Bug 13799 JAR exporter exports class files from output folder
There was a problem with the output folder not being detected as such.
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/jarpackager/JarFileExportOperation.java
try {
						new ProgressMonitorDialog(fParentShell).run(false, false, createSaveModifiedResourcesRunnable(dirtyFiles));
						retVal[0]= true;
					} finally {
						description.setAutoBuilding(autoBuild);
						workspace.setDescription(description);
					}
					
				} catch (InvocationTargetException ex) {
					addError(JarPackagerMessages.getString("JarFileExportOperation.errorSavingModifiedResources"), ex); 
					JavaPlugin.log(ex);
					retVal[0]= false;
				} catch (InterruptedException ex) {
						Assert.isTrue(false); 
						retVal[0]= false;
				} catch (CoreException ex) {
					addError(JarPackagerMessages.getString("JarFileExportOperation.errorSavingModifiedResources"), ex); 
					JavaPlugin.log(ex);
					retVal[0]= false;
				}
	 		}
		};
		display.syncExec(runnable);
		return retVal[0];
	}
	private IRunnableWithProgress createSaveModifiedResourcesRunnable(final IFile[] dirtyFiles) {
		return new IRunnableWithProgress() {
			public void run(final IProgressMonitor pm) {
				IEditorPart[] editorsToSave= JavaPlugin.getDirtyEditors();
				pm.beginTask(JarPackagerMessages.getString("JarFileExportOperation.savingModifiedResources"), editorsToSave.length);