Make the dndck4 ckeditor plugin to be the default configuration of scald for new installs only

not a lot of things can be done.

Two contributions about this, more related to Easier way of setting the mee_store_format variable, but this issue is fixed, and this is related to manage coexistence of the two systems;

1 - about the plugins
I can make two assertions :
a) The use of the legacy plugin makes sense if and only if mee_store_format is 'sas'
b) The use of the dndck4 plugin makes sense if and only if mee_store_format is 'embed_div'
If these are valid, then we can register only one plugin:

function dnd_ckeditor_plugin() {
  $plugins = array();
  $mee_store_format = (module_exists('mee')) ? mee_store_format() : '';
  if ($mee_store_format == 'sas') {
    $plugins['dnd'] = array(
      'name' => 'dnd',
      'desc' => t('Scald Drag and Drop integration'),
      'path' =>  drupal_get_path('module', 'dnd') . '/plugins/ckeditor/',
      'buttons' => array(),
    );
  }
  elseif ($mee_store_format == 'embed_div' && version_compare(ckeditor_get_version(), '4.3.0') >= 0) {
    $plugins['dndck4'] = array(
      'name' => 'dndck4',
      'desc' => t('Scald Drag and Drop integration - CKEditor 4 widgets'),
      'path' =>  drupal_get_path('module', 'dnd') . '/plugins/dndck4/',
      'buttons' => array(),
    );
  }
  return $plugins;
}

The user will still have to check boxes in ckeditor profiles, but he/she will be sure to select the "right" plugin

2 - About the input text filter
If mee_store_format is 'embed_div', the mee_filter_process() function MUST be executed, but it is not technically necessary that this be in a filter context;
So the filter activation may be an optimisation option, just as "Always rebuild rendered content"
mee_field_attach_view_alter() could manage both cases as follow:

function mee_field_attach_view_alter(&$output, $context) {
  $store_format = mee_store_format();
  if ($store_format == 'sas' || $store_format == 'embed_div') {
    list($id, $revision_id, $bundle) = entity_extract_ids($context['entity_type'], $context['entity']);
    $fields = field_info_instances($context['entity_type'], $bundle);
    foreach ($fields as $name => $field) {
      if (!empty($field['settings']['dnd_enabled']) && isset($output[$name])) {
        foreach (element_children($output[$name]) as $key) {
          if ($store_format == 'embed_div') {
            $input_format = $output[$name]['#items'][$key]['format'];
            $list = filter_list_format($input_format);
            if (empty($list['mee_scald_widgets']) || $list['mee_scald_widgets']->status != 1) {
              $output[$name][$key]['#markup'] = mee_filter_process($output[$name][$key]['#markup']);
            }
          }
          $output[$name][$key]['#markup'] = scald_sas_to_rendered($output[$name][$key]['#markup'], $field['settings']['context']);
        }
      }
    }
  }
}

How to check "the case of new installs" is another problem, but the two patches above can make life easyer ;-)

The "wrong" plugin is automatically de-activated when you visit admin/config/content/ckeditor, which you have to do, in order to activate the new one for the given profile(s) - so there cannot be any conflict

Well, this is for the stable release of CKEditor module, but now that "CKEditor plugin system is modular and clean", everything can happen >>)

about "Also to set the default value of the mee store format variable", I have no idea how we can know that this is a "new install" (because we should not change the store format at an upgrade, not even at a disable/enable sequence).
Perhaps checking the mee_resource table is empty ? - it records the embedded atoms, so if it is empty, no storage_format has been in effect... but is it allowed to issue a db query in mee.install ?

Here is a patch for this;
I use the filter bypass for months, the plugin pre selection works with latest ckeditor dev, but the install trick is untested...

you can double check.

Just a side note for testers/debuggers : the check of ckeditor_get_version() fails if you are using ckeditor-dev (from github) at the source level, because of :

    if ($ckeditor_version == '%VERSION%') {
      $ckeditor_version = '4.0.0';
    }

This is of course totally irrelevant for this issue, which is about "the next stable release"

ckeditor_version was a joke : Right after preparing the patch, I installed latest ckeditor module (modular and clean) and latest ckeditor library (branch major) - I spent a couple of minutes to figure out why it was not working...

But now, any up to date site will use ckeditor from CDN, and dndck4 works with the default ckeditor settings
(//cdn.ckeditor.com/4.4.3/full-all) unaltered: the widget plugin is dynamically loaded after dndck4 statement :

CKEDITOR.plugins.add('dndck4', {
  lang: 'en',
  requires: 'widget',

Anyway, the plugin activation is at profile level, and scald cannot know which profile(s) is/are relevant for use with dnd/mee