Index: pym/portage.py
===================================================================
--- pym/portage.py	(revision 6016)
+++ pym/portage.py	(working copy)
@@ -2692,8 +2692,11 @@
 				writemsg("!!! Invalid SRC_URI for '%s'.\n" % cpv, noiselevel=-1)
 				del e
 				return 0
+		mytree = os.path.dirname(os.path.dirname(mysettings["O"]))
+		manifest1_compat = not os.path.exists(
+			os.path.join(mytree, "manifest1_obsolete"))
 		mf = Manifest(mysettings["O"], mysettings["DISTDIR"],
-			fetchlist_dict=fetchlist_dict)
+			fetchlist_dict=fetchlist_dict, manifest1_compat=manifest1_compat)
 		# Don't require all hashes since that can trigger excessive
 		# fetches when sufficient digests already exist.  To ease transition
 		# while Manifest 1 is being removed, only require hashes that will
Index: pym/portage_manifest.py
===================================================================
--- pym/portage_manifest.py	(revision 6016)
+++ pym/portage_manifest.py	(working copy)
@@ -425,7 +425,8 @@
 		else:
 			distfilehashes = {}
 		self.__init__(self.pkgdir, self.distdir,
-			fetchlist_dict=self.fetchlist_dict, from_scratch=True)
+			fetchlist_dict=self.fetchlist_dict, from_scratch=True,
+			manifest1_compat=self.compat)
 		for pkgdir, pkgdir_dirs, pkgdir_files in os.walk(self.pkgdir):
 			break
 		for f in pkgdir_files: