diff -r 39d1f83eb05d -r 63c817ea4a70 mercurial/localrepo.py
--- a/mercurial/localrepo.py	Tue Apr 24 16:32:44 2012 +0200
+++ b/mercurial/localrepo.py	Sat Apr 28 15:01:57 2012 +0200
@@ -1147,6 +1147,9 @@
                 and wctx.branch() == wctx.p1().branch()):
                 return None
 
+            if merge and changes[3]:
+                raise util.Abort(_("cannot commit merge with missing files"))
+
             ms = mergemod.mergestate(self)
             for f in changes[0]:
                 if f in ms and ms[f] == 'u':