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 {
					List dirtyFilesList= Arrays.asList(dirtyFiles);
					for (int i= 0; i < editorsToSave.length; i++) {
						if (editorsToSave[i].getEditorInput() instanceof IFileEditorInput) {
							IFile dirtyFile= ((IFileEditorInput)editorsToSave[i].getEditorInput()).getFile();					
							if (dirtyFilesList.contains((dirtyFile)))
								editorsToSave[i].doSave(new SubProgressMonitor(pm, 1));
						}
						pm.worked(1);
					}
				} finally {
					pm.done();
				}
			}
		};
	}
	protected void saveFiles() {
		
		if (fJarPackage.isManifestGenerated() && fJarPackage.isManifestSaved()) {
			try {
				saveManifest();
			} catch (CoreException ex) {
				addError(JarPackagerMessages.getString("JarFileExportOperation.errorSavingManifest"), ex); 
			} catch (IOException ex) {
				addError(JarPackagerMessages.getString("JarFileExportOperation.errorSavingManifest"), ex); 
			}
		}
		
		
		if (fJarPackage.isDescriptionSaved()) {