Fix test.py and tests to use an explicit --packages flag.

tests/standalone/package/scenarios/packages_file_strange_formatting/empty_package_dir_test.dart

 // Copyright (c) 2015, the Dart project authors.  Please see the AUTHORS file
 // for details. All rights reserved. Use of this source code is governed by a
 // BSD-style license that can be found in the LICENSE file.
 
-// PackageRoot=none
 // Packages=empty_package_dir.packages
 
 // In this test, we give a packages file that associates the package 'foo' with
 // the empty string. This causes both the VM and dart2js to resolve
 // 'package:foo' imports relative to the root directory. So the import statement
 // `import 'package:foo/foo.dart'` is equivalent to `import '/foo.dart'`.
 library empty_package_dir_test;
 
 import 'package:foo/foo.dart';
 
 main() {
 }