Bug 58542 Dangerous change to setSystem in MarkersViews
In MarkerView.refresh() there is the line uiJob.setSystem(true); Which may happen after the uiJob has run. As a result it is possible that it is not being used to decrement the count of jobs and the progress monitor can run forever.
bundles/org.eclipse.ui.ide/src/org/eclipse/ui/views/markers/internal/MarkerView.java
protected IResource[] focusResources;
	private Clipboard clipboard;
	IResourceChangeListener resourceListener = new IResourceChangeListener() {
		public void resourceChanged(IResourceChangeEvent event) {
			String[] markerTypes = getMarkerTypes();
			boolean refreshNeeded = false;
			
			for (int idx = 0; idx < markerTypes.length; idx++) {					
				IMarkerDelta[] markerDeltas = event.findMarkerDeltas(markerTypes[idx], true);
				List changes = new ArrayList(markerDeltas.length);
				
				examineDelta(markerDeltas, changes);
				
				if (markerDeltas.length != changes.size()) {
					refreshNeeded = true;
				}
				
				change(MarkerList.createMarkersIgnoringErrors(changes));
			}
						
			
			if (refreshNeeded) {
				markerCountDirty = true;
				refresh();
			}
		}
	};
	
	protected ActionCopyMarker copyAction;
	protected ActionPasteMarker pasteAction;