Put more logic into Filter from theme preprocess function.

bibcite_footnotes.module

@@ -10,6 +10,7 @@ use Drupal\Core\Routing\RouteMatchInterface;
 use Drupal\Core\Url;
 use Drupal\Core\Link;
 use Drupal\bibcite_footnotes\CitationTools;
+use Drupal\bibcite_footnotes\Plugin\Filter\ReferenceFootnotesFilter;
 
 /**
  * Implements hook_theme().
@@ -60,20 +61,20 @@ function bibcite_footnotes_help($route_name, RouteMatchInterface $route_match) {
  * @throws \Drupal\Component\Plugin\Exception\PluginNotFoundException
  */
 function bibcite_footnotes_preprocess_bibcite_footnote_list(&$variables) {
-  $config = \Drupal::config('filter.format.rich_text_references');//filters.filter_reference_footnotes.settings');
-  $footnotes = $variables['footnotes'];
+  $config = $variables['config'];
+  $footnotes = $variables['notes'];
 
   $notes = [
     '#theme' => 'item_list',
     '#list_type' => 'ul',
-    '#title' => $config->get('filters.filter_reference_footnotes.settings.notes_section_label'),
+    '#title' => $variables['note_type'] == ReferenceFootnotesFilter::ENDNOTE ? $config['notes_section_label'] : $config['references_section_label'],
     '#attributes' => ['class' => 'footnotes'],
     '#wrapper_attributes' => ['class' => 'container'],
   ];
 
   $notes['#attached']['library'][] = 'bibcite_footnotes/reference_footnote';
-  $dont_show_backlink_text = $config->get('filters.filter_reference_footnotes.settings.reference_dont_show_backlink_text');
-  $sort_references_by = $config->get('filters.filter_reference_footnotes.settings.reference_sort_by');
+  $dont_show_backlink_text = $config['dont_show_backlink_text'];
+  $sort_references_by = $config['reference_sort_by'];
   $citation_tools = new CitationTools();
   foreach ($footnotes as $fn) {
     $item = [
@@ -111,21 +112,16 @@ function bibcite_footnotes_preprocess_bibcite_footnote_list(&$variables) {
       $override_page_in_citation = FALSE;
     }
 
-    if (!empty($fn['text'])) {
+    if (!empty($fn['text']) && $variables['note_type'] == ReferenceFootnotesFilter::ENDNOTE) {
       // Handle the case where an endnote contains text and a reference.
       // It will appear in both lists. But the link text for the endnote should
       // always be the title of the note. So make a copy of the biuld arrray
       // and change the link text.
-      $note_build = $build + ['#type' => 'markup', '#markup' => ' <span class="endnote-text">' . $fn['text'] . '</span>'];
-      $note_build['footnote-link'] = Link::fromTextAndUrl($fn['value'], $url)->toRenderable();
-      if (!empty($reference_entity_id)) {
-        $citation_build = $citation_tools->getRenderableReference($reference_entity_id);
-        $note_build[] = $citation_build;
-      }
-      $note_item = [] + $item;
-      $note_item['#markup'] = render($note_build);
+      $build['#type'] = 'markup';
+      $build['#markup'] = ' <span class="endnote-text">' . $fn['text'] . '</span>';
+      $build['footnote-link'] = Link::fromTextAndUrl($fn['value'], $url)->toRenderable();
+
 
-      $notes['#items'][] = $note_item;
     }
 
     if (!empty($reference_entity_id)) {
@@ -135,20 +131,17 @@ function bibcite_footnotes_preprocess_bibcite_footnote_list(&$variables) {
       }
       $build[] = $citation_build;
       $render = render($build);
-      $item['#markup'] = $render;
-      $item['sort'] = trim(strip_tags(render($citation_build)));
-      $references['#items'][] = $item;
 
+      $item['sort'] = trim(strip_tags(render($citation_build)));
     }
-
+    $item['#markup'] = $render;
+    $notes['#items'][] = $item;
   }
 
-  $variables['notes'] = $notes;
-
-  if ($sort_references_by == 'alphabetical') {
-    usort($references['#items'], '_bibcite_footnotes_reference_array_cmp');
+  if ($sort_references_by == 'alphabetical' && $variables['note_type'] == ReferenceFootnotesFilter::REFERENCE) {
+    usort($notes['#items'], '_bibcite_footnotes_reference_array_cmp');
   }
-  $variables['references'] = $references;
+  $variables['notes'] = $notes;
 }
 
 function _bibcite_footnotes_reference_array_cmp($a, $b) {

src/Plugin/Filter/ReferenceFootnotesFilter.php

@@ -10,7 +10,7 @@ use Drupal\footnotes\Plugin\Filter\FootnotesFilter;
  * Provides a base filter for Reference Footnotes filter.
  *
  * @Filter(
- *   id = "filter_reference_footnotes",
+ *   id = "filter_reference_footnotes",footnote_list
  *   module = "bibcite_footnotes",
  *   title = @Translation("Reference Footnotes filter"),
  *   description = @Translation("You can insert footnotes directly into texts."),
@@ -155,11 +155,19 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
         // themed as a list
         $markup = [
           '#theme' => 'bibcite_footnote_list',
-          '#footnotes' => $notes,
+          '#notes' => $notes,
           '#note_type' => self::ENDNOTE,
           '#config' => $this->settings,
         ];
         $str = \Drupal::service('renderer')->render($markup, FALSE);
+
+        $markup = [
+          '#theme' => 'bibcite_footnote_list',
+          '#notes' => $references,
+          '#note_type' => self::REFERENCE,
+          '#config' => $this->settings,
+        ];
+        $str .= \Drupal::service('renderer')->render($markup, FALSE);
       }
       // Reset the static variables so they can be used again next time.
       $n = 0;
@@ -336,7 +344,6 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
       $prev_reference_id = $fn['reference']; // Could be empty, that's OK.
 
     }
-    ksm($footnotes);
   }
 
   protected function extractNotesByType($type, $footnotes) {
@@ -344,7 +351,7 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
     foreach ($footnotes as $fn) {
       switch ($type) {
         case self::ENDNOTE:
-          if (!empty(fn['text'])) {
+          if (!empty($fn['text'])) {
             $notes[] = $fn;
           }
           break;
@@ -354,7 +361,6 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
           }
           break;
       }
-      ksm($fn);
     }
     return $notes;
   }