Bug 310266 PartRenderingEngine shuts down when just one MWindow is destroyed
PartRenderingEngine's run(MApplicationElement, IEclipseContext) method has a big, inlined "HACK!!" comment in it. The problem is that it only checks for the disposal of one single shell. So if you have other shells hanging around (other MWindows), your whole application will be brought down even if you've only just closed one window.
bundles/org.eclipse.e4.ui.workbench.swt/src/org/eclipse/e4/ui/workbench/swt/internal/PartRenderingEngine.java
runContext.set(IResourceUtiltities.class.getName(),
						new ResourceUtility(Activator.getDefault()
								.getBundleAdmin()));
				
				KeyBindingDispatcher dispatcher = (KeyBindingDispatcher) ContextInjectionFactory
						.make(KeyBindingDispatcher.class, runContext);
				runContext.set(KeyBindingDispatcher.class.getName(), dispatcher);
				org.eclipse.swt.widgets.Listener listener = dispatcher
						.getKeyDownFilter();
				display.addFilter(SWT.KeyDown, listener);
				display.addFilter(SWT.Traverse, listener);
				
				
				
				
				testShell = null;
				theApp = null;
				boolean spinOnce = true;
				if (uiRoot instanceof MApplication) {
					spinOnce = false; 
					theApp = (MApplication) uiRoot;
					
					for (MWindow window : theApp.getChildren()) {
						testShell = (Shell) createGui(window);
					}
					
					
				} else if (uiRoot instanceof MUIElement) {
					if (uiRoot instanceof MWindow) {
						testShell = (Shell) createGui((MUIElement) uiRoot);