Call refresh_cache() when updating the user index for --only commits.

We're guaranteeing the user that the index will be stat-clean after
git commit. Thus, we need to call refresh_cache() for the user index too,
in the 'git commit <paths>' case.
Signed-off-by: NKristian Høgsberg <krh@redhat.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

builtin-commit.c

@@ -109,6 +109,7 @@ static char *prepare_index(const char **files, const char *prefix)
 
 	/* update the user index file */
 	add_files_to_cache(verbose, prefix, files);
+	refresh_cache(REFRESH_QUIET);
 	if (write_cache(fd, active_cache, active_nr) || close(fd))
 		die("unable to write new_index file");