ResourceException: Problems encountered while copying resources.

I started getting the error below popping up every once in a while since upgrading to one of the later releases.

Environment

• Operating System: OSX Sierra - 10.12.3
• JDK version: 8.121
• Visual Studio Code version: 1.10.2
• Java extension version: 0.0.13

Steps To Reproduce

1. Ever since the latest update I have been receiving the error below. This is happening on an Android project.

[Error - 5:00:10 PM] Mar 20, 2017 2:50:47 PM JavaBuilder handling ImageBuilderInternalException while building: jdt.ls-java-project
Problems encountered while copying resources.
org.eclipse.core.internal.resources.ResourceException: Problems encountered while copying resources.
	at org.eclipse.core.internal.localstore.FileSystemResourceManager.copy(FileSystemResourceManager.java:336)
	at org.eclipse.core.internal.resources.Resource.copy(Resource.java:545)
	at org.eclipse.jdt.internal.core.builder.AbstractImageBuilder.copyResource(AbstractImageBuilder.java:383)
	at org.eclipse.jdt.internal.core.builder.BatchImageBuilder$3.visit(BatchImageBuilder.java:231)
	at org.eclipse.core.internal.resources.Resource$1.visitElement(Resource.java:84)
	at org.eclipse.core.internal.watson.ElementTreeIterator.doIteration(ElementTreeIterator.java:82)
	at org.eclipse.core.internal.watson.ElementTreeIterator.doIteration(ElementTreeIterator.java:87)
	at org.eclipse.core.internal.watson.ElementTreeIterator.iterate(ElementTreeIterator.java:129)
	at org.eclipse.core.internal.resources.Resource.accept(Resource.java:94)
	at org.eclipse.core.internal.resources.Resource.accept(Resource.java:52)
	at org.eclipse.jdt.internal.core.builder.BatchImageBuilder.copyExtraResourcesBack(BatchImageBuilder.java:200)
	at org.eclipse.jdt.internal.core.builder.BatchImageBuilder.cleanOutputFolders(BatchImageBuilder.java:124)
	at org.eclipse.jdt.internal.core.builder.BatchImageBuilder.build(BatchImageBuilder.java:47)
	at org.eclipse.jdt.internal.core.builder.JavaBuilder.buildAll(JavaBuilder.java:256)
	at org.eclipse.jdt.internal.core.builder.JavaBuilder.build(JavaBuilder.java:180)
	at org.eclipse.core.internal.events.BuildManager$2.run(BuildManager.java:735)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.internal.events.BuildManager.basicBuild(BuildManager.java:206)
	at org.eclipse.core.internal.events.BuildManager.basicBuild(BuildManager.java:246)
	at org.eclipse.core.internal.events.BuildManager$1.run(BuildManager.java:301)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.internal.events.BuildManager.basicBuild(BuildManager.java:304)
	at org.eclipse.core.internal.events.BuildManager.basicBuildLoop(BuildManager.java:360)
	at org.eclipse.core.internal.events.BuildManager.build(BuildManager.java:383)
	at org.eclipse.core.internal.events.AutoBuildJob.doBuild(AutoBuildJob.java:142)
	at org.eclipse.core.internal.events.AutoBuildJob.run(AutoBuildJob.java:232)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:56)
Contains: Resource '/jdt.ls-java-project/src/pom.xml' does not exist.

Unfortunately, I am not able to upload a sample project right now.

Start by reproducing the intermittent failure in an Android project using the reported VS Code and Java extension environment. Trace the ResourceException from JavaBuilder through BatchImageBuilder.copyExtraResourcesBack, focusing on the missing jdt.ls-java-project/src/pom.xml resource. Done means the copying failure is understood and no longer occurs under the reported conditions.