diff -r bb45190a54b7 -r fb92927f9775 mercurial/verify.py
--- a/mercurial/verify.py	Tue Feb 02 17:31:17 2016 -0800
+++ b/mercurial/verify.py	Thu Feb 04 08:34:07 2016 -0800
@@ -284,7 +284,7 @@
         for f, f2, size in repo.store.datafiles():
             if not f:
                 self.err(None, _("cannot decode filename '%s'") % f2)
-            elif size > 0 or not revlogv1:
+            elif (size > 0 or not revlogv1) and f.startswith('data/'):
                 storefiles.add(_normpath(f))
 
         files = sorted(set(filenodes) | set(filelinkrevs))