Trouble with Digest/Email Frequency Integration

I just battled with both modules as well, and after a lengthy debugging session I discovered what I think are potential flaws in both modules. My conclusion is as follows:

message_digest\plugins\notifier\abstract.inc, public function agregate()

$start is set to the $interval (1 day or 1 week) prior to now:
$start = strtotime('-' . $interval);

This is the query that gets message digest entries (all entries larger than $start):
$query->condition('timestamp', $start, '>');

Should this query not rather grab all entries that are smaller than $start?
$query->condition('timestamp', $start, '<');

Then coming to the message_subscribe_email_frequency.module:

function message_subscribe_email_frequency_message_subscribe_get_subscribers_alter(&$uids, $values) {
  if (empty($uids)) {
    // Nobody is subscribed to the content.
    return;
  }

  // Get the frequency setting for any users subscribed to the content.
  // We don't use the Field API to get these values as we want to get the
  // settings for all the users with a single query.
  $query = "
    SELECT
      entity_id, message_subscribe_email_freq_value
    FROM
      {field_data_message_subscribe_email_freq}
    WHERE
      deleted != 1
    AND
      entity_id IN (:entity_ids)
  ";

  $result = db_query($query, array(':entity_ids' => array_keys($uids)))->fetchAll();

  foreach ($result as $row) {
    // Add notifier based on frequency selected by user.
    $frequency = $row->message_subscribe_email_freq_value;
    // Unset the notifier if the user has chosen to never receive email
    // notifications for subscribed content.
    if ($frequency == MESSAGE_SUBSCRIBE_EMAIL_FREQUENCY_NEVER) {
      unset($uids[$row->entity_id]['notifiers']['email']);
    }
    // We only change the frequency if the user should have been emailed in the
    // first place but does not want to receive the email immediately.
    if (isset($uids[$row->entity_id]['notifiers']['email']) && $frequency != 'email') {
      unset($uids[$row->entity_id]['notifiers']['email']);
      $uids[$row->entity_id]['notifiers'][$frequency] = $frequency;
    }
  }
}

Does this code make sense? Having followed the module's instructions, I removed all default notifiers. But then $uids[$row->entity_id]['notifiers'] has no value, and it is not set to anything at all.

So I replaced it with this:

function message_subscribe_email_frequency_message_subscribe_get_subscribers_alter(&$uids, $values) {
  if (empty($uids)) {
    // Nobody is subscribed to the content.
    return;
  }

  // Get the frequency setting for any users subscribed to the content.
  // We don't use the Field API to get these values as we want to get the
  // settings for all the users with a single query.
  $query = "
    SELECT
      entity_id, message_subscribe_email_freq_value
    FROM
      {field_data_message_subscribe_email_freq}
    WHERE
      deleted != 1
    AND
      entity_id IN (:entity_ids)
  ";

  $result = db_query($query, array(':entity_ids' => array_keys($uids)))->fetchAll();

  foreach ($result as $row) {
    // Add notifier based on frequency selected by user.
    $frequency = $row->message_subscribe_email_freq_value;
    if (isset($frequency) && $frequency != MESSAGE_SUBSCRIBE_EMAIL_FREQUENCY_NEVER) {
      $uids[$row->entity_id]['notifiers'][$frequency] = $frequency;
    }
  }
}

And so far everything seems to work.

@WillowDigit: Thank you so much for your work on this! Without your comment, I would have never gotten all of this to work.

There is already a patch that fixes the Message Digest problem here: #2238833: Incompatibilities with message queue logic means some digested messages may never get sent.

And for Message Subscribe Frequency, I have made a patch based on the work from #1. I will also move this issue to the respective project page.

Please review :)