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 {
				saveDescription();
			} catch (CoreException ex) {
				addError(JarPackagerMessages.getString("JarFileExportOperation.errorSavingDescription"), ex); 
			} catch (IOException ex) {
				addError(JarPackagerMessages.getString("JarFileExportOperation.errorSavingDescription"), ex); 
			}
		}
	}
	protected void saveDescription() throws CoreException, IOException {
		
		if (fJarPackage.isManifestReused())
			fJarPackage.setGenerateManifest(false);
		ByteArrayOutputStream objectStreamOutput= new ByteArrayOutputStream();
		IJarDescriptionWriter writer= fJarPackage.createJarDescriptionWriter(objectStreamOutput);
		ByteArrayInputStream fileInput= null;
		try {
			writer.write(fJarPackage);
			fileInput= new ByteArrayInputStream(objectStreamOutput.toByteArray());
			IFile descriptionFile= fJarPackage.getDescriptionFile();
			if (descriptionFile.isAccessible() && (fJarPackage.allowOverwrite() || JarPackagerUtil.askForOverwritePermission(fParentShell, descriptionFile.getFullPath().toString())))
					descriptionFile.setContents(fileInput, true, true, null);
			else {
				descriptionFile.create(fileInput, true, null);	
			}
		} finally {
			if (fileInput != null)
				fileInput.close();
			if (writer != null)
				writer.close();