Implement applying the patch to the index using git-apply.

If a file is unchanged but stat-dirty, git-apply may erroneously fail to
apply patches, thinking that they conflict with a dirty working tree.

As such, since 2a6f08ac (am: refresh the index at start and --resolved,
2011-08-15), git-am will refresh the index before applying patches.
Re-implement this behavior.
Helped-by: NJunio C Hamano <gitster@pobox.com>
Signed-off-by: NPaul Tan <pyokagan@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>