The email_to_user function does not accept multiple attachments, even though the base class PHPMailer supports such behavior with multiple calls to $mailer->AddAttachment.

My suggestion is to make the 6th and 7th argument to email_to_user accept array values with their string content. Such a solution would be backward compatible with the existing behavior, and support the desired behavior. Here's an example of what some client code would look like:

$attachments = array();

foreach ($file in $files) {

  $attachment[$file->get_filename()] = $file->get_filepath();

}

$filenames = array_keys($attachments);

$filepaths = array_values($attachments);

email_to_user($user, $USER, 'Multiple attachments', '', '', $filenames, $filepaths);

I've attached a patch that allows for this behavior (I think).