diff -r f0e9f38d250f -r 54522bbe1597 mercurial/context.py
--- a/mercurial/context.py	Tue Jan 12 13:43:41 2016 -0800
+++ b/mercurial/context.py	Tue Jan 12 12:43:36 2016 -0800
@@ -140,9 +140,15 @@
                 added.append(fn)
             elif node2 is None:
                 removed.append(fn)
+            elif node2 != _newnode:
+                # The file was not a new file in mf2, so an entry
+                # from diff is really a difference.
+                modified.append(fn)
             elif flag1 != flag2:
                 modified.append(fn)
             elif self[fn].cmp(other[fn]):
+                # node2 was newnode, but the working file doesn't
+                # match the one in mf1.
                 modified.append(fn)
             else:
                 clean.append(fn)