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.

Comienza reproduciendo una compilación Maven clean desde la CLI mientras jdt.ls está en ejecución, usando la JavaBuilder CoreException reportada como el fallo observado. Rastrea cómo el servidor gestiona los cambios del sistema de archivos durante la compilación externa; se considera terminado cuando el estado de jdt.ls permanece sincronizado con el sistema de archivos y el error deja de aparecer.