External clean build gets jdt.ls out-of-sync

As reported by @xuaveneg in #306, during the execution of a build task (using maven), The errors showing in the output console are:

[Error - 10:27:32] 2 oct. 2017 10:26:41 JavaBuilder handling CoreException
File not found: [filename].
org.eclipse.core.runtime.CoreException: File not found: [filename].
	at org.eclipse.core.internal.filesystem.Policy.error(Policy.java:45)
	at org.eclipse.core.internal.filesystem.local.LocalFile.openInputStream(LocalFile.java:406)
	at org.eclipse.core.internal.localstore.FileSystemResourceManager.read(FileSystemResourceManager.java:849)
	at org.eclipse.core.internal.resources.File.getContents(File.java:277)
	at org.eclipse.jdt.internal.core.util.Util.getResourceContentsAsByteArray(Util.java:1135)
	at org.eclipse.jdt.internal.core.builder.IncrementalImageBuilder.writeClassFileCheck(IncrementalImageBuilder.java:889)
	at org.eclipse.jdt.internal.core.builder.IncrementalImageBuilder.writeClassFileContents(IncrementalImageBuilder.java:831)
	at org.eclipse.jdt.internal.core.builder.AbstractImageBuilder.writeClassFile(AbstractImageBuilder.java:860)
	at org.eclipse.jdt.internal.core.builder.AbstractImageBuilder.acceptResult(AbstractImageBuilder.java:191)
	at org.eclipse.jdt.internal.compiler.Compiler.processCompiledUnits(Compiler.java:593)
	at org.eclipse.jdt.internal.compiler.Compiler.compile(Compiler.java:462)
	at org.eclipse.jdt.internal.compiler.Compiler.compile(Compiler.java:417)
	at org.eclipse.jdt.internal.core.builder.AbstractImageBuilder.compile(AbstractImageBuilder.java:368)
	at org.eclipse.jdt.internal.core.builder.IncrementalImageBuilder.compile(IncrementalImageBuilder.java:330)
	at org.eclipse.jdt.internal.core.builder.AbstractImageBuilder.compile(AbstractImageBuilder.java:305)
	at org.eclipse.jdt.internal.core.builder.IncrementalImageBuilder.build(IncrementalImageBuilder.java:135)
	at org.eclipse.jdt.internal.core.builder.JavaBuilder.buildDeltas(JavaBuilder.java:267)
	at org.eclipse.jdt.internal.core.builder.JavaBuilder.build(JavaBuilder.java:195)
	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)
Caused by: java.io.FileNotFoundException: [filename] (Le chemin d’accès spécifié est introuvable)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at org.eclipse.core.internal.filesystem.local.LocalFile.openInputStream(LocalFile.java:401)
	... 28 more

Running a clean build from CLI, causes a discrepancy between the jdt.ls server state and the file system. We need to handle that better.

Start by reproducing a Maven clean build from the CLI while jdt.ls is running, using the reported JavaBuilder CoreException as the observed failure. Trace how the server handles filesystem changes during the external build; done means the jdt.ls state stays synchronized with the filesystem and the error no longer appears.