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.

Beginne damit, einen Maven clean build über die CLI zu reproduzieren, während jdt.ls läuft, und verwende die gemeldete JavaBuilder CoreException als beobachteten Fehler. Verfolge, wie der Server während des externen Builds Änderungen am Dateisystem verarbeitet. Fertig ist die Aufgabe, wenn der Zustand von jdt.ls mit dem Dateisystem synchron bleibt und der Fehler nicht mehr auftritt.