On a regular basis I get the NPE from below, restarting Eclipse fixes that. Refreshing the project explorer for the affected resources does not make a difference.

java.lang.NullPointerException: Cannot invoke "org.eclipse.jface.text.IDocument.get()" because "document" is null
at org.eclipse.pde.internal.core.text.AbstractEditingModel.getInputStream(AbstractEditingModel.java:162)
at org.eclipse.pde.internal.core.text.AbstractEditingModel.load(AbstractEditingModel.java:121)
at org.eclipse.pde.internal.ui.editor.plugin.BundleInputContext.createModel(BundleInputContext.java:87)
at org.eclipse.pde.internal.ui.editor.context.InputContext.create(InputContext.java:165)
at org.eclipse.pde.internal.ui.editor.plugin.BundleInputContext.(BundleInputContext.java:64)
at org.eclipse.pde.internal.ui.editor.plugin.ManifestEditor.createResourceContexts(ManifestEditor.java:264)
at org.eclipse.pde.internal.ui.editor.PDEFormEditor.createInputContexts(PDEFormEditor.java:229)
at org.eclipse.pde.internal.ui.editor.PDEFormEditor.createPages(PDEFormEditor.java:270)
at org.eclipse.ui.part.MultiPageEditorPart.createPartControl(MultiPageEditorPart.java:387)
at org.eclipse.ui.internal.e4.compatibility.CompatibilityPart.createPartControl(CompatibilityPart.java:160)
at org.eclipse.ui.internal.e4.compatibility.CompatibilityEditor.createPartControl(CompatibilityEditor.java:98)
at org.eclipse.ui.internal.e4.compatibility.CompatibilityPart.create(CompatibilityPart.java:367)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:58)
at org.eclipse.e4.core.internal.di.InjectorImpl.processAnnotated(InjectorImpl.java:1037)
at org.eclipse.e4.core.internal.di.InjectorImpl.processAnnotated(InjectorImpl.java:998)
at org.eclipse.e4.core.internal.di.InjectorImpl.internalInject(InjectorImpl.java:142)
at org.eclipse.e4.core.internal.di.InjectorImpl.internalMake(InjectorImpl.java:401)
at org.eclipse.e4.core.internal.di.InjectorImpl.make(InjectorImpl.java:319)
at org.eclipse.e4.core.contexts.ContextInjectionFactory.make(ContextInjectionFactory.java:203)
at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.createFromBundle(ReflectionContributionFactory.java:90)
at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.doCreate(ReflectionContributionFactory.java:59)
at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.create(ReflectionContributionFactory.java:42)
at org.eclipse.ui.internal.WorkbenchContributionFactory.create(WorkbenchContributionFactory.java:46)
at org.eclipse.e4.ui.workbench.renderers.swt.ContributedPartRenderer.createWidget(ContributedPartRenderer.java:133)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.createWidget(PartRenderingEngine.java:987)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.safeCreateGui(PartRenderingEngine.java:658)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.safeCreateGui(PartRenderingEngine.java:762)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$2.run(PartRenderingEngine.java:726)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:47)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.createGui(PartRenderingEngine.java:710)
at org.eclipse.e4.ui.internal.workbench.PartServiceImpl.lambda$0(PartServiceImpl.java:105)
at org.eclipse.e4.ui.services.internal.events.UIEventHandler.lambda$0(UIEventHandler.java:38)
at org.eclipse.swt.widgets.Synchronizer.syncExec(Synchronizer.java:183)
at org.eclipse.ui.internal.UISynchronizer.syncExec(UISynchronizer.java:136)
at org.eclipse.swt.widgets.Display.syncExec(Display.java:5994)
at org.eclipse.e4.ui.workbench.swt.DisplayUISynchronize.syncExec(DisplayUISynchronize.java:34)
at org.eclipse.e4.ui.services.internal.events.UIEventHandler.handleEvent(UIEventHandler.java:38)
at org.eclipse.equinox.internal.event.EventHandlerWrapper.handleEvent(EventHandlerWrapper.java:206)
at org.eclipse.equinox.internal.event.EventHandlerTracker.dispatchEvent(EventHandlerTracker.java:201)
at org.eclipse.equinox.internal.event.EventHandlerTracker.dispatchEvent(EventHandlerTracker.java:1)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:151)
at org.eclipse.equinox.internal.event.EventAdminImpl.dispatchEvent(EventAdminImpl.java:132)
at org.eclipse.equinox.internal.event.EventAdminImpl.sendEvent(EventAdminImpl.java:73)
at org.eclipse.equinox.internal.event.EventComponent.sendEvent(EventComponent.java:48)
at org.eclipse.e4.ui.services.internal.events.EventBroker.send(EventBroker.java:55)
at org.eclipse.e4.ui.internal.workbench.UIEventPublisher.notifyChanged(UIEventPublisher.java:61)
at org.eclipse.emf.common.notify.impl.BasicNotifierImpl.eNotify(BasicNotifierImpl.java:424)
at org.eclipse.e4.ui.model.application.ui.impl.ElementContainerImpl.setSelectedElementGen(ElementContainerImpl.java:168)
at org.eclipse.e4.ui.model.application.ui.impl.ElementContainerImpl.setSelectedElement(ElementContainerImpl.java:187)
at org.eclipse.e4.ui.internal.workbench.ModelServiceImpl.showElementInWindow(ModelServiceImpl.java:650)
at org.eclipse.e4.ui.internal.workbench.ModelServiceImpl.bringToTop(ModelServiceImpl.java:614)
at org.eclipse.e4.ui.internal.workbench.PartServiceImpl.delegateBringToTop(PartServiceImpl.java:805)
at org.eclipse.e4.ui.internal.workbench.PartServiceImpl.bringToTop(PartServiceImpl.java:406)
at org.eclipse.e4.ui.internal.workbench.PartServiceImpl.showPart(PartServiceImpl.java:1277)
at org.eclipse.ui.internal.WorkbenchPage.busyOpenEditor(WorkbenchPage.java:3220)
at org.eclipse.ui.internal.WorkbenchPage.lambda$11(WorkbenchPage.java:3110)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:67)
at org.eclipse.ui.internal.WorkbenchPage.openEditor(WorkbenchPage.java:3108)
at org.eclipse.ui.internal.WorkbenchPage.openEditor(WorkbenchPage.java:3078)
at org.eclipse.ui.internal.WorkbenchPage.openEditor(WorkbenchPage.java:3069)
at org.eclipse.ui.ide.IDE.openEditor(IDE.java:550)
at org.eclipse.ui.ide.IDE.openEditor(IDE.java:510)
at org.eclipse.jdt.internal.ui.javaeditor.EditorUtility.openInEditor(EditorUtility.java:377)
at org.eclipse.jdt.internal.ui.javaeditor.EditorUtility.openInSpecificEditor(EditorUtility.java:176)
at org.eclipse.jdt.internal.ui.javaeditor.EditorUtility.openInEditor(EditorUtility.java:169)
at org.eclipse.jdt.ui.actions.OpenAction.run(OpenAction.java:288)
at org.eclipse.jdt.ui.actions.OpenAction.run(OpenAction.java:254)
at org.eclipse.jdt.ui.actions.SelectionDispatchAction.dispatchRun(SelectionDispatchAction.java:274)
at org.eclipse.jdt.ui.actions.SelectionDispatchAction.run(SelectionDispatchAction.java:252)
at org.eclipse.jdt.internal.ui.navigator.OpenAndExpand.run(OpenAndExpand.java:53)
at org.eclipse.ui.actions.RetargetAction.run(RetargetAction.java:215)
at org.eclipse.ui.navigator.CommonNavigatorManager$1.open(CommonNavigatorManager.java:184)
at org.eclipse.ui.OpenAndLinkWithEditorHelper$InternalListener.open(OpenAndLinkWithEditorHelper.java:48)
at org.eclipse.jface.viewers.StructuredViewer$2.run(StructuredViewer.java:801)
at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:47)
at org.eclipse.jface.util.SafeRunnable.run(SafeRunnable.java:169)
at org.eclipse.jface.viewers.StructuredViewer.fireOpen(StructuredViewer.java:798)
at org.eclipse.jface.viewers.StructuredViewer.handleOpen(StructuredViewer.java:1113)
at org.eclipse.ui.navigator.CommonViewer.handleOpen(CommonViewer.java:470)
at org.eclipse.jface.util.OpenStrategy.fireOpenEvent(OpenStrategy.java:295)
at org.eclipse.jface.util.OpenStrategy$1.handleEvent(OpenStrategy.java:330)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:91)
at org.eclipse.swt.widgets.Display.sendEvent(Display.java:5889)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1656)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:5104)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:4545)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$5.run(PartRenderingEngine.java:1147)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:339)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1038)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:153)
at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:677)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:339)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:583)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:173)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:185)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:219)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:149)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:115)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:467)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:298)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:627)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:575)
at org.eclipse.equinox.launcher.Main.run(Main.java:1431)
at org.eclipse.equinox.launcher.Main.main(Main.java:1403)