The specified line with the clean() call is the same. The only difference in the files is that the messageClass gets a suffix for encrypted messages:
322,323c322,333
< // @TODO: add messageClass suffix for encrypted messages
< $result['messageClass'] = 'IPM.Note';
---
> if ($headers->ctype == 'multipart/signed'
> && count($message->attachments) == 1 && $message->attachments[0]->mimetype == 'application/pkcs7-signature'
> ) {
> $result['messageClass'] = 'IPM.Note.SMIME.MultipartSigned';
> }
> else if ($headers->ctype == 'application/pkcs7-mime' || $headers->ctype == 'application/x-pkcs7-mime') {
> $result['messageClass'] = 'IPM.Note.SMIME';
> }
> else {
> $result['messageClass'] = 'IPM.Note';
> }
>