Extension causes `bad class file` and `ClassNotFoundException` in Maven build

I have a Maven project with submodules. When I open it in VS Code with this extension installed everything seems to work perfectly (code completion, javadoc, go to definition...). But when I run mvn clean install externally extension starts throwing tens of BadLocationExceptions (displayed in Output tab).

Moreover maven build fails! I can see some bad class file errors from maven-compiler-plugin and bellow TypeNotPresentException caused by ClassNotFoundException from some test run by maven-surefire-plugin. When I close VS Code Maven build works.

Environment

• Operating System: Window 10
• JDK version: 1.8.0_112
• Visual Studio Code version: 1.17.0
• Java extension version: 0.11.0

Steps To Reproduce

1. clone https://github.com/vojtechhabarta/typescript-generator.git
2. open folder in VS Code
3. check that it works
4. run mvn clean install
5. build fails with TypeNotPresentException in tests

BadLocationException in VS Code Output window:

org.eclipse.jface.text.BadLocationException
	at org.eclipse.jface.text.ListLineTracker.getLineOffset(ListLineTracker.java:191)
	at org.eclipse.jface.text.AbstractLineTracker.getLineOffset(AbstractLineTracker.java:157)
	at org.eclipse.jface.text.AbstractDocument.getLineOffset(AbstractDocument.java:873)
	at org.eclipse.jdt.ls.core.internal.handlers.WorkspaceDiagnosticsHandler.convertRange(WorkspaceDiagnosticsHandler.java:164)
	at org.eclipse.jdt.ls.core.internal.handlers.WorkspaceDiagnosticsHandler.toDiagnostic(WorkspaceDiagnosticsHandler.java:144)
	at org.eclipse.jdt.ls.core.internal.handlers.WorkspaceDiagnosticsHandler.lambda$0(WorkspaceDiagnosticsHandler.java:129)
	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
	at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
	at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
	at org.eclipse.jdt.ls.core.internal.handlers.WorkspaceDiagnosticsHandler.toDiagnosticsArray(WorkspaceDiagnosticsHandler.java:131)
	at org.eclipse.jdt.ls.core.internal.handlers.WorkspaceDiagnosticsHandler.visit(WorkspaceDiagnosticsHandler.java:115)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:64)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:75)
	at org.eclipse.core.internal.events.ResourceDelta.accept(ResourceDelta.java:48)
	at org.eclipse.jdt.ls.core.internal.handlers.WorkspaceDiagnosticsHandler.resourceChanged(WorkspaceDiagnosticsHandler.java:62)
	at org.eclipse.core.internal.events.NotificationManager$1.run(NotificationManager.java:299)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.internal.events.NotificationManager.notify(NotificationManager.java:289)
	at org.eclipse.core.internal.events.NotificationManager.broadcastChanges(NotificationManager.java:152)
	at org.eclipse.core.internal.resources.Workspace.broadcastPostChange(Workspace.java:374)
	at org.eclipse.core.internal.resources.Workspace.endOperation(Workspace.java:1469)
	at org.eclipse.core.internal.events.AutoBuildJob.doBuild(AutoBuildJob.java:157)
	at org.eclipse.core.internal.events.AutoBuildJob.run(AutoBuildJob.java:232)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:56)

Sample error in maven-compiler-plugin:

cz/habarta/typescript/generator/ext/AxiosClientExtensionTest.java:[4,39] cannot access cz.habarta.typescript.generator.Input
  bad class file: ...\typescript-generator\typescript-generator-core\target\classes\cz\habarta\typescript\generator\Input.class
    unable to access file: ...\typescript-generator\typescript-generator-core\target\classes\cz\habarta\typescript\generator\Input.class (The system cannot find the file specified)
    Please remove or make sure it appears in the correct subdirectory of the classpath.

Sample error from test in maven-surefire-plugin:

java.lang.TypeNotPresentException: Type ImmutableRectangle not present
	at sun.reflect.annotation.TypeNotPresentExceptionProxy.generateException(TypeNotPresentExceptionProxy.java:46)
	at sun.reflect.annotation.AnnotationInvocationHandler.invoke(AnnotationInvocationHandler.java:84)
	at com.sun.proxy.$Proxy24.as(Unknown Source)
	at com.fasterxml.jackson.databind.introspect.JacksonAnnotationIntrospector.findSerializationType(JacksonAnnotationIntrospector.java:758)
	at com.fasterxml.jackson.databind.AnnotationIntrospector.refineSerializationType(AnnotationIntrospector.java:843)
	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:152)
	at cz.habarta.typescript.generator.parser.Jackson2Parser.getBeanHelper(Jackson2Parser.java:243)
	at cz.habarta.typescript.generator.parser.Jackson2Parser.parseBean(Jackson2Parser.java:70)
	at cz.habarta.typescript.generator.parser.Jackson2Parser.parseClass(Jackson2Parser.java:63)
	at cz.habarta.typescript.generator.parser.ModelParser.parseQueue(ModelParser.java:67)
	at cz.habarta.typescript.generator.parser.ModelParser.parseModel(ModelParser.java:36)
	at cz.habarta.typescript.generator.TypeScriptGenerator.generateTypeScript(TypeScriptGenerator.java:51)
	at cz.habarta.typescript.generator.TypeScriptGenerator.generateTypeScript(TypeScriptGenerator.java:43)
	at cz.habarta.typescript.generator.TypeScriptGenerator.generateTypeScript(TypeScriptGenerator.java:38)
	at cz.habarta.typescript.generator.ImmutablesTest.testImmutables(ImmutablesTest.java:17)
	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:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
	at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:367)
	at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:274)
	at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
	at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:161)
	at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:290)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:242)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:121)
Caused by: java.lang.ClassNotFoundException: ImmutableRectangle
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:348)
	at sun.reflect.generics.factory.CoreReflectionFactory.makeNamedType(CoreReflectionFactory.java:114)
	at sun.reflect.generics.visitor.Reifier.visitClassTypeSignature(Reifier.java:125)
	at sun.reflect.generics.tree.ClassTypeSignature.accept(ClassTypeSignature.java:49)
	at sun.reflect.annotation.AnnotationParser.parseSig(AnnotationParser.java:439)
	at sun.reflect.annotation.AnnotationParser.parseClassValue(AnnotationParser.java:420)
	at sun.reflect.annotation.AnnotationParser.parseMemberValue(AnnotationParser.java:349)
	at sun.reflect.annotation.AnnotationParser.parseAnnotation2(AnnotationParser.java:286)
	at sun.reflect.annotation.AnnotationParser.parseAnnotations2(AnnotationParser.java:120)
	at sun.reflect.annotation.AnnotationParser.parseAnnotations(AnnotationParser.java:72)
	at java.lang.Class.createAnnotationData(Class.java:3521)
	at java.lang.Class.annotationData(Class.java:3510)
	at java.lang.Class.getAnnotation(Class.java:3415)
	at cz.habarta.typescript.generator.parser.JaxrsApplicationParser.tryParse(JaxrsApplicationParser.java:78)
	at cz.habarta.typescript.generator.parser.ModelParser.parseQueue(ModelParser.java:55)
	... 29 more

Tái hiện sự cố bằng cách mở typescript-generator trong VS Code và chạy mvn clean install, sau đó so sánh bản build khi VS Code đã đóng. Bắt đầu từ WorkspaceDiagnosticsHandler.convertRange và các lỗi được báo cáo của AxiosClientExtensionTest và ImmutablesTest; hoàn tất khi bản build Maven thành công với extension đang hoạt động và không xuất hiện BadLocationException.