IndexNotReadyException when add files/directories using ModuleBuilderListener

I have a custom module builder

public class CustomModuleBuilder extends JavaModuleBuilder implements ModuleBuilderListener

And I want all modules of this type to start out with a directory structure, class, format the class, and add two libraries.  My moduleCreated is below

@Override
public void moduleCreated(@NotNull Module module) {
    VirtualFile[] sourceRoots = ModuleRootManager.getInstance(module).getSourceRoots();
    VirtualFile root = sourceRoots[0];
    PsiDirectory sourceDirectory = PsiManager.getInstance(module.getProject()).findDirectory(root);
    PsiDirectory classDirectory;
    classDirectory = PackageUtil.findOrCreateDirectoryForPackage(module, "com.my.custompackage", sourceDirectory, false);

    NOTE!! : The function  createFileFromText(@NonNls @NotNull String fileName, @NotNull FileType fileType, @NotNull CharSequence text); failed becuase it said eventSystemEnabled was false
    PsiFile functionPsiFile = PsiFileFactory.getInstance(module.getProject()).createFileFromText(“CustomClsas.java", JavaFileType.INSTANCE, createCustomClassCode(), LocalTimeCounter.currentTime(), true);
    WriteCommandAction.runWriteCommandAction(module.getProject(), new Runnable() {
        @Override
        public void run() {
            try {
                classDirectory.add(functionPsiFile);
            } catch (IndexNotReadyException e) {
                e.printStackTrace();
                //Throws but works fine
            }
            //shorten class references, and add the necessary import statements
            PsiDocumentManager documentManager = PsiDocumentManager.getInstance(module.getProject());
            Document document = documentManager.getDocument(functionPsiFile);
            documentManager.commitDocument(document);
            PsiClass functionClass = ((PsiJavaFile) functionPsiFile).getClasses()[0];
            CodeStyleManager.getInstance(module.getProject()).reformat(functionClass);
            try {
                //This does not work becuase of thrown error
                JavaCodeStyleManager.getInstance(module.getProject()).shortenClassReferences(functionClass);
            } catch (IndexNotReadyException e){
                e.printStackTrace();
            }
        }
    });
}

The package, class directory, library and class all get created (Though adding the newly created class directory throws the exception as show, stack trace below).  But the class does not get it's references references shortened.  Both stack traces are very similar (and end in the same FileBasedIndexImple calls.  I have used the same code to format/shorted references in actions that are called via right-clicking on open class editor --> generate code --> format generated code. Incase you missed it, I'm not sure if the following was relavent

    NOTE!! : The function  createFileFromText(@NonNls @NotNull String fileName, @NotNull FileType fileType, @NotNull CharSequence text); failed becuase it said eventSystemEnabled was false
    PsiFile functionPsiFile = PsiFileFactory.getInstance(module.getProject()).createFileFromText(“CustomClsas.java", JavaFileType.INSTANCE, createCustomClassCode(), LocalTimeCounter.currentTime(), true);

at com.intellij.util.indexing.FileBasedIndexImpl.handleDumbMode(FileBasedIndexImpl.java:855)
 at com.intellij.util.indexing.FileBasedIndexImpl.ensureUpToDate(FileBasedIndexImpl.java:804)
 at com.intellij.util.indexing.FileBasedIndexImpl.ensureUpToDate(FileBasedIndexImpl.java:788)
 at com.intellij.psi.stubs.StubIndexImpl.processElements(StubIndexImpl.java:250)
 at com.intellij.psi.stubs.StubIndexImpl.processElements(StubIndexImpl.java:238)
 at com.intellij.psi.stubs.StubIndex.process(StubIndex.java:76)
 at com.intellij.psi.stubs.StubIndex.process(StubIndex.java:95)
 at com.intellij.psi.stubs.StubIndexImpl.get(StubIndexImpl.java:227)
 at com.intellij.psi.stubs.StubIndex.getElements(StubIndex.java:144)
 at com.intellij.psi.stubs.StubIndex.getElements(StubIndex.java:134)
 at com.intellij.psi.impl.java.stubs.index.JavaFullClassNameIndex.get(JavaFullClassNameIndex.java:48)
 at com.intellij.psi.impl.file.impl.JavaFileManagerImpl.findClassInIndex(JavaFileManagerImpl.java:145)
 at com.intellij.psi.impl.file.impl.JavaFileManagerImpl.findClass(JavaFileManagerImpl.java:129)
 at com.intellij.psi.impl.PsiElementFinderImpl.findClass(PsiElementFinderImpl.java:54)
 at com.intellij.psi.impl.JavaPsiFacadeImpl.findClass(JavaPsiFacadeImpl.java:102)
 at com.intellij.psi.impl.PsiElementFactoryImpl.createTypeByFQClassName(PsiElementFactoryImpl.java:411)
 at com.intellij.psi.PsiType.getTypeByName(PsiType.java:147)
 at com.intellij.psi.PsiType.getJavaLangObject(PsiType.java:159)
 at com.intellij.psi.impl.PsiClassImplUtil.getSuperTypes(PsiClassImplUtil.java:902)
 at com.intellij.psi.impl.source.PsiClassImpl.getSuperTypes(PsiClassImpl.java:249)
 at com.intellij.psi.impl.PsiClassImplUtil.processSuperTypes(PsiClassImplUtil.java:774)
 at com.intellij.psi.impl.PsiClassImplUtil.processDeclarationsInClassNotCached(PsiClassImplUtil.java:709)
 at com.intellij.psi.impl.PsiClassImplUtil.processDeclarationsInClass(PsiClassImplUtil.java:478)
 at com.intellij.psi.impl.PsiClassImplUtil.processDeclarationsInClass(PsiClassImplUtil.java:448)
 at com.intellij.psi.impl.source.PsiClassImpl.processDeclarations(PsiClassImpl.java:488)
 at com.intellij.psi.scope.util.PsiScopesUtil.treeWalkUp(PsiScopesUtil.java:72)
 at com.intellij.psi.scope.util.PsiScopesUtil.treeWalkUp(PsiScopesUtil.java:54)
 at com.intellij.psi.scope.util.PsiScopesUtil.resolveAndWalk(PsiScopesUtil.java:215)
 at com.intellij.psi.scope.util.PsiScopesUtil.resolveAndWalk(PsiScopesUtil.java:146)
 at com.intellij.psi.impl.source.PsiJavaCodeReferenceElementImpl.resolve(PsiJavaCodeReferenceElementImpl.java:438)
 at com.intellij.psi.impl.source.PsiJavaCodeReferenceElementImpl.access$100(PsiJavaCodeReferenceElementImpl.java:55)
 at com.intellij.psi.impl.source.PsiJavaCodeReferenceElementImpl$OurGenericsResolver.resolve(PsiJavaCodeReferenceElementImpl.java:339)
 at com.intellij.psi.impl.source.PsiJavaCodeReferenceElementImpl$OurGenericsResolver.resolve(PsiJavaCodeReferenceElementImpl.java:331)
 at com.intellij.psi.impl.source.resolve.ResolveCache$4.compute(ResolveCache.java:191)
 at com.intellij.psi.impl.source.resolve.ResolveCache$4.compute(ResolveCache.java:188)
 at com.intellij.openapi.util.RecursionManager$2.doPreventingRecursion(RecursionManager.java:112)
 at com.intellij.psi.impl.source.resolve.ResolveCache.resolveWithCaching(ResolveCache.java:188)
 at com.intellij.psi.impl.PsiImplUtil.multiResolveImpl(PsiImplUtil.java:779)
 at com.intellij.psi.impl.PsiImplUtil.multiResolveImpl(PsiImplUtil.java:769)
 at com.intellij.psi.impl.source.PsiJavaCodeReferenceElementImpl.multiResolve(PsiJavaCodeReferenceElementImpl.java:366)
 at com.intellij.psi.impl.source.PsiJavaCodeReferenceElementImpl.advancedResolve(PsiJavaCodeReferenceElementImpl.java:359)
 at com.intellij.psi.impl.source.PsiJavaCodeReferenceElementImpl.resolve(PsiJavaCodeReferenceElementImpl.java:328)
 at com.intellij.psi.impl.source.tree.JavaTreeCopyHandler.encodeInformationInRef(JavaTreeCopyHandler.java:207)
 at com.intellij.psi.impl.source.tree.JavaTreeCopyHandler.encodeInformation(JavaTreeCopyHandler.java:141)
 at com.intellij.psi.impl.source.tree.ChangeUtil.encodeInformation(ChangeUtil.java:62)
 at com.intellij.psi.impl.source.tree.ChangeUtil.encodeInformation(ChangeUtil.java:69)
 at com.intellij.psi.impl.source.tree.ChangeUtil.encodeInformation(ChangeUtil.java:69)
 at com.intellij.psi.impl.source.tree.ChangeUtil.encodeInformation(ChangeUtil.java:69)
 at com.intellij.psi.impl.source.tree.ChangeUtil.encodeInformation(ChangeUtil.java:69)
 at com.intellij.psi.impl.source.tree.ChangeUtil.encodeInformation(ChangeUtil.java:69)
 at com.intellij.psi.impl.source.tree.ChangeUtil.encodeInformation(ChangeUtil.java:53)
 at com.intellij.psi.impl.source.tree.ChangeUtil.encodeInformation(ChangeUtil.java:47)
 at com.intellij.psi.impl.file.PsiDirectoryImpl.updateAddedFile(PsiDirectoryImpl.java:392)
 at com.intellij.psi.impl.file.PsiDirectoryImpl.add(PsiDirectoryImpl.java:456)
 at com.intellij.psi.impl.file.PsiJavaDirectoryImpl.add(PsiJavaDirectoryImpl.java:64)
 at com.custom.custom.CustomModuleBuilder$1.run(CustomModuleBuilder.java:70)
 at com.intellij.openapi.command.WriteCommandAction$4.run(WriteCommandAction.java:176)
 at com.intellij.openapi.command.WriteCommandAction$Simple.run(WriteCommandAction.java:166)
 at com.intellij.openapi.application.RunResult.run(RunResult.java:38)
 at com.intellij.openapi.command.WriteCommandAction$2$1.run(WriteCommandAction.java:114)
 at com.intellij.openapi.application.impl.ApplicationImpl.runWriteAction(ApplicationImpl.java:931)
 at com.intellij.openapi.command.WriteCommandAction$2.run(WriteCommandAction.java:111)
 at com.intellij.openapi.command.impl.CoreCommandProcessor.executeCommand(CoreCommandProcessor.java:124)
 at com.intellij.openapi.command.impl.CoreCommandProcessor.executeCommand(CoreCommandProcessor.java:99)
 at com.intellij.openapi.command.WriteCommandAction.performWriteCommandAction(WriteCommandAction.java:108)
 at com.intellij.openapi.command.WriteCommandAction.execute(WriteCommandAction.java:80)
 at com.intellij.openapi.command.WriteCommandAction.runWriteCommandAction(WriteCommandAction.java:173)
 at com.custom.custom.Custom.CustomModuleBuilder.moduleCreated(CustomModuleBuilder.java:66)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:497)
 at com.intellij.util.EventDispatcher.dispatch(EventDispatcher.java:88)
 at com.intellij.util.EventDispatcher.access$100(EventDispatcher.java:34)
 at com.intellij.util.EventDispatcher$1.invoke(EventDispatcher.java:68)
 at com.sun.proxy.$Proxy110.moduleCreated(Unknown Source)
 at com.intellij.ide.util.projectWizard.ModuleBuilder.onModuleInitialized(ModuleBuilder.java:279)
 at com.intellij.ide.util.projectWizard.ModuleBuilder.access$000(ModuleBuilder.java:56)
 at com.intellij.ide.util.projectWizard.ModuleBuilder$3$1.run(ModuleBuilder.java:311)
 at com.intellij.openapi.application.impl.ApplicationImpl.runWriteAction(ApplicationImpl.java:931)
 at com.intellij.ide.util.projectWizard.ModuleBuilder$3.run(ModuleBuilder.java:308)
 at com.intellij.ide.startup.impl.StartupManagerImpl$7.run(StartupManagerImpl.java:369)
 at com.intellij.util.ui.UIUtil.invokeLaterIfNeeded(UIUtil.java:2350)
 at com.intellij.ide.startup.impl.StartupManagerImpl.runWhenProjectIsInitialized(StartupManagerImpl.java:365)
 at com.intellij.ide.util.projectWizard.ModuleBuilder.createAndCommitIfNeeded(ModuleBuilder.java:305)
 at com.intellij.ide.util.projectWizard.ModuleBuilder$4.compute(ModuleBuilder.java:355)
 at com.intellij.ide.util.projectWizard.ModuleBuilder$4.compute(ModuleBuilder.java:352)
 at com.intellij.openapi.application.impl.ApplicationImpl.runWriteAction(ApplicationImpl.java:955)
 at com.intellij.ide.util.projectWizard.ModuleBuilder.commitModule(ModuleBuilder.java:352)
 at com.intellij.openapi.roots.ui.configuration.actions.NewModuleAction.createModuleFromWizard(NewModuleAction.java:82)
 at com.intellij.openapi.roots.ui.configuration.actions.NewModuleAction.actionPerformed(NewModuleAction.java:61)
 at com.intellij.openapi.actionSystem.ex.ActionUtil.performActionDumbAware(ActionUtil.java:182)
 at com.intellij.openapi.actionSystem.impl.ActionMenuItem$ActionTransmitter$1.run(ActionMenuItem.java:312)
 at com.intellij.openapi.wm.impl.FocusManagerImpl.runOnOwnContext(FocusManagerImpl.java:958)
 at com.intellij.openapi.wm.impl.IdeFocusManagerImpl.runOnOwnContext(IdeFocusManagerImpl.java:124)
 at com.intellij.openapi.actionSystem.impl.ActionMenuItem$ActionTransmitter.actionPerformed(ActionMenuItem.java:282)
 at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
 at com.intellij.openapi.actionSystem.impl.ActionMenuItem.fireActionPerformed(ActionMenuItem.java:109)
 at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
 at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
 at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:308)
 at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
 at com.apple.laf.ScreenMenuItemCheckbox.itemStateChanged(ScreenMenuItemCheckbox.java:193)
 at java.awt.CheckboxMenuItem.processItemEvent(CheckboxMenuItem.java:389)
 at java.awt.CheckboxMenuItem.processEvent(CheckboxMenuItem.java:357)
 at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:351)
 at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:339)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:761)
 at java.awt.EventQueue.access$500(EventQueue.java:97)
 at java.awt.EventQueue$3.run(EventQueue.java:709)
 at java.awt.EventQueue$3.run(EventQueue.java:703)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
 at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
 at java.awt.EventQueue$4.run(EventQueue.java:731)
 at java.awt.EventQueue$4.run(EventQueue.java:729)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
 at com.intellij.ide.IdeEventQueue.defaultDispatchEvent(IdeEventQueue.java:734)
 at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:569)
 at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:382)
 at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Any help would be appreciated!

Thanks,
Weston