlugin.java:288)
at org.eclipse.ui.internal.EarlyStartupRunnable.getExecutableExtension(EarlyStartupRunnable.java:120)
at org.eclipse.ui.internal.EarlyStartupRunnable.run(EarlyStartupRunnable.java:68)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.ui.internal.Workbench$56.run(Workbench.java:2812)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Caused by: java.lang.NullPointerException
at org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer.<init>(PreferenceInitializer.java:46)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:184)
... 11 more
!SUBENTRY 1 org.eclipse.equinox.registry 4 1 2015-12-30 08:00:41.371
!MESSAGE Plug-in "org.eclipse.swtbot.eclipse.ui" was unable to instantiate class "org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer".
!STACK 0
java.lang.NullPointerException
at org.eclipse.swtbot.eclipse.ui.preferences.PreferenceInitializer.<init>(PreferenceInitializer.java:46)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
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.ui.internal.WorkbenchPlugin$1.run(WorkbenchPlugin.java:293)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at org.eclipse.ui.internal.WorkbenchPlugin.createExtension(WorkbenchPlugin.java:288)
at org.eclipse.ui.internal.EarlyStartupRunnable.getExecutableExtension(EarlyStartupRunnable.java:120)
at org.eclipse.ui.internal.EarlyStartupRunnable.run(EarlyStartupRunnable.java:68)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.ui.internal.Workbench$56.run(Workbench.java:2812)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
!ENTRY org.eclipse.ui.workbench 4 2 2015-12-30 08:00:41.373
!MESSAGE Problems occurred when invoking code from plug-in: "org.eclipse.ui.workbench".
!STACK 0
java.lang.NullPointerException
at org.eclipse.ui.internal.monitoring.MonitoringStartup.earlyStartup(MonitoringStartup.java:33)
at org.eclipse.ui.internal.EarlyStartupRunnable.runEarlyStartup(EarlyStartupRunnable.java:90)
at org.eclipse.ui.internal.EarlyStartupRunnable.run(EarlyStartupRunnable.java:68)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.ui.internal.Workbench$56.run(Workbench.java:2812)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
!ENTRY org.eclipse.ui 4 4 2015-12-30 08:00:41.373
!MESSAGE Unhandled Exception
!ENTRY org.eclipse.ui.monitoring 4 0 2015-12-30 08:00:41.374
!MESSAGE Unable to execute early startup code for an extension
!STACK 0
java.lang.NullPointerException
at org.eclipse.ui.internal.monitoring.MonitoringStartup.earlyStartup(MonitoringStartup.java:33)
at org.eclipse.ui.internal.EarlyStartupRunnable.runEarlyStartup(EarlyStartupRunnable.java:90)
at org.eclipse.ui.internal.EarlyStartupRunnable.run(EarlyStartupRunnable.java:68)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
at org.eclipse.ui.internal.Workbench$56.run(Workbench.java:2812)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
!ENTRY org.eclipse.core.jobs 2 2 2015-12-30 08:00:42.189
!MESSAGE Job found still running after platform shutdown. Jobs should be canceled by the plugin that scheduled them during shutdown: org.eclipse.epp.internal.logging.aeri.ide.Startup$1
Job found still running after platform shutdown. Jobs should be canceled by the plugin that scheduled them during shutdown: org.eclipse.epp.internal.logging.aeri.ide.Startup$1
!ENTRY org.eclipse.core.jobs 2 2 2015-12-30 08:00:42.190
!MESSAGE Job found still running after platform shutdown. Jobs should be canceled by the plugin that scheduled them during shutdown: org.eclipse.epp.internal.mpc.ui.wizards.MarketplaceDropAdapter$1
Job found still running after platform shutdown. Jobs should be canceled by the plugin that scheduled them during shutdown: org.eclipse.epp.internal.mpc.ui.wizards.MarketplaceDropAdapter$1
The exception from first error log is thrown here (but it is not the LinkageError, just Exception):
try {
result = classInstance.newInstance();
} catch (Exception e) {
throwException(NLS.bind(RegistryMessages.plugin_instantiateClassError, contributingBundle.getSymbolicName(), className), e);
} catch (LinkageError e1) {
I tried to remove:
.metadata.plugins
.metadata.plugins\org.eclipse.e4.workbench\workingsets.xml
but the problem still exists
EDIT: Problem is resolved. I started application with clear flag (Run Configuration->Main(bookmark)->Workspace Data (Area)->Clear (Flag) and errors disappeared)