java.lang.Throwable: Indexing process should not rely on non-indexed file data. 5.0.1-alpha

[VitaliyBoyko]

Describe the bug (*)

A clear and concise description of what the bug is.

java.lang.Throwable: Indexing process should not rely on non-indexed file data.
Indexing file = /home/vitaliy/projects/tccupdate/src/app/code/.../AdvancedBreadcrumbs/etc/di.xml, file id = 8201, queried file id = 8206
	at com.intellij.openapi.diagnostic.Logger.error(Logger.java:202)
	at com.intellij.indexing.composite.CompositeInvertedIndexBase.doGetIndexedFileData(CompositeInvertedIndexBase.java:162)
	at com.intellij.indexing.composite.CompositeInvertedIndexBase.getIndexedFileData(CompositeInvertedIndexBase.java:144)
	at com.intellij.psi.stubs.StubProcessingHelper.retrieveStubIdList(StubProcessingHelper.java:38)
	at com.intellij.psi.stubs.StubIndexEx.lambda$processElements$6(StubIndexEx.java:198)
	at java.base/java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1708)
	at com.intellij.psi.stubs.StubIndexEx.processElements(StubIndexEx.java:197)
	at com.intellij.psi.stubs.StubIndex.getElements(StubIndex.java:103)
	at com.intellij.psi.stubs.StubIndex.getElements(StubIndex.java:91)
	at com.jetbrains.php.PhpIndexImpl.getElements(PhpIndexImpl.java:639)
	at com.jetbrains.php.PhpIndexImpl.getByName(PhpIndexImpl.java:1076)
	at com.jetbrains.php.PhpIndexImpl.getByFQN(PhpIndexImpl.java:1053)
	at com.jetbrains.php.PhpIndexImpl.getByFqnCacheAware(PhpIndexImpl.java:1134)
	at com.jetbrains.php.PhpIndexImpl.getClassesByFQNInternal(PhpIndexImpl.java:1129)
	at com.jetbrains.php.PhpIndexImpl.getAnyByFQN(PhpIndexImpl.java:1168)
	at com.magento.idea.magento2plugin.stubs.indexes.PluginIndex$1.getPluginsForType(PluginIndex.java:104)
	at com.magento.idea.magento2plugin.stubs.indexes.PluginIndex$1.map(PluginIndex.java:78)
	at com.magento.idea.magento2plugin.stubs.indexes.PluginIndex$1.map(PluginIndex.java:49)
	at com.intellij.util.indexing.impl.MapReduceIndex.mapByIndexer(MapReduceIndex.java:317)
	at com.intellij.util.indexing.impl.MapReduceIndex.mapInput(MapReduceIndex.java:308)
	at com.intellij.util.indexing.impl.storage.VfsAwareMapReduceIndex.mapInput(VfsAwareMapReduceIndex.java:176)
	at com.intellij.util.indexing.impl.storage.VfsAwareMapReduceIndex.mapInput(VfsAwareMapReduceIndex.java:40)
	at com.intellij.util.indexing.impl.MapReduceIndex.mapInputAndPrepareUpdate(MapReduceIndex.java:253)
	at com.intellij.indexing.composite.CompositeInvertedIndexBase.updateBaseIndex(CompositeInvertedIndexBase.java:284)
	at com.intellij.indexing.composite.CompositeInvertedIndexBase.mapInputAndPrepareUpdate(CompositeInvertedIndexBase.java:62)
	at com.intellij.indexing.composite.CompositeInvertedIndexBase.mapInputAndPrepareUpdate(CompositeInvertedIndexBase.java:28)
	at com.intellij.util.indexing.FileBasedIndexImpl.createSingleIndexValueApplier(FileBasedIndexImpl.java:1608)
	at com.intellij.util.indexing.FileBasedIndexImpl.lambda$doIndexFileContent$25(FileBasedIndexImpl.java:1473)
	at com.intellij.openapi.fileTypes.impl.FileTypeManagerImpl.freezeFileTypeTemporarilyWithProvidedValueIn(FileTypeManagerImpl.java:670)
	at com.intellij.util.indexing.FileBasedIndexImpl.doIndexFileContent(FileBasedIndexImpl.java:1421)
	at com.intellij.util.indexing.FileBasedIndexImpl.indexFileContent(FileBasedIndexImpl.java:1394)
	at com.intellij.util.indexing.FileBasedIndexImpl.processRefreshedFile(FileBasedIndexImpl.java:1342)
	at com.intellij.util.indexing.FileBasedIndexImpl$VirtualFileUpdateTask.doProcess(FileBasedIndexImpl.java:1743)
	at com.intellij.util.indexing.FileBasedIndexImpl$VirtualFileUpdateTask.doProcess(FileBasedIndexImpl.java:1740)
	at com.intellij.util.indexing.UpdateTask.process(UpdateTask.java:63)
	at com.intellij.util.indexing.UpdateTask.processAll(UpdateTask.java:32)
	at com.intellij.util.indexing.FileBasedIndexImpl.forceUpdate(FileBasedIndexImpl.java:1760)
	at com.intellij.util.indexing.FileBasedIndexImpl.ensureUpToDate(FileBasedIndexImpl.java:808)
	at com.intellij.psi.stubs.StubIndexEx.processAllKeys(StubIndexEx.java:305)
	at com.intellij.psi.stubs.StubIndex.processAllKeys(StubIndex.java:71)
	at com.intellij.psi.stubs.StubIndexEx.getAllKeys(StubIndexEx.java:293)
	at com.intellij.lang.javascript.psi.stubs.JSLazyIndexedPackagesIndex.getPackagesToIndex(JSLazyIndexedPackagesIndex.java:75)
	at com.intellij.javascript.nodejs.library.NodeModulesIndexingRulesProvider.updateRequest$lambda-2$lambda-0(NodeModulesIndexingRulesProvider.kt:70)
	at com.intellij.openapi.application.impl.NonBlockingReadActionImpl$OTelMonitor.callWrapped(NonBlockingReadActionImpl.java:746)
	at com.intellij.openapi.application.impl.NonBlockingReadActionImpl$OTelMonitor$MonitoredComputation.call(NonBlockingReadActionImpl.java:778)
	at com.intellij.openapi.application.impl.NonBlockingReadActionImpl$Submission.insideReadAction(NonBlockingReadActionImpl.java:573)
	at com.intellij.openapi.application.impl.NonBlockingReadActionImpl$Submission.lambda$attemptComputation$3(NonBlockingReadActionImpl.java:537)
	at com.intellij.openapi.application.impl.ApplicationImpl.tryRunReadAction(ApplicationImpl.java:1086)
	at com.intellij.openapi.progress.util.ProgressIndicatorUtils.lambda$runInReadActionWithWriteActionPriority$0(ProgressIndicatorUtils.java:71)
	at com.intellij.openapi.progress.util.ProgressIndicatorUtilService.runActionAndCancelBeforeWrite(ProgressIndicatorUtilService.java:63)
	at com.intellij.openapi.progress.util.ProgressIndicatorUtils.runActionAndCancelBeforeWrite(ProgressIndicatorUtils.java:128)
	at com.intellij.openapi.progress.util.ProgressIndicatorUtils.lambda$runWithWriteActionPriority$1(ProgressIndicatorUtils.java:109)
	at com.intellij.openapi.progress.ProgressManager.lambda$runProcess$0(ProgressManager.java:68)
	at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$runProcess$2(CoreProgressManager.java:190)
	at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$executeProcessUnderProgress$13(CoreProgressManager.java:591)
	at com.intellij.openapi.progress.impl.CoreProgressManager.registerIndicatorAndRun(CoreProgressManager.java:666)
	at com.intellij.openapi.progress.impl.CoreProgressManager.computeUnderProgress(CoreProgressManager.java:622)
	at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:590)
	at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:60)
	at com.intellij.openapi.progress.impl.CoreProgressManager.runProcess(CoreProgressManager.java:177)
	at com.intellij.openapi.progress.ProgressManag

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4. See error

Expected behavior (*)

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Please complete the following information: (*)

• OS: Linux 5.19.0-26-generic
• PhpStorm/Intellij version: 2022.3
• Plugin Version: 5.0.1-alpha-2022-12-23-10-43

Additional context

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[m2-assistant]

Hi @VitaliyBoyko. Thank you for your report.
To speed up processing of this issue, make sure that you provided sufficient information.

Add a comment to assign the issue: @magento I am working on this

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