Refactorings and Typecheckerstate behave incoherently which may lead to an NPE

[sxhya]

To reproduce on vclang-lib library:

• typecheck "Trunc.vc";
• rename some function lying in different module, say rename "Pointed" from Spheres.vc to "PointedType" using Shift+F6;
• open Spheres.vc and notice that typechecker state is incorrect (i.e. icons that vizualize it are little green circles while in reality they all should have been reset);
• try to modify the contents of the definition of PointedType in any way;
• get an NPE as below:

Element class com.intellij.psi.impl.source.tree.CompositeElement of type DEF_FUNCTION (class org.vclang.psi.stubs.VcDefFunctionStub$Type)
com.intellij.psi.PsiInvalidElementAccessException: Element class com.intellij.psi.impl.source.tree.CompositeElement of type DEF_FUNCTION (class org.vclang.psi.stubs.VcDefFunctionStub$Type)
at com.intellij.psi.PsiInvalidElementAccessException.createByNode(PsiInvalidElementAccessException.java:96)
at com.intellij.psi.impl.source.SubstrateRef$2.getContainingFile(SubstrateRef.java:101)
at com.intellij.extapi.psi.StubBasedPsiElementBase.getContainingFile(StubBasedPsiElementBase.java:275)
at org.vclang.typechecking.TypeCheckingServiceImpl$VcSourceInfoProvider.sourceOf(TypeCheckingService.kt:272)
at org.vclang.typechecking.TypeCheckingServiceImpl$VcSourceInfoProvider.sourceOf(TypeCheckingService.kt:265)
at com.jetbrains.jetpad.vclang.module.caching.sourceless.CacheSourceInfoProvider.sourceOf(CacheSourceInfoProvider.java:18)
at com.jetbrains.jetpad.vclang.module.caching.LocalizedTypecheckerState.getLocal(LocalizedTypecheckerState.java:41)
at com.jetbrains.jetpad.vclang.module.caching.LocalizedTypecheckerState.reset(LocalizedTypecheckerState.java:54)
at com.jetbrains.jetpad.vclang.typechecking.order.DependencyCollector.update(DependencyCollector.java:55)
at org.vclang.typechecking.TypeCheckingServiceImpl$TypeCheckerPsiTreeChangeListener.processParent(TypeCheckingService.kt:242)
at org.vclang.typechecking.TypeCheckingServiceImpl$TypeCheckerPsiTreeChangeListener.beforeChildReplacement(TypeCheckingService.kt:226)
at com.intellij.psi.impl.PsiManagerImpl.fireEvent(PsiManagerImpl.java:386)
at com.intellij.psi.impl.PsiManagerImpl.beforeChildReplacement(PsiManagerImpl.java:257)
at com.intellij.psi.impl.source.text.DiffLog$ReplaceEntry.doActualPsiChange(DiffLog.java:115)
at com.intellij.psi.impl.source.text.DiffLog.performActualPsiChange(DiffLog.java:54)
at com.intellij.psi.impl.DocumentCommitThread$2.runInner(DocumentCommitThread.java:871)
at com.intellij.pom.impl.PomTransactionBase.run(PomTransactionBase.java:46)
at com.intellij.pom.core.impl.PomModelImpl.runTransaction(PomModelImpl.java:158)
at com.intellij.psi.impl.DocumentCommitThread.lambda$doActualPsiChange$8(DocumentCommitThread.java:868)
at com.intellij.psi.impl.source.codeStyle.CodeStyleManagerImpl.lambda$performActionWithFormatterDisabled$5(CodeStyleManagerImpl.java:676)
at com.intellij.psi.impl.source.PostprocessReformattingAspect.disablePostprocessFormattingInside(PostprocessReformattingAspect.java:116)
at com.intellij.psi.impl.source.codeStyle.CodeStyleManagerImpl.lambda$performActionWithFormatterDisabled$7(CodeStyleManagerImpl.java:705)
at com.intellij.formatting.FormatterImpl.runWithFormattingDisabled(FormatterImpl.java:903)
at com.intellij.psi.impl.source.codeStyle.CodeStyleManagerImpl.performActionWithFormatterDisabled(CodeStyleManagerImpl.java:703)
at com.intellij.psi.impl.source.codeStyle.CodeStyleManagerImpl.performActionWithFormatterDisabled(CodeStyleManagerImpl.java:675)
at com.intellij.psi.impl.DocumentCommitThread.doActualPsiChange(DocumentCommitThread.java:855)
at com.intellij.psi.impl.DocumentCommitThread.lambda$doCommit$7(DocumentCommitThread.java:774)
at com.intellij.psi.impl.PsiDocumentManagerBase.commitToExistingPsi(PsiDocumentManagerBase.java:399)
at com.intellij.psi.impl.PsiDocumentManagerBase.finishCommitInWriteAction(PsiDocumentManagerBase.java:375)
at com.intellij.psi.impl.PsiDocumentManagerImpl.finishCommitInWriteAction(PsiDocumentManagerImpl.java:145)
at com.intellij.psi.impl.PsiDocumentManagerBase$3.run(PsiDocumentManagerBase.java:333)
at com.intellij.openapi.application.impl.ApplicationImpl.runWriteAction(ApplicationImpl.java:1031)
at com.intellij.psi.impl.PsiDocumentManagerBase.finishCommit(PsiDocumentManagerBase.java:340)
at com.intellij.psi.impl.DocumentCommitThread.lambda$createEdtRunnable$5(DocumentCommitThread.java:592)
at com.intellij.openapi.application.TransactionGuardImpl.runSyncTransaction(TransactionGuardImpl.java:86)
at com.intellij.openapi.application.TransactionGuardImpl.lambda$submitTransaction$1(TransactionGuardImpl.java:109)
at com.intellij.openapi.application.impl.LaterInvocator$FlushQueue.runNextEvent(LaterInvocator.java:416)
at com.intellij.openapi.application.impl.LaterInvocator$FlushQueue.run(LaterInvocator.java:399)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
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.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at com.intellij.ide.IdeEventQueue.defaultDispatchEvent(IdeEventQueue.java:821)
at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:649)
at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:365)
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)