(from a customer).

Sometimes, Eclipse gets into a state where class files that the Scala compiler should generate are not present in the output folder. Unfortunately the problem is very difficult to reproduce, so there is no reliable repro project I can send, but I have two observations that may help: one, in the failure case, the progress window indicates a normal build process, which is then unexpectedly followed by a "Cleaning output folder for ..." stage that wipes out the previously (correctly) built class files.

Captured stacktrace in the debugger:

Thread [Worker-23] (Suspended (entry into method delete in File))
File.delete() line: 1028 [local variables unavailable]
LocalFile.internalDelete(File, String, MultiStatus, IProgressMonitor) line: 221
LocalFile.internalDelete(File, String, MultiStatus, IProgressMonitor) line: 241
LocalFile.internalDelete(File, String, MultiStatus, IProgressMonitor) line: 241
LocalFile.internalDelete(File, String, MultiStatus, IProgressMonitor) line: 241
LocalFile.delete(int, IProgressMonitor) line: 129
DeleteVisitor.delete(UnifiedTreeNode, boolean) line: 63
DeleteVisitor.visit(UnifiedTreeNode) line: 150
UnifiedTree.accept(IUnifiedTreeVisitor, int) line: 109
FileSystemResourceManager.delete(IResource, int, IProgressMonitor) line: 349
ResourceTree.internalDeleteFolder(IFolder, int, IProgressMonitor) line: 352
ResourceTree.standardDeleteFolder(IFolder, int, IProgressMonitor) line: 798
Folder(Resource).unprotectedDelete(ResourceTree, int, IProgressMonitor) line: 1977
Folder(Resource).delete(int, IProgressMonitor) line: 803
BatchImageBuilder.cleanOutputFolders(boolean) line: 116
BatchImageBuilder.build() line: 48
GeneralScalaJavaBuilder(JavaBuilder).buildAll() line: 254
GeneralScalaJavaBuilder(JavaBuilder).build(int, Map, IProgressMonitor) line: 178
GeneralScalaJavaBuilder(ScalaJavaBuilder).build(int, Map, IProgressMonitor) line: 27
JavaEclipseCompiler.compile(File[], File[], Output, String[], Logger) line: 47
AggressiveCompile$$anonfun$3$$anonfun$compileJava$1$1.apply$mcV$sp() line: 126
AggressiveCompile$$anonfun$3$$anonfun$compileJava$1$1.apply() line: 126
AggressiveCompile$$anonfun$3$$anonfun$compileJava$1$1.apply() line: 126
AggressiveCompile.sbt$compiler$AggressiveCompile$$timed(String, Logger, Function0<T>) line: 159
AggressiveCompile$$anonfun$3.compileJava$1(AnalysisCallback, Seq) line: 125
AggressiveCompile$$anonfun$3.apply(Set<File>, DependencyChanges, AnalysisCallback) line: 142
AggressiveCompile$$anonfun$3.apply(Object, Object, Object) line: 86
IncrementalCompile$$anonfun$doCompile$1.apply(Set<File>, DependencyChanges) line: 38
IncrementalCompile$$anonfun$doCompile$1.apply(Object, Object) line: 36
Incremental$.cycle(Set<File>, Set<File>, DependencyChanges, Analysis, Function2<Set<File>,DependencyChanges,Analysis>, ClassfileManager, int, Logger, IncOptions) line: 73
Incremental$$anonfun$1.apply(ClassfileManager) line: 33
Incremental$$anonfun$1.apply(Object) line: 32
Incremental$.manageClassfiles(IncOptions, Function1<ClassfileManager,T>) line: 41
Incremental$.compile(Set<File>, Function1<String,Option<File>>, Analysis, ReadStamps, Function1<File,Option<Analysis>>, Function2<Set<File>,DependencyChanges,Analysis>, Logger, IncOptions, Equiv<Stamp>) line: 32
IncrementalCompile$.apply(Set<File>, Function1<String,Option<File>>, Function3<Set<File>,DependencyChanges,AnalysisCallback,BoxedUnit>, Analysis, Function1<File,Option<Analysis>>, Output, Logger, IncOptions) line: 26
AggressiveCompile.compile2(CompileConfiguration, Logger, Equiv<CompileSetup>) line: 150
AggressiveCompile.compile1(Seq<File>, Seq<File>, CompileSetup, Option<CompileProgress>, AnalysisStore, Function1<File,Option<Analysis>>, Function1<File,Function1<String,Object>>, AnalyzingCompiler, JavaCompiler, Reporter, boolean, GlobalsCache, IncOptions, Logger) line: 70
AggressiveCompile.apply(AnalyzingCompiler, JavaCompiler, Seq<File>, Seq<File>, Output, GlobalsCache, Option<CompileProgress>, Seq<String>, Seq<String>, Function1<File,Option<Analysis>>, Function1<File,Function1<String,Object>>, Reporter, CompileOrder, boolean, IncOptions, Logger) line: 45
IC$.compile(Inputs<Analysis,AnalyzingCompiler>, Logger) line: 22
EclipseSbtBuildManager.runCompiler(Seq<File>) line: 133
EclipseSbtBuildManager.update(Set<AbstractFile>, Set<AbstractFile>) line: 124
EclipseSbtBuildManager.build(Set<IFile>, Set<IFile>, SubMonitor) line: 178
ScalaProject.build(Set<IFile>, Set<IFile>, SubMonitor) line: 666
ScalaBuilder.build(int, Map<String,String>, IProgressMonitor) line: 119
BuildManager$3.run() line: 783
SafeRunner.run(ISafeRunnable) line: 42
BuildManager.basicBuild(int, IncrementalProjectBuilder, Map<String,String>, MultiStatus, IProgressMonitor) line: 212
BuildManager.basicBuild(IBuildConfiguration, int, IBuildContext, ICommand[], MultiStatus, IProgressMonitor) line: 257
BuildManager$1.run() line: 310
SafeRunner.run(ISafeRunnable) line: 42
BuildManager.basicBuild(IBuildConfiguration, int, IBuildContext, MultiStatus, IProgressMonitor) line: 313
BuildManager.basicBuildLoop(IBuildConfiguration[], IBuildConfiguration[], int, MultiStatus, IProgressMonitor) line: 369
BuildManager.build(IBuildConfiguration[], IBuildConfiguration[], int, IProgressMonitor) line: 422
Workspace.buildInternal(IBuildConfiguration[], int, boolean, IProgressMonitor) line: 513
Workspace.build(IBuildConfiguration[], int, boolean, IProgressMonitor) line: 432
BuildAction$1.runInWorkspace(IProgressMonitor) line: 305
BuildAction$1(InternalWorkspaceJob).run(IProgressMonitor) line: 38
Worker.run() line: 54