JBDS fails to restart with "SWTException: Invalid thread access" after crash

Issue

Dev Studio crashed in the middle of a "Refactor->Rename Class" operation. The log shows there was an OutOfMemoryError: PermGen space, and when I try to restart, the $WORKSPACE/.metadata/.log shows

  java.lang.ExceptionInInitializerError
    at org.eclipse.jdt.ui.PreferenceConstants.initializeDefaultValues(PreferenceConstants.java:3739)
    at org.eclipse.jdt.internal.ui.JavaUIPreferenceInitializer.initializeDefaultPreferences(JavaUIPreferenceInitializer.java:38)
    at org.eclipse.core.internal.preferences.PreferenceServiceRegistryHelper$1.run(PreferenceServiceRegistryHelper.java:300)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.core.internal.preferences.PreferenceServiceRegistryHelper.runInitializer(PreferenceServiceRegistryHelper.java:303)
    at org.eclipse.core.internal.preferences.PreferenceServiceRegistryHelper.applyRuntimeDefaults(PreferenceServiceRegistryHelper.java:131)
    at org.eclipse.core.internal.preferences.PreferencesService.applyRuntimeDefaults(PreferencesService.java:368)
    at org.eclipse.core.internal.preferences.DefaultPreferences.applyRuntimeDefaults(DefaultPreferences.java:166)
    at org.eclipse.core.internal.preferences.DefaultPreferences.load(DefaultPreferences.java:237)
    at org.eclipse.core.internal.preferences.EclipsePreferences.create(EclipsePreferences.java:410)
    at org.eclipse.core.internal.preferences.EclipsePreferences.internalNode(EclipsePreferences.java:663)
    at org.eclipse.core.internal.preferences.EclipsePreferences.node(EclipsePreferences.java:805)
    at org.eclipse.core.internal.preferences.AbstractScope.getNode(AbstractScope.java:38)
    at org.eclipse.core.runtime.preferences.DefaultScope.getNode(DefaultScope.java:76)
    at org.eclipse.ui.preferences.ScopedPreferenceStore.getDefaultPreferences(ScopedPreferenceStore.java:250)
    at org.eclipse.ui.preferences.ScopedPreferenceStore.getPreferenceNodes(ScopedPreferenceStore.java:285)
    at org.eclipse.ui.preferences.ScopedPreferenceStore.internalGet(ScopedPreferenceStore.java:475)
    at org.eclipse.ui.preferences.ScopedPreferenceStore.getBoolean(ScopedPreferenceStore.java:387)
    at org.eclipse.jdt.internal.ui.preferences.MembersOrderPreferenceCache.install(MembersOrderPreferenceCache.java:61)
    at org.eclipse.jdt.internal.ui.JavaPlugin.ensurePreferenceStoreBackwardsCompatibility(JavaPlugin.java:426)
    at org.eclipse.jdt.internal.ui.JavaPlugin.start(JavaPlugin.java:373)
    ...
Caused by: org.eclipse.swt.SWTException: Invalid thread access
    at org.eclipse.swt.SWT.error(SWT.java:4361)
    at org.eclipse.swt.SWT.error(SWT.java:4276)
    at org.eclipse.swt.SWT.error(SWT.java:4247)
    at org.eclipse.swt.widgets.Display.error(Display.java:1258)
    at org.eclipse.swt.widgets.Display.checkDevice(Display.java:764)
    at org.eclipse.swt.widgets.Display.getSystemFont(Display.java:2459)
    at org.eclipse.jface.preference.PreferenceConverter.<clinit>(PreferenceConverter.java:84)
    ... 76 more