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

Reproduce the issue by opening typescript-generator in VS Code and running mvn clean install, then compare the build with VS Code closed. Start at WorkspaceDiagnosticsHandler.convertRange and the reported AxiosClientExtensionTest and ImmutablesTest failures; done means the Maven build passes with the extension active and no BadLocationException appears.