diff --git a/bibcite_footnotes.module b/bibcite_footnotes.module
index 39c617e..754f094 100644
--- a/bibcite_footnotes.module
+++ b/bibcite_footnotes.module
@@ -11,6 +11,27 @@ use Drupal\Core\Url;
 use Drupal\Core\Link;
 use Drupal\bibcite_footnotes\CitationTools;
 
+/**
+ * Implements hook_theme().
+ */
+function bibcite_footnotes_theme() {
+  return [
+    'bibcite_footnote_link' => [
+      'render element' => 'fn',
+      'template' => 'footnote-link',
+    ],
+    'bibcite_footnote_list' => [
+      'render element' => 'footnotes',
+      'path' => drupal_get_path('module', 'bibcite_footnotes') . '/templates',
+      'template' => 'footnote-list',
+      'variables' => [
+        'notes' => [],
+        'note_type' => [],
+      ],
+    ],
+  ];
+}
+
 /**_bibcite_foot
  * Implements hook_help().
  */
@@ -49,14 +70,6 @@ function bibcite_footnotes_preprocess_footnote_list(&$variables) {
     '#wrapper_attributes' => ['class' => 'container'],
   ];
 
-  $references= [
-    '#theme' => 'item_list',
-    '#list_type' => 'ul',
-    '#title' => $config->get('filters.filter_reference_footnotes.settings.references_section_label'),
-    '#attributes' => ['class' => 'footnotes'],
-    '#wrapper_attributes' => ['class' => 'container'],
-
-  ];
   $references['#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 = $config->get('filters.filter_reference_footnotes.settings.reference_sort_by');
@@ -169,17 +182,3 @@ function bibcite_footnotes_preprocess_footnote_link(&$variables) {
   $link = Link::fromTextAndUrl($fn['value'], $url)->toRenderable();
   $variables['fn']['fn'][] = $link;
 }
-
-function bibcite_footnotes_theme_registry_alter(&$theme_registry) {
-  unset($theme_registry['footnote_list']['function']);
-  $theme_registry['footnote_list']['path'] = drupal_get_path('module', 'bibcite_footnotes') . '/templates';
-  $theme_registry['footnote_list']['template'] = 'footnote-list';
-  $theme_registry['footnote_list']['variables']['notes'] = [];
-  $theme_registry['footnote_list']['variables']['references'] = [];
-  $theme_registry['footnote_list']['variables']['footnotes'] = [];
-
-  unset($theme_registry['footnote_link']['function']);
-  $theme_registry['footnote_link']['path'] = drupal_get_path('module', 'bibcite_footnotes') . '/templates';
-  $theme_registry['footnote_link']['template'] = 'footnote-link';
-}
-
diff --git a/src/Plugin/Filter/ReferenceFootnotesFilter.php b/src/Plugin/Filter/ReferenceFootnotesFilter.php
index fcddbf7..faeacda 100644
--- a/src/Plugin/Filter/ReferenceFootnotesFilter.php
+++ b/src/Plugin/Filter/ReferenceFootnotesFilter.php
@@ -26,6 +26,8 @@ use Drupal\footnotes\Plugin\Filter\FootnotesFilter;
  * )
  */
 class ReferenceFootnotesFilter extends FootnotesFilter {
+  const ENDNOTE = 0;
+  const REFERENCE = 1;
 
   /**
    * Object with configuration for reference footnotes.
@@ -142,16 +144,15 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
       if ($this->settings['footnotes_ibid']) {
         $this->ibidemify($store_matches);
       }
+
       if (count($store_matches) > 0) {
+        // Separate out endontes and reference notes.
+        $notes = $this->extractNotesByType(self::NOTES, $store_matches);
+        $references = $this->extractNotesByType(self::REFERENCES, $store_matches);
+
+
         // Only if there are stored fn matches, pass the array of fns to be
-        // themed as a list Drupal 7 requires we use "render element" which
-        // just introduces a wrapper around the old array.
-        // @FIXME
-        // theme() has been renamed to _theme() and should NEVER be called
-        // directly. Calling _theme() directly can alter the expected output and
-        // potentially introduce  security issues
-        // (see https://www.drupal.org/node/2195739). You should use renderable
-        // arrays instead. @see https://www.drupal.org/node/2195739
+        // themed as a list
         $markup = [
           '#theme' => 'footnote_list',
           '#footnotes' => $store_matches,
@@ -258,6 +259,8 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
       '#theme' => 'footnote_link',
       'fn' => $fn,
     ];
+
+
     $result = \Drupal::service('renderer')->render($fn, FALSE);
 
     return $result;
@@ -333,4 +336,10 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
     }
     ksm($footnotes);
   }
+
+  protected function extractNotesByType($type, $footnotes) {
+    foreach ($footnotes as $fn) {
+
+    }
+  }
 }