diff --git a/tests/wpt/manifestupdate.py b/tests/wpt/manifestupdate.py
index 3615d6c3e05..63178726f73 100644
--- a/tests/wpt/manifestupdate.py
+++ b/tests/wpt/manifestupdate.py
@@ -6,6 +6,7 @@ import argparse
 import imp
 import os
 import sys
+import tempfile
 from collections import defaultdict
 
 from mozlog.structured import commandline
@@ -77,10 +78,28 @@ def _check_clean(logger, test_paths):
     for url_base, paths in test_paths.iteritems():
         tests_path = paths["tests_path"]
         manifest_path = os.path.join(paths["metadata_path"], "MANIFEST.json")
-        old_manifest = manifest.manifest.load(tests_path, manifest_path)
-        new_manifest = manifest.manifest.Manifest.from_json(tests_path,
-                                                            old_manifest.to_json())
-        manifest.update.update(tests_path, new_manifest, working_copy=True)
+
+        old_manifest = manifest.manifest.load_and_update(tests_path,
+                                                         manifest_path,
+                                                         url_base,
+                                                         working_copy=False,
+                                                         update=False,
+                                                         write_manifest=False,)
+
+        # Even if no cache is specified, one will be used automatically by the
+        # VCS integration. Create a brand new cache every time to ensure that
+        # the VCS integration always thinks that any file modifications in the
+        # working directory are new and interesting.
+        cache_root = tempfile.mkdtemp()
+        new_manifest = manifest.manifest.load_and_update(tests_path,
+                                                         manifest_path,
+                                                         url_base,
+                                                         working_copy=True,
+                                                         update=True,
+                                                         cache_root=cache_root,
+                                                         write_manifest=False,
+                                                         allow_cached=False)
+
         manifests_by_path[manifest_path] = (old_manifest, new_manifest)
 
     for manifest_path, (old_manifest, new_manifest) in manifests_by_path.iteritems():