Patch Set 4:

First hit (getFlags() ==0)
org.eclipse.egit.core.synchronize.GitSubscriberMergeContext$2.resourceChanged(GitSubscriberMergeContext.java:71)
	at org.eclipse.core.internal.events.NotificationManager$1.run(NotificationManager.java:291)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.internal.events.NotificationManager.notify(NotificationManager.java:285)
	at org.eclipse.core.internal.events.NotificationManager.broadcastChanges(NotificationManager.java:149)
	at org.eclipse.core.internal.resources.Workspace.broadcastPostChange(Workspace.java:395)
	at org.eclipse.core.internal.resources.Workspace.endOperation(Workspace.java:1530)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2353)
	at org.eclipse.ui.actions.WorkspaceModifyOperation.run(WorkspaceModifyOperation.java:118)
	at org.eclipse.ui.internal.editors.text.WorkspaceOperationRunner.run(WorkspaceOperationRunner.java:75)
	at org.eclipse.ui.internal.editors.text.WorkspaceOperationRunner.run(WorkspaceOperationRunner.java:65)
	at org.eclipse.ui.editors.text.TextFileDocumentProvider.executeOperation(TextFileDocumentProvider.java:456)
	at org.eclipse.ui.editors.text.TextFileDocumentProvider.saveDocument(TextFileDocumentProvider.java:772)
	at org.eclipse.ui.texteditor.AbstractTextEditor.performSave(AbstractTextEditor.java:5048)
	at org.eclipse.ui.texteditor.AbstractTextEditor.doSave(AbstractTextEditor.java:4837)
	at org.eclipse.ui.texteditor.AbstractTextEditor$TextEditorSavable.doSave(AbstractTextEditor.java:7177)
	at org.eclipse.ui.Saveable.doSave(Saveable.java:214)
	at org.eclipse.ui.internal.SaveableHelper.doSaveModel(SaveableHelper.java:349)
	at org.eclipse.ui.internal.SaveableHelper$3.run(SaveableHelper.java:195)
	at org.eclipse.ui.internal.SaveableHelper$5.run(SaveableHelper.java:277)
	at org.eclipse.jface.operation.ModalContext.runInCurrentThread(ModalContext.java:464)
	at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:372)
	at org.eclipse.jface.window.ApplicationWindow$1.run(ApplicationWindow.java:759)
	at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
	at org.eclipse.jface.window.ApplicationWindow.run(ApplicationWindow.java:756)
	at org.eclipse.ui.internal.WorkbenchWindow.run(WorkbenchWindow.java:2642)
	at org.eclipse.ui.internal.SaveableHelper.runProgressMonitorOperation(SaveableHelper.java:285)
	at org.eclipse.ui.internal.SaveableHelper.runProgressMonitorOperation(SaveableHelper.java:264)
	at org.eclipse.ui.internal.SaveableHelper.saveModels(SaveableHelper.java:207)
	at org.eclipse.ui.internal.SaveableHelper.savePart(SaveableHelper.java:144)
	at org.eclipse.ui.internal.EditorManager.savePart(EditorManager.java:1399)
	at org.eclipse.ui.internal.WorkbenchPage.savePart(WorkbenchPage.java:3416)
	at org.eclipse.ui.internal.WorkbenchPage.saveEditor(WorkbenchPage.java:3429)
	at org.eclipse.ui.internal.handlers.SaveHandler.execute(SaveHandler.java:54)
	at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:293)
	at org.eclipse.core.commands.Command.executeWithChecks(Command.java:476)
	at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:508)
	at org.eclipse.ui.internal.handlers.HandlerService.executeCommand(HandlerService.java:169)
	at org.eclipse.ui.internal.keys.WorkbenchKeyboard.executeCommand(WorkbenchKeyboard.java:468)
	at org.eclipse.ui.internal.keys.WorkbenchKeyboard.press(WorkbenchKeyboard.java:786)
	at org.eclipse.ui.internal.keys.WorkbenchKeyboard.processKeyEvent(WorkbenchKeyboard.java:885)
	at org.eclipse.ui.internal.keys.WorkbenchKeyboard.filterKeySequenceBindings(WorkbenchKeyboard.java:567)
	at org.eclipse.ui.internal.keys.WorkbenchKeyboard.access$3(WorkbenchKeyboard.java:508)
	at org.eclipse.ui.internal.keys.WorkbenchKeyboard$KeyDownFilter.handleEvent(WorkbenchKeyboard.java:123)
	at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
	at org.eclipse.swt.widgets.Display.filterEvent(Display.java:1531)
	at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1257)
	at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1282)
	at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1267)
	at org.eclipse.swt.widgets.Widget.sendKeyEvent(Widget.java:1294)
	at org.eclipse.swt.widgets.Widget.gtk_key_press_event(Widget.java:730)
	at org.eclipse.swt.widgets.Control.gtk_key_press_event(Control.java:3019)
	at org.eclipse.swt.widgets.Composite.gtk_key_press_event(Composite.java:734)
	at org.eclipse.swt.widgets.Widget.windowProc(Widget.java:1743)
	at org.eclipse.swt.widgets.Control.windowProc(Control.java:5016)
	at org.eclipse.swt.widgets.Display.windowProc(Display.java:4408)
	at org.eclipse.swt.internal.gtk.OS._gtk_main_do_event(Native Method)
	at org.eclipse.swt.internal.gtk.OS.gtk_main_do_event(OS.java:8422)
	at org.eclipse.swt.widgets.Display.eventProc(Display.java:1245)
	at org.eclipse.swt.internal.gtk.OS._g_main_context_iteration(Native Method)
	at org.eclipse.swt.internal.gtk.OS.g_main_context_iteration(OS.java:2276)
	at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3207)
	at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2696)
	at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2660)
	at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2494)
	at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:674)
	at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
	at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:667)
	at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
	at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:123)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
	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:601)
	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)


Second hit (getFlags() == 131072)
org.eclipse.egit.core.synchronize.GitSubscriberMergeContext$2.resourceChanged(GitSubscriberMergeContext.java:71)
	at org.eclipse.core.internal.events.NotificationManager$1.run(NotificationManager.java:291)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.internal.events.NotificationManager.notify(NotificationManager.java:285)
	at org.eclipse.core.internal.events.NotificationManager.broadcastChanges(NotificationManager.java:149)
	at org.eclipse.core.internal.resources.Workspace.broadcastPostChange(Workspace.java:395)
	at org.eclipse.core.internal.resources.Workspace.endOperation(Workspace.java:1530)
	at org.eclipse.core.internal.events.AutoBuildJob.doBuild(AutoBuildJob.java:156)
	at org.eclipse.core.internal.events.AutoBuildJob.run(AutoBuildJob.java:241)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54)