t4111 (apply): refresh index before applying patches to it

"git apply", like most plumbing, does not automatically refresh the
index file even if it is only stat-dirty.  So unless the two "cp"
commands in reset_preimage() for a given file happen to have the same
time stamp, there will be a spurious

	error: sub/dir/file: does not match index

Refresh the index to eliminate this timing dependency.  Noticed by
running the test with --valgrind (which slows things down a lot).

Reported-by: Thomas Rast <trast@student.ethz.ch>
Signed-off-by: Jonathan Nieder <jrnieder@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

t/t4111-apply-subdir.sh

@@ -36,7 +36,8 @@ test_expect_success 'setup: subdir' '
 		cp "$2" file &&
 		cp "$2" sub/dir/file &&
 		cp "$2" sub/dir/b/file &&
-		cp "$2" objects/file
+		cp "$2" objects/file &&
+		test_might_fail git update-index --refresh -q
 	}
 '