Project with _tests_ breaks when used with a plugin combo of `war` and `liberty` with gradle.

A plain gradle webapp project with war plugin that has tests will completely break in vscode the moment the plugin id "io.openliberty.tools.gradle.Liberty" version "3.1-SNAPSHOT" is introduced into the build. Autocompletion dies, errors appear on every class there is in the main and test trees. If the plugin is removed, it goes back to normal. Alternatively, If the src/test folder is removed and liberty plugin kept, project goes back to normal.

From command line, everything is normal, project builds/tests without issues.

Environment

• Operating System: Ubuntu 20.04.1 LTS
• JDK version: 14 - Oracle and openjdk
• Visual Studio Code version: latest
• Java extension version: latest
• With Gradle 6.6

Steps To Reproduce

1. Make a new gradle webapp project with the war plugin.
2. Add some plain junit test.
3. Introduce the io.openliberty.tools.gradle.Liberty to the build.
4. Everything breaks in vscode, but can run the build from command line (build, test, etc).
5. Remove the war and its place add java-library plugin and in vscode everything returns to normal.
6. Alternatively to 5, keep the war plugin and remove the src/test folder and in vscode everything return to normal.

Error taken from the Output of Language Support for Java:

WARNING: Using incubator modules: jdk.incubator.foreign, jdk.incubator.jpackage
[Error - 6:15:59 PM] Aug 20, 2020, 6:15:59 PM Failed to configure project war-liberty-sample
Test source folder 'src/test/java' in project 'war-liberty-sample' must have an output folder that is not also used for main sources
Java Model Exception: Java Model Status [Test source folder 'src/test/java' in project 'war-liberty-sample' must have an output folder that is not also used for main sources]
	at org.eclipse.jdt.internal.core.JavaModelOperation.runOperation(JavaModelOperation.java:798)
	at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3608)
	at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3568)
	at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3624)
	at org.eclipse.buildship.core.internal.workspace.SourceFolderUpdater.updateSourceFolders(SourceFolderUpdater.java:71)
	at org.eclipse.buildship.core.internal.workspace.SourceFolderUpdater.update(SourceFolderUpdater.java:169)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.synchronizeJavaProjectInTransaction(BaseConfigurator.java:116)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.access$000(BaseConfigurator.java:40)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator$1.run(BaseConfigurator.java:105)
	at org.eclipse.jdt.internal.core.BatchOperation.executeOperation(BatchOperation.java:41)
	at org.eclipse.jdt.internal.core.JavaModelOperation.run(JavaModelOperation.java:736)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2292)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2317)
	at org.eclipse.jdt.core.JavaCore.run(JavaCore.java:5895)
	at org.eclipse.jdt.core.JavaCore.run(JavaCore.java:5852)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.synchronizeJavaProject(BaseConfigurator.java:101)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.configure(BaseConfigurator.java:91)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.configure(BaseConfigurator.java:66)
	at org.eclipse.buildship.core.internal.extension.InternalProjectConfigurator.configure(InternalProjectConfigurator.java:65)
	at org.eclipse.buildship.core.internal.workspace.ProjectConfigurators.configureConfigurators(ProjectConfigurators.java:70)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.synchronizeOpenWorkspaceProject(SynchronizeGradleBuildOperation.java:163)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.synchronizeWorkspaceProject(SynchronizeGradleBuildOperation.java:137)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.synchronizeGradleProjectWithWorkspaceProject(SynchronizeGradleBuildOperation.java:127)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.access$000(SynchronizeGradleBuildOperation.java:42)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation$1.run(SynchronizeGradleBuildOperation.java:85)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2292)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2312)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.synchronizeProjectsWithWorkspace(SynchronizeGradleBuildOperation.java:82)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.run(SynchronizeGradleBuildOperation.java:64)
	at org.eclipse.buildship.core.internal.DefaultGradleBuild$SynchronizeOperation.runInToolingApi(DefaultGradleBuild.java:230)
	at org.eclipse.buildship.core.internal.operation.DefaultToolingApiOperationManager$WorkspaceRunnableAdapter.run(DefaultToolingApiOperationManager.java:58)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2292)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2317)
	at org.eclipse.buildship.core.internal.operation.DefaultToolingApiOperationManager.run(DefaultToolingApiOperationManager.java:39)
	at org.eclipse.buildship.core.internal.DefaultGradleBuild$SynchronizeOperation.run(DefaultGradleBuild.java:192)
	at org.eclipse.buildship.core.internal.DefaultGradleBuild.synchronize(DefaultGradleBuild.java:100)
	at org.eclipse.buildship.core.internal.DefaultGradleBuild.synchronize(DefaultGradleBuild.java:86)
	at org.eclipse.jdt.ls.core.internal.managers.GradleProjectImporter.startSynchronization(GradleProjectImporter.java:238)
	at org.eclipse.jdt.ls.core.internal.managers.GradleProjectImporter.importDir(GradleProjectImporter.java:127)
	at org.eclipse.jdt.ls.core.internal.managers.GradleProjectImporter.lambda$0(GradleProjectImporter.java:119)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at java.base/java.util.Collections$UnmodifiableCollection.forEach(Collections.java:1087)
	at org.eclipse.jdt.ls.core.internal.managers.GradleProjectImporter.importToWorkspace(GradleProjectImporter.java:119)
	at org.eclipse.jdt.ls.core.internal.managers.ProjectsManager.importProjects(ProjectsManager.java:108)
	at org.eclipse.jdt.ls.core.internal.managers.ProjectsManager.initializeProjects(ProjectsManager.java:98)
	at org.eclipse.jdt.ls.core.internal.handlers.InitHandler$1.runInWorkspace(InitHandler.java:195)
	at org.eclipse.core.internal.resources.InternalWorkspaceJob.run(InternalWorkspaceJob.java:42)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)

[Error - 6:15:59 PM] Aug 20, 2020, 6:15:59 PM Failed to configure project war-liberty-sample
Test source folder 'src/test/java' in project 'war-liberty-sample' must have an output folder that is not also used for main sources
Java Model Exception: Java Model Status [Test source folder 'src/test/java' in project 'war-liberty-sample' must have an output folder that is not also used for main sources]
	at org.eclipse.jdt.internal.core.JavaModelOperation.runOperation(JavaModelOperation.java:798)
	at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3608)
	at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3568)
	at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3624)
	at org.eclipse.buildship.core.internal.workspace.SourceFolderUpdater.updateSourceFolders(SourceFolderUpdater.java:71)
	at org.eclipse.buildship.core.internal.workspace.SourceFolderUpdater.update(SourceFolderUpdater.java:169)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.synchronizeJavaProjectInTransaction(BaseConfigurator.java:116)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.access$000(BaseConfigurator.java:40)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator$1.run(BaseConfigurator.java:105)
	at org.eclipse.jdt.internal.core.BatchOperation.executeOperation(BatchOperation.java:41)
	at org.eclipse.jdt.internal.core.JavaModelOperation.run(JavaModelOperation.java:736)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2292)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2317)
	at org.eclipse.jdt.core.JavaCore.run(JavaCore.java:5895)
	at org.eclipse.jdt.core.JavaCore.run(JavaCore.java:5852)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.synchronizeJavaProject(BaseConfigurator.java:101)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.configure(BaseConfigurator.java:91)
	at org.eclipse.buildship.core.internal.workspace.BaseConfigurator.configure(BaseConfigurator.java:66)
	at org.eclipse.buildship.core.internal.extension.InternalProjectConfigurator.configure(InternalProjectConfigurator.java:65)
	at org.eclipse.buildship.core.internal.workspace.ProjectConfigurators.configureConfigurators(ProjectConfigurators.java:70)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.synchronizeOpenWorkspaceProject(SynchronizeGradleBuildOperation.java:163)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.synchronizeWorkspaceProject(SynchronizeGradleBuildOperation.java:137)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.synchronizeGradleProjectWithWorkspaceProject(SynchronizeGradleBuildOperation.java:127)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.access$000(SynchronizeGradleBuildOperation.java:42)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation$1.run(SynchronizeGradleBuildOperation.java:85)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2292)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2312)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.synchronizeProjectsWithWorkspace(SynchronizeGradleBuildOperation.java:82)
	at org.eclipse.buildship.core.internal.workspace.SynchronizeGradleBuildOperation.run(SynchronizeGradleBuildOperation.java:64)
	at org.eclipse.buildship.core.internal.DefaultGradleBuild$SynchronizeOperation.runInToolingApi(DefaultGradleBuild.java:230)
	at org.eclipse.buildship.core.internal.operation.DefaultToolingApiOperationManager$WorkspaceRunnableAdapter.run(DefaultToolingApiOperationManager.java:58)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2292)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2317)
	at org.eclipse.buildship.core.internal.operation.DefaultToolingApiOperationManager.run(DefaultToolingApiOperationManager.java:39)
	at org.eclipse.buildship.core.internal.DefaultGradleBuild$SynchronizeOperation.run(DefaultGradleBuild.java:192)
	at org.eclipse.buildship.core.internal.DefaultGradleBuild.synchronize(DefaultGradleBuild.java:100)
	at org.eclipse.buildship.core.internal.DefaultGradleBuild.synchronize(DefaultGradleBuild.java:86)
	at org.eclipse.jdt.ls.core.internal.managers.GradleProjectImporter.startSynchronization(GradleProjectImporter.java:238)
	at org.eclipse.jdt.ls.core.internal.managers.GradleProjectImporter.importDir(GradleProjectImporter.java:127)
	at org.eclipse.jdt.ls.core.internal.managers.GradleProjectImporter.lambda$0(GradleProjectImporter.java:119)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at java.base/java.util.Collections$UnmodifiableCollection.forEach(Collections.java:1087)
	at org.eclipse.jdt.ls.core.internal.managers.GradleProjectImporter.importToWorkspace(GradleProjectImporter.java:119)
	at org.eclipse.jdt.ls.core.internal.managers.ProjectsManager.importProjects(ProjectsManager.java:108)
	at org.eclipse.jdt.ls.core.internal.managers.ProjectsManager.initializeProjects(ProjectsManager.java:98)
	at org.eclipse.jdt.ls.core.internal.handlers.InitHandler$1.runInWorkspace(InitHandler.java:195)
	at org.eclipse.core.internal.resources.InternalWorkspaceJob.run(InternalWorkspaceJob.java:42)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)

[Error - 6:16:00 PM] Aug 20, 2020, 6:16:00 PM An internal error occurred during: "Initialize workspace".
Path must include project and resource name: /war-liberty-sample
java.lang.IllegalArgumentException: Path must include project and resource name: /war-liberty-sample
	at org.eclipse.core.runtime.Assert.isLegal(Assert.java:66)
	at org.eclipse.core.internal.resources.Workspace.newResource(Workspace.java:2122)
	at org.eclipse.core.internal.resources.Container.getFolder(Container.java:205)
	at org.eclipse.jdt.ls.core.internal.managers.StandardProjectsManager.registerWatchers(StandardProjectsManager.java:335)
	at org.eclipse.jdt.ls.core.internal.handlers.JDTLanguageServer$2.run(JDTLanguageServer.java:300)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)

[Error - 6:16:00 PM] Aug 20, 2020, 6:16:00 PM An internal error occurred during: "Register Watchers".
Path must include project and resource name: /war-liberty-sample
java.lang.IllegalArgumentException: Path must include project and resource name: /war-liberty-sample
	at org.eclipse.core.runtime.Assert.isLegal(Assert.java:66)
	at org.eclipse.core.internal.resources.Workspace.newResource(Workspace.java:2122)
	at org.eclipse.core.internal.resources.Container.getFolder(Container.java:205)
	at org.eclipse.jdt.ls.core.internal.managers.StandardProjectsManager.registerWatchers(StandardProjectsManager.java:335)
	at org.eclipse.jdt.ls.core.internal.managers.StandardProjectsManager$1.run(StandardProjectsManager.java:99)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)

Current Result

Attaching minimum sample. In build.gradle -> plugins can switch between the id 'java-library' and id 'war' plugins. When the war plugin is active, project breaks in vscode (errors on every class, no autocomplete) if there is src/test.

Try remove the src/test folder and it returns to normal.

Expected Result

Additional Informations

Tried cleaning all conceivable caches - gradle and vscode included. Ran it in a fresh VM as well with the same gradle/java combo. Affects local vscode development as well as the remote option (via ssh).

tar -xzvf
war-liberty-sample.tar.gz

Reproduce the failure with a Gradle webapp using the war and Liberty plugins plus src/test/java. Start from the reported SourceFolderUpdater.updateSourceFolders stack-trace entry and inspect the Gradle project import path. Done means VS Code configures both main and test sources without the output-folder error while command-line build and tests continue to work.