corrected info yaml file

README.md

@@ -6,42 +6,95 @@ Contents
 
  * Introduction
  * Installation
- * Configuration
+ * Use
  * Current Maintainers
 
 Introduction
 ------------
 
-A plugin for the Footnotes module (https://www.drupal.org/project/footnotes) 
-that lets a user insert references created or importeed using the Bibliography 
-and Citation project (https://www.drupal.org/project/bibcite).
-
 Provides a CKEditor plugin that lets a user select from a list of citations which
-appear in a formatted at the bottom of the text area that contains the footnote.
+appear in a formatted list at the bottom of the text that contains endnotes
+and references.
 
 Installation
 ------------
 
-Install and set up the Footnotes module as per its installation instructions, including
-enabling and configuring the Footnotes text filter. If the 'Allowed HTML tags' filter is enabled
-you will need to add the following HTML tags for the reference footnotes to display properly.:
+### Works Cited field
+
+1. Go to Administration > Structure > Content Types and edit the type that will include Reference Footnotes
+2. In the Manage Fields tab, press Add Field.
+3. In "Re-use an existing field" select "Entity reference: field_bibcite_fn_works_cited".
+4. Enter an appropriate label and press 'Save and continue'.
+5. On the next page select all the items in "Reference type" that should be available to choose from as footnotes.
+6. Customize the field under "Manage form display" and "Manage display", typically you'll want to 
+   place the Works Cited field directly under the Body field. See below for configuring with 
+   Inline Entity Form.
+7. In "Manage display", select "Rendered entity" in the Format drop-down for the Works Cited field.
+8. Press the Settings icon and under "View mode" choose "Citation" - a new view mode created 
+   by this module.
+
+#### Inline Enity Form
+
+It's recommended to also install [Inline Entity Form][1] which allowes a user to
+create new references directly in the node edit form.
+
+1. In "Entity Form Display", select ''Inline Entity Form - complex".
+2. Press the settings button in the rightmost column.
+3. Enabling  "Allow users to add new reference entities" and
+   "Allow users to add existing reference entities" is recommended. 
+
+[1]: https://www.drupal.org/project/inline_entity_form
+
+### CKEditor filter and toolbar button
+
+1. Enable the module.
+2. Go to Administration > Configuration > Content authoring > Text formats and editors.
+ 3. Edit the text format you want to add Reference Footnotes to
+4. Enable the Reference Footnotes Filter
+5. Drag the Reference Footnotes button into the active buttons toolbar.
+6. Configure the options for the Reference Footnotes Filter.
+
+If the 'Allowed HTML tags' filter is enabled add these HTML tags to the allowed list:
 
 ```html
-    <a class href id> <div class id> <span class id> <ul class id type> 
-	<ol class id start type> <sup> <li class id>
+    <a class href id> <div class id> <span class id> <ol class id type> 
+	<sup> <li class id>
 ```
 
-Configuration
--------------
+Use
+---
+
+See the documentation for [Bibliography and Citation - Import][2] module for how to
+add citations exported from a citation management system like RefWorks or EndNote.
 
-Drag the Reference Footnotes button into the active set of buttons in the text format
-you want to use References in and save the settings.
+[2]: https://www.drupal.org/project/bibcite
 
-You will then need to create or import one or more references using the Bibliography &
-Citations project. Those will then appear in a select list when you are editing a text area
-and click on the Reference Footnote button.
+### Adding a Works Cited item
+
+If Inline Entity Form is enabled, an author can create new citations or add references to 
+previously-imported or created references directly with the 'Add new reference' and 
+'Add existing reference' buttons.
+
+With Inline Entity Form, newly-added citations are immediately selectable in the 
+Reference Footnotes dialog.
+
+If not using the inline entity form, you can select previously imported or created references 
+
+When you edit the node again, and you click on the Reference Footnote editor toolbar button,
+a list of citations will be available to choose from.
+
+### Citation Formatting
+
+The Works Cited field will use the Default style selected in the 
+Bibliography & Citation administration pages at Administration > Configuration > 
+Bibliography & Citation > Settings in the Processing tab under Processor.'
 
 Current Maintainers
 -------------------
 
  * Alexander O'Neill (https://www.drupal.org/u/alxp)
+
+Sponsors
+--------
+
+ * This work is supported by the [University of Prince Edward Island Robertson Library](https://library.upei.ca).

bibcite_footnotes.info.yml

@@ -1,9 +1,11 @@
 name: 'BibCite Footnotes'
 type: module
 description: 'Inline footnote links for BibCite References'
-core: 8.x
+core_version_requirement: ^8.0 || ^9 || ^10
 package: 'Bibliography & Citation'
 dependencies:
   - bibcite:bibcite
   - bibcite:bibcite_entity
-  - footnotes:footnotes
+  - fakeobjects:fakeobjects
+
+

bibcite_footnotes.libraries.yml

@@ -3,3 +3,13 @@ reference_footnote:
   css:
     theme:
       css/reference_footnote.css: {}
+  dependencies:
+    - core/jquery
+    - core/drupalSettings
+replace_citations:
+  version: VERSION
+  js:
+    js/replace_citations.js: {}
+  dependencies:
+    - core/jquery
+    - core/drupalSettings

bibcite_footnotes.module

@@ -5,12 +5,14 @@
  * Contains bibcite_footnotes.module.
  */
 
+use Drupal\Core\Field\EntityReferenceFieldItemListInterface;
 use Drupal\Core\Form\FormStateInterface;
 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;
+use Drupal\field\Entity\FieldConfig;
 
 /**
  * Implements hook_theme().
@@ -23,7 +25,7 @@ function bibcite_footnotes_theme() {
     ],
     'bibcite_footnote_list' => [
       'render element' => 'footnotes',
-      'path' => drupal_get_path('module', 'bibcite_footnotes') . '/templates',
+      'path' => \Drupal::service('extension.list.module')->getPath('bibcite_footnotes') . '/templates',
       'template' => 'bibcite-footnote-list',
       'variables' => [
         'notes' => [],
@@ -67,14 +69,14 @@ function bibcite_footnotes_preprocess_bibcite_footnote_list(&$variables) {
   $notes = [
     '#theme' => 'item_list',
     '#list_type' => 'ul',
-    '#title' => $variables['note_type'] == ReferenceFootnotesFilter::ENDNOTE ? $config['notes_section_label'] : $config['references_section_label'],
+    '#title' => $variables['note_type'] == $config['notes_section_label'],
     '#attributes' => ['class' => 'footnotes'],
     '#wrapper_attributes' => ['class' => 'container'],
   ];
 
   $notes['#attached']['library'][] = 'bibcite_footnotes/reference_footnote';
   $dont_show_backlink_text = $config['reference_dont_show_backlink_text'];
-  $sort_references_by = $config['reference_sort_by'];
+
   $citation_tools = new CitationTools();
   if (empty($footnotes)) {
     return;
@@ -89,7 +91,7 @@ function bibcite_footnotes_preprocess_bibcite_footnote_list(&$variables) {
     $build = [];
     $reference_entity_id = $fn['reference'];
 
-    $footnote_link_text = ($dont_show_backlink_text && $reference_entity_id) ? '^' : $fn['value'];
+    $footnote_link_text = ($dont_show_backlink_text) ? '^' : $fn['value'];
     if (!is_array($fn['ref_id'])) {
       $url = Url::fromUserInput('#' . $fn['ref_id'], ['attributes' => ['id' => $fn['fn_id'], 'class' => 'footnote-link']]);
       $link = Link::fromTextAndUrl(($footnote_link_text), $url)->toRenderable();
@@ -124,8 +126,8 @@ function bibcite_footnotes_preprocess_bibcite_footnote_list(&$variables) {
           . '</span>',
       ];
     }
-    else if (!empty($fn['text']) && $variables['note_type'] == ReferenceFootnotesFilter::ENDNOTE) {
-      $build['footnote-link'] = Link::fromTextAndUrl($fn['value'], $url)->toRenderable();
+    else if (!empty($fn['text'])) {
+      $build['footnote-link'] = Link::fromTextAndUrl($footnote_link_text, $url)->toRenderable();
       $build['footnote-text'] = [
         '#type' => 'markup',
         '#markup' => ' <span class="endnote-text">' . $fn['text'] . '</span>',
@@ -143,8 +145,9 @@ function bibcite_footnotes_preprocess_bibcite_footnote_list(&$variables) {
         $build[] = $citation_build;
       }
 
-      $render = render($build);
-      $item['sort'] = trim(strip_tags(render($citation_build)));
+      //$render = render($build);
+      $citation_build_render = \Drupal::service('renderer')->render($citation_build);
+      $item['sort'] = trim(strip_tags($citation_build_render));
     }
 
 //    $item['#markup'] = $render;
@@ -153,9 +156,6 @@ function bibcite_footnotes_preprocess_bibcite_footnote_list(&$variables) {
     $render = FALSE;
   }
 
-  if ($sort_references_by == 'alphabetical' && $variables['note_type'] == ReferenceFootnotesFilter::REFERENCE) {
-    usort($notes['#items'], '_bibcite_footnotes_reference_array_cmp');
-  }
   $variables['notes'] = $notes;
 }
 
@@ -192,18 +192,175 @@ function bibcite_footnotes_preprocess_bibcite_footnote_link(&$variables) {
   $citation_data = $citation_tools->getRenderableReference($citation_entity_id);
 
   // Citation contains a page reference, so construct parenthetical footnote.
-  if (!empty($fn['page'])) {
+  // @TODO: Make it explicit.
+  if (!empty($fn['page'] && !is_numeric($fn['value']))) {
     $fn['value'] = "({$fn['value']}, {$fn['page']})";
     $citation_data['#data']['page'] = $fn['page'];
     $class .= '-inline';
   }
-
-  $title = trim(strip_tags(render($citation_data)));
+  $citation_data_render = \Drupal::service('renderer')->render($citation_data);
+  $title = trim(strip_tags($citation_data_render));
   $url = Url::fromUserInput('#' . $fn['fn_id'], ['attributes' => ['id' => $fn['ref_id'], 'class' => $class, 'title' => $title]]);
-  
+
 
   $link = Link::fromTextAndUrl($fn['value'], $url)->toRenderable();
   unset($variables['fn']['fn']);
   $variables['fn']['fn'] = $link;
 //  $variables['fn']['fn'][] = $link;
 }
+
+/**
+ * Implementation of hook_inline_entity_form_entity_form_alter().
+ *
+ * Force all entities to be saved once they are created.
+ *
+ * @TODO: Add cleanup batch task for orphaned References.
+ *
+ * @param $form
+ * @param \Drupal\Core\Form\FormStateInterface $form_state
+ */
+function bibcite_footnotes_inline_entity_form_entity_form_alter(&$form, FormStateInterface &$form_state) {
+  $form['#save_entity'] = TRUE;
+}
+
+/**
+ * Implementation of hook_form_node_form_alter().
+ *
+ * This function populates the Reference list drop-down in the CKEditor drop-down.
+ * It gathers all referenced entities of type bibcite_reference and puts them
+ * into a JavaScript setting under drupalSettings.bibcite_footnotes.references.
+ *
+ * @param $form
+ * @param \Drupal\Core\Form\FormStateInterface $form_state
+ */
+function bibcite_footnotes_form_node_form_alter(&$form, FormStateInterface &$form_state) {
+  $ief = $form_state->get('inline_entity_form');
+  if ($ief) {
+    // Inline entity storage uses hashes to separate out the field instances.
+    $bibcite_references = [];
+    foreach ($ief as $ief_instance) {
+      /**
+       * @var FieldConfig $field_config
+       */
+      if ($field_config = $ief_instance['instance']) {
+
+        // Check if this is a bibcite_reference field type.
+        if ($field_config->getSetting('handler') == 'default:bibcite_reference') {
+          $field_name = $field_config->get('field_name');
+          if (!empty($ief_instance['entities'])) {
+
+            foreach ($ief_instance['entities'] as $entity_wrapper) {
+              /**
+               * @var \Drupal\core\Entity\EntityInterface $entity
+               */
+              $entity = $entity_wrapper['entity'];
+              if ($entity->getEntityTypeId() == 'bibcite_reference') {
+                list($citation_text, $citation_key) = bibcite_footnotes_get_ckeditor_select_item($entity);
+                $bibcite_references[] = [$citation_text, $citation_key];
+              }
+            }
+          }
+        }
+      }
+    }
+
+    $triggering_element = $form_state->getTriggeringElement();
+    if (!$triggering_element) {
+      $form['#attached']['drupalSettings']['bibcite_footnotes']['references'] = $bibcite_references;
+    }
+    else {
+      $form[$triggering_element['#parents'][0]]['widget']['#attached']['library'][] = 'bibcite_footnotes/replace_citations';
+      $form[$triggering_element['#parents'][0]]['widget']['#attached']['drupalSettings']['bibcite_footnotes']['references'] = $bibcite_references;
+    }
+  }
+  else {
+    // Not using Inline Entity Form, get the references if they exist
+    $entity = $form_state->getFormObject()->getEntity();
+    $fields = $entity->getFields();
+    $reference_field = FALSE;
+    foreach ($fields as $field) {
+      $type = $field->getFieldDefinition();
+      if ($type->getType() == 'entity_reference') {
+        if ($type->getSetting('handler') == 'default:bibcite_reference') {
+          $referenced_entities = $field->referencedEntities();
+          $bibcite_references = [];
+          foreach ($referenced_entities as $referenced_entity) {
+            list($citation_text, $citation_key) = bibcite_footnotes_get_ckeditor_select_item($referenced_entity);
+            $bibcite_references[] = [$citation_text, $citation_key];
+          }
+          $form['#attached']['drupalSettings']['bibcite_footnotes']['references'] = $bibcite_references;
+        }
+      }
+    }
+  }
+}
+
+/**
+ * Construct an item to go into the CKEditor Reference drop-down list.
+ *
+ * @param $entity
+ *
+ * @return array
+ *   The form of the array is ["Citation string", [reference entity id].
+ */
+function bibcite_footnotes_get_ckeditor_select_item($entity): array {
+  $serializer = \Drupal::service('serializer');
+
+  $data = $serializer->normalize($entity, 'csl');
+  $build = ['#theme' => 'bibcite_citation', '#data' => $data];
+  $build_render = \Drupal::service('renderer')->render($build);
+  $citation_text = trim(strip_tags($build_render));
+  // Attempt to match up pre-saved entities with the eventual saved ones.
+  $citation_key = $entity->id->first()->getValue()['value'];
+  return [$citation_text, $citation_key];
+}
+
+/**
+ * Implementation of hook_preprocess_field().
+ * Sort the works cited list by rendered text, which results in author(s) then title.
+ *
+ * @param $variables
+ * @param $hook
+ */
+function bibcite_footnotes_preprocess_field(&$variables, $hook) {
+  $citation_tools = new CitationTools();
+  if ($variables['field_name'] == 'field_bibcite_fn_works_cited') {
+
+    foreach($variables['element'] as $index => $element) {
+      if (is_numeric($index)) {
+        $renderable = $citation_tools->getRenderableReference($element['#bibcite_reference']);
+        $renderable = \Drupal::service('renderer')->render($renderable);
+        $items[] = [
+          'orig_index' => $index,
+          'orig_element' => $element,
+          'rendered' => trim(strip_tags($renderable)),
+        ];
+      }
+    }
+    uasort($items, '_bibcite_footnotes_sort_rendered_references');
+    $i = 0;
+    foreach ($items as $item) {
+      $variables['element'][$i] = $item['orig_element'];
+      $variables['element']['#items'][$i] = $item['orig_element'];
+      $variables['items'][$i]['content'] = $item['orig_element'];
+      $i += 1;
+    }
+  }
+}
+
+/**
+ * Comparator function for theme field preprocess.
+ *
+ * @param $a
+ *   The first renderable element.
+ * @param $b
+ *   The second renderable element.
+ *
+ * @return int
+ */
+function _bibcite_footnotes_sort_rendered_references($a, $b) {
+  if ($a['rendered'] == $b['rendered']) {
+    return 0;
+  }
+  return strtolower($a['rendered']) < strtolower($b['rendered']) ? -1 : 1;
+}

bibcite_footnotes_article_with_citations/README.md

@@ -0,0 +1,4 @@
+Description
+-----------
+
+Example content type and text format to demonstrate a fully-configured Reference Footnotes setup.

bibcite_footnotes_article_with_citations/bibcite_footnotes_article_with_citations.info.yml

@@ -0,0 +1,13 @@
+name: 'BibCite Footnotes Article with Citations'
+type: module
+description: 'Example module to show a fully-configured content type and text format with Reference Footnotes.'
+core_version_requirement: ^8 || ^9 || ^10
+package: 'Bibliography & Citation'
+dependencies:
+  - bibcite_footnotees:bibcite_footnotes
+  - bibcite:bibcite_import
+  - bibcite:bibcite_bibtex
+  - bibcite:bibcite_endnote
+  - bibcite:bibcite_ris
+  - bibcite:bibcite_marc
+  - inline_entity_form:inline_entity_form

bibcite_footnotes_article_with_citations/config/install/core.entity_form_display.node.bibcite_fn_article_references.default.yml

@@ -0,0 +1,113 @@
+langcode: en
+status: true
+dependencies:
+  config:
+    - field.field.node.bibcite_fn_article_references.body
+    - field.field.node.bibcite_fn_article_references.field_bibcite_fn_works_cited
+    - field.field.node.bibcite_fn_article_references.field_image
+    - field.field.node.bibcite_fn_article_references.field_tags
+    - image.style.thumbnail
+    - node.type.bibcite_fn_article_references
+  module:
+    - image
+    - inline_entity_form
+    - path
+    - text
+id: node.bibcite_fn_article_references.default
+targetEntityType: node
+bundle: bibcite_fn_article_references
+mode: default
+content:
+  body:
+    type: text_textarea_with_summary
+    weight: 7
+    settings:
+      rows: 9
+      summary_rows: 3
+      placeholder: ''
+    third_party_settings: {  }
+    region: content
+  created:
+    type: datetime_timestamp
+    weight: 2
+    region: content
+    settings: {  }
+    third_party_settings: {  }
+  field_bibcite_fn_works_cited:
+    weight: 8
+    settings:
+      form_mode: default
+      label_singular: ''
+      label_plural: ''
+      allow_new: true
+      allow_existing: true
+      match_operator: CONTAINS
+      override_labels: false
+      collapsible: false
+      collapsed: false
+      allow_duplicate: false
+    third_party_settings: {  }
+    type: inline_entity_form_complex
+    region: content
+  field_image:
+    weight: 10
+    settings:
+      progress_indicator: throbber
+      preview_image_style: thumbnail
+    third_party_settings: {  }
+    type: image_image
+    region: content
+  field_tags:
+    weight: 9
+    settings:
+      match_operator: CONTAINS
+      size: 60
+      placeholder: ''
+    third_party_settings: {  }
+    type: entity_reference_autocomplete
+    region: content
+  path:
+    type: path
+    weight: 5
+    region: content
+    settings: {  }
+    third_party_settings: {  }
+  promote:
+    type: boolean_checkbox
+    settings:
+      display_label: true
+    weight: 3
+    region: content
+    third_party_settings: {  }
+  status:
+    type: boolean_checkbox
+    settings:
+      display_label: true
+    weight: 6
+    region: content
+    third_party_settings: {  }
+  sticky:
+    type: boolean_checkbox
+    settings:
+      display_label: true
+    weight: 4
+    region: content
+    third_party_settings: {  }
+  title:
+    type: string_textfield
+    weight: 0
+    region: content
+    settings:
+      size: 60
+      placeholder: ''
+    third_party_settings: {  }
+  uid:
+    type: entity_reference_autocomplete
+    weight: 1
+    settings:
+      match_operator: CONTAINS
+      size: 60
+      placeholder: ''
+    region: content
+    third_party_settings: {  }
+hidden: {  }

bibcite_footnotes_article_with_citations/config/install/core.entity_view_display.node.bibcite_fn_article_references.default.yml

@@ -0,0 +1,57 @@
+langcode: en
+status: true
+dependencies:
+  config:
+    - field.field.node.bibcite_fn_article_references.body
+    - field.field.node.bibcite_fn_article_references.field_bibcite_fn_works_cited
+    - field.field.node.bibcite_fn_article_references.field_image
+    - field.field.node.bibcite_fn_article_references.field_tags
+    - node.type.bibcite_fn_article_references
+  module:
+    - image
+    - text
+    - user
+id: node.bibcite_fn_article_references.default
+targetEntityType: node
+bundle: bibcite_fn_article_references
+mode: default
+content:
+  body:
+    label: hidden
+    type: text_default
+    weight: 1
+    settings: {  }
+    third_party_settings: {  }
+    region: content
+  field_bibcite_fn_works_cited:
+    weight: 2
+    label: above
+    settings:
+      view_mode: citation
+      link: false
+    third_party_settings: {  }
+    type: entity_reference_entity_view
+    region: content
+  field_image:
+    weight: 4
+    label: above
+    settings:
+      image_style: ''
+      image_link: ''
+    third_party_settings: {  }
+    type: image
+    region: content
+  field_tags:
+    weight: 3
+    label: above
+    settings:
+      link: true
+    third_party_settings: {  }
+    type: entity_reference_label
+    region: content
+  links:
+    weight: 0
+    region: content
+    settings: {  }
+    third_party_settings: {  }
+hidden: {  }

bibcite_footnotes_article_with_citations/config/install/editor.editor.basic_html_with_references.yml

@@ -0,0 +1,51 @@
+langcode: en
+status: true
+dependencies:
+  config:
+    - filter.format.basic_html_with_references
+  module:
+    - ckeditor
+format: basic_html_with_references
+editor: ckeditor
+settings:
+  toolbar:
+    rows:
+      -
+        -
+          name: Formatting
+          items:
+            - Bold
+            - Italic
+        -
+          name: Links
+          items:
+            - DrupalLink
+            - DrupalUnlink
+        -
+          name: Lists
+          items:
+            - BulletedList
+            - NumberedList
+        -
+          name: Media
+          items:
+            - Blockquote
+            - DrupalImage
+        -
+          name: Tools
+          items:
+            - Source
+            - reference_footnotes
+  plugins:
+    stylescombo:
+      styles: ''
+    language:
+      language_list: un
+image_upload:
+  status: false
+  scheme: public
+  directory: inline-images
+  max_size: ''
+  max_dimensions:
+    width: null
+    height: null

bibcite_footnotes_article_with_citations/config/install/field.field.node.bibcite_fn_article_references.body.yml

@@ -0,0 +1,21 @@
+langcode: en
+status: true
+dependencies:
+  config:
+    - field.storage.node.body
+    - node.type.bibcite_fn_article_references
+  module:
+    - text
+id: node.bibcite_fn_article_references.body
+field_name: body
+entity_type: node
+bundle: bibcite_fn_article_references
+label: Body
+description: ''
+required: false
+translatable: true
+default_value: {  }
+default_value_callback: ''
+settings:
+  display_summary: true
+field_type: text_with_summary

bibcite_footnotes_article_with_citations/config/install/field.field.node.bibcite_fn_article_references.field_bibcite_fn_works_cited.yml

@@ -0,0 +1,98 @@
+langcode: en
+status: true
+dependencies:
+  config:
+    - bibcite_entity.bibcite_reference_type.artwork
+    - bibcite_entity.bibcite_reference_type.audiovisual
+    - bibcite_entity.bibcite_reference_type.bill
+    - bibcite_entity.bibcite_reference_type.book
+    - bibcite_entity.bibcite_reference_type.book_chapter
+    - bibcite_entity.bibcite_reference_type.broadcast
+    - bibcite_entity.bibcite_reference_type.case
+    - bibcite_entity.bibcite_reference_type.chart
+    - bibcite_entity.bibcite_reference_type.classical
+    - bibcite_entity.bibcite_reference_type.conference_paper
+    - bibcite_entity.bibcite_reference_type.conference_proceedings
+    - bibcite_entity.bibcite_reference_type.database
+    - bibcite_entity.bibcite_reference_type.film
+    - bibcite_entity.bibcite_reference_type.government_report
+    - bibcite_entity.bibcite_reference_type.hearing
+    - bibcite_entity.bibcite_reference_type.journal
+    - bibcite_entity.bibcite_reference_type.journal_article
+    - bibcite_entity.bibcite_reference_type.legal_ruling
+    - bibcite_entity.bibcite_reference_type.magazine_article
+    - bibcite_entity.bibcite_reference_type.manuscript
+    - bibcite_entity.bibcite_reference_type.map
+    - bibcite_entity.bibcite_reference_type.miscellaneous
+    - bibcite_entity.bibcite_reference_type.miscellaneous_section
+    - bibcite_entity.bibcite_reference_type.newspaper_article
+    - bibcite_entity.bibcite_reference_type.patent
+    - bibcite_entity.bibcite_reference_type.personal
+    - bibcite_entity.bibcite_reference_type.presentation
+    - bibcite_entity.bibcite_reference_type.report
+    - bibcite_entity.bibcite_reference_type.software
+    - bibcite_entity.bibcite_reference_type.statute
+    - bibcite_entity.bibcite_reference_type.thesis
+    - bibcite_entity.bibcite_reference_type.unpublished
+    - bibcite_entity.bibcite_reference_type.web_article
+    - bibcite_entity.bibcite_reference_type.web_project_page
+    - bibcite_entity.bibcite_reference_type.web_service
+    - bibcite_entity.bibcite_reference_type.website
+    - field.storage.node.field_bibcite_fn_works_cited
+    - node.type.bibcite_fn_article_references
+id: node.bibcite_fn_article_references.field_bibcite_fn_works_cited
+field_name: field_bibcite_fn_works_cited
+entity_type: node
+bundle: bibcite_fn_article_references
+label: 'Works Cited'
+description: 'List of works mentioned in this article.'
+required: false
+translatable: true
+default_value: {  }
+default_value_callback: ''
+settings:
+  handler: 'default:bibcite_reference'
+  handler_settings:
+    target_bundles:
+      artwork: artwork
+      audiovisual: audiovisual
+      bill: bill
+      book: book
+      book_chapter: book_chapter
+      broadcast: broadcast
+      case: case
+      chart: chart
+      classical: classical
+      conference_paper: conference_paper
+      conference_proceedings: conference_proceedings
+      database: database
+      film: film
+      government_report: government_report
+      hearing: hearing
+      journal: journal
+      journal_article: journal_article
+      legal_ruling: legal_ruling
+      magazine_article: magazine_article
+      manuscript: manuscript
+      map: map
+      miscellaneous: miscellaneous
+      miscellaneous_section: miscellaneous_section
+      newspaper_article: newspaper_article
+      patent: patent
+      personal: personal
+      presentation: presentation
+      report: report
+      software: software
+      statute: statute
+      thesis: thesis
+      unpublished: unpublished
+      web_article: web_article
+      web_project_page: web_project_page
+      web_service: web_service
+      website: website
+    sort:
+      field: title
+      direction: ASC
+    auto_create: false
+    auto_create_bundle: artwork
+field_type: entity_reference

bibcite_footnotes_article_with_citations/config/install/field.field.node.bibcite_fn_article_references.field_image.yml

@@ -0,0 +1,37 @@
+langcode: en
+status: true
+dependencies:
+  config:
+    - field.storage.node.field_image
+    - node.type.bibcite_fn_article_references
+  module:
+    - image
+id: node.bibcite_fn_article_references.field_image
+field_name: field_image
+entity_type: node
+bundle: bibcite_fn_article_references
+label: Image
+description: ''
+required: false
+translatable: true
+default_value: {  }
+default_value_callback: ''
+settings:
+  file_directory: '[date:custom:Y]-[date:custom:m]'
+  file_extensions: 'png gif jpg jpeg'
+  max_filesize: ''
+  max_resolution: ''
+  min_resolution: ''
+  alt_field: true
+  alt_field_required: true
+  title_field: false
+  title_field_required: false
+  default_image:
+    uuid: ''
+    alt: ''
+    title: ''
+    width: null
+    height: null
+  handler: 'default:file'
+  handler_settings: {  }
+field_type: image

bibcite_footnotes_article_with_citations/config/install/field.field.node.bibcite_fn_article_references.field_tags.yml

@@ -0,0 +1,28 @@
+langcode: en
+status: true
+dependencies:
+  config:
+    - field.storage.node.field_tags
+    - node.type.bibcite_fn_article_references
+    - taxonomy.vocabulary.tags
+id: node.bibcite_fn_article_references.field_tags
+field_name: field_tags
+entity_type: node
+bundle: bibcite_fn_article_references
+label: Tags
+description: 'Enter a comma-separated list. For example: Amsterdam, Mexico City, "Cleveland, Ohio"'
+required: false
+translatable: true
+default_value: {  }
+default_value_callback: ''
+settings:
+  handler: 'default:taxonomy_term'
+  handler_settings:
+    target_bundles:
+      tags: tags
+    sort:
+      field: name
+      direction: asc
+    auto_create: true
+    auto_create_bundle: ''
+field_type: entity_reference

bibcite_footnotes_article_with_citations/config/install/filter.format.basic_html_with_references.yml

@@ -0,0 +1,87 @@
+langcode: en
+status: true
+dependencies:
+  module:
+    - bibcite_footnotes
+    - editor
+    - footnotes
+name: 'Basic HTML with References'
+format: basic_html_with_references
+weight: 0
+filters:
+  filter_reference_footnotes:
+    id: filter_reference_footnotes
+    provider: bibcite_footnotes
+    status: true
+    weight: -50
+    settings:
+      footnotes_collapse: '1'
+      footnotes_ibid: '0'
+      notes_section_label: Notes
+      reference_dont_show_backlink_text: '0'
+      works_cited_sort_by: alphabetical
+  editor_file_reference:
+    id: editor_file_reference
+    provider: editor
+    status: true
+    weight: -45
+    settings: {  }
+  filter_html_image_secure:
+    id: filter_html_image_secure
+    provider: filter
+    status: true
+    weight: -46
+    settings: {  }
+  filter_url:
+    id: filter_url
+    provider: filter
+    status: false
+    weight: -41
+    settings:
+      filter_url_length: 72
+  filter_html:
+    id: filter_html
+    provider: filter
+    status: true
+    weight: -49
+    settings:
+      allowed_html: '<a href hreflang id class="" title> <div id class=""> <em> <strong> <cite> <blockquote cite> <code> <ul type class=""> <ol id type class=""> <li id class=""> <dl> <dt> <dd> <h2 id> <h3 id> <h4 id> <h5 id> <h6 id> <span id class=""> <sup> <img src alt data-entity-type data-entity-uuid data-align data-caption> <p> <fn id>'
+      filter_html_help: true
+      filter_html_nofollow: false
+  filter_autop:
+    id: filter_autop
+    provider: filter
+    status: false
+    weight: -42
+    settings: {  }
+  filter_align:
+    id: filter_align
+    provider: filter
+    status: true
+    weight: -48
+    settings: {  }
+  filter_caption:
+    id: filter_caption
+    provider: filter
+    status: true
+    weight: -47
+    settings: {  }
+  filter_htmlcorrector:
+    id: filter_htmlcorrector
+    provider: filter
+    status: false
+    weight: -40
+    settings: {  }
+  filter_html_escape:
+    id: filter_html_escape
+    provider: filter
+    status: false
+    weight: -43
+    settings: {  }
+  filter_footnotes:
+    id: filter_footnotes
+    provider: footnotes
+    status: false
+    weight: -44
+    settings:
+      footnotes_collapse: '0'

bibcite_footnotes_article_with_citations/config/install/node.type.bibcite_fn_article_references.yml

@@ -0,0 +1,17 @@
+langcode: en
+status: true
+dependencies:
+  module:
+    - menu_ui
+third_party_settings:
+  menu_ui:
+    available_menus:
+      - main
+    parent: 'main:'
+name: 'Article with References'
+type: bibcite_fn_article_references
+description: 'Article that includes a Works Cited field and in-text references.'
+help: ''
+new_revision: true
+preview_mode: 1
+display_submitted: true

composer.json

@@ -0,0 +1,23 @@
+{
+    "name": "roblib/bibcite_footnotes",
+    "description": "Add citation footnotes with automatic numbering.",
+    "type": "drupal-module",
+    "homepage": "https://drupal.org/project/bibcite_footnotes",
+    "authors": [
+        {
+            "name": "Alexander O'Neill (alxp)",
+            "homepage": "https://www.drupal.org/u/alxp",
+            "role": "Maintainer"
+        }
+    ],
+    "support": {
+        "issues": "https://drupal.org/project/issues/bibcite_footnotes",
+        "source": "https://cgit.drupalcode.org/bibcite_footnotes"
+    },
+    "license": "GPL-2.0+",
+    "minimum-stability": "dev",
+    "require": {
+        "drupal/core": ">=8.6",
+        "drupal/fakeobjects": "^1.0"
+    }
+}

config/optional/field.storage.node.field_bibcite_fn_works_cited.yml

@@ -0,0 +1,24 @@
+langcode: en
+status: true
+dependencies:
+  module:
+    - bibcite_entity
+    - node
+third_party_settings:
+  field_permissions:
+    permission_type: public
+_core:
+  default_config_hash: pxSiuPskUjLuu_0TFIFVYFyZtkIelIPBysbXt_LyLVk
+id: node.field_bibcite_fn_works_cited
+field_name: field_bibcite_fn_works_cited
+entity_type: node
+type: entity_reference
+settings:
+  target_type: bibcite_reference
+module: core
+locked: false
+cardinality: -1
+translatable: true
+indexes: {  }
+persist_with_no_fields: false
+custom_storage: false

css/reference_footnote.css

@@ -7,4 +7,89 @@
 .footnote-list .footnotes .footnote-multi::after {
   content: " ";
   white-space: pre;
-}
+}
+
+/*
+ * CSS specific to Bibcite Footnotes module.
+ * (Borrowed from Footnotes module.
+ *
+*
+* Thanks to binford2k@lug.wsu.edu for this tip and drinkypoo
+* for the question leading up to it. http://drupal.org/node/80538
+*/
+
+/* Add empty space before footnotes and a black line on top. */
+.footnotes {
+  clear: both;
+  margin-top: 4em;
+  margin-bottom: 2em;
+  border-top: 1px solid #000;
+}
+/* Make footnotes appear in a smaller font */
+.footnotes {
+  font-size: 0.9em;
+}
+/*
+  Make the footnote a supertext^1
+*/
+.see-footnote {
+  vertical-align: top;
+  position: relative;
+  top: -0.25em;
+  font-size: 0.9em;
+}
+/* Hide the bullet of the UL list of footnotes */
+
+ul.footnotes {
+  list-style-type: none;
+  margin-left: 0;
+  padding-left: 0;
+}
+ul.footnotes li {
+  margin-left: 2.5em;
+  list-style-type: none;
+  background: none; /* Garland theme sets a bullet via background image, this must be unset! See bug 861634 */
+}
+/* Move the footnote number outside of the margin for footnote text (hanging indent) */
+ul.footnotes {
+  /* This is apparently very needed for the "position: absolute;" below to work correctly */
+  position: relative;
+}
+.footnotes .footnote-label {
+  position: absolute;
+  left: 0;
+  z-index: 2;
+}
+/* Highlight the target footnote (or ref number, if a backlink was used) when user clicks a footnote. */
+.see-footnote:target,
+.footnotes .footnote:target {
+  background-color: #eee;
+}
+.see-footnote:target {
+  border: solid 1px #aaa;
+}
+/* Note: This CSS has a minor bug on all versions of IE in that the footnote numbers
+are aligned with the absolute bottom of their space, thus being a couple of pixels
+lower than their corresponding line of text. IE5.5 has a serious bug in that the numbers
+are not shifted left at all, thus being garbled together with the start of their text. */
+
+/*
+  Make the multiple backlinks a supertext^1
+*/
+.footnotes .footnote-multi {
+  vertical-align: top;
+  position: relative;
+  top: -0.25em;
+  font-size: 0.75em;
+}
+/*
+ * Textile Footnotes
+ */
+/* First footnote */
+#fn1 {
+  border-top: 1px solid #000;
+  margin-top: 3em;
+}
+.footnote {
+  font-size: 0.9em;
+}

js/plugins/reference_footnotes/dialogs/footnotes.js

@@ -14,7 +14,7 @@
                           {
                             id: 'reference',
                             type: 'select',
-                            items: editor.config.referenceFootnotes_list,
+                            items: [[" - None - ", 0]].concat(typeof(drupalSettings.bibcite_footnotes) !== 'undefined' ? drupalSettings.bibcite_footnotes.references : []),
                             label: Drupal.t('Reference Footnote item:'),
                             setup: function (element) {
                               if (isEdit)
@@ -27,13 +27,18 @@
                             label: Drupal.t('Or add free-form footnote text :'),
                             setup: function (element) {
                                 if (isEdit) {
-                                  var text = element.getText();
+                                  var markup = element.getHtml();
 
-                                  this.setValue(text);
+                                  this.setValue(markup);
 
                                 }
                             }
                           },
+                          {
+                            id: 'html-help',
+                            type: 'html',
+                            html: 'HTML tags can be used, e.g., <strong>, <em>, <a href="...">',
+                          },
                           {
                             id: 'page',
                             type: 'text',
@@ -56,16 +61,40 @@
                                     if (isEdit)
                                         this.setValue(element.getAttribute('value'));
                                 }
-                            }
+
+                            },
+                          {
+                            id: 'value-help',
+                            type: 'html',
+                            html: 'Leave blank for an automatic sequential reference number, or enter a custom footnote value',
+                          }
                         ],
                 }
             ],
             onShow : function() {
-                if (isEdit) {
-                    this.fakeObj = CKEDITOR.plugins.reference_footnotes.getSelectedFootnote( editor );
-                    this.realObj = editor.restoreRealElement( this.fakeObj );
-                }
-                this.setupContent( this.realObj );
+              if (isEdit) {
+                this.fakeObj = CKEDITOR.plugins.reference_footnotes.getSelectedFootnote(editor);
+                this.realObj = editor.restoreRealElement(this.fakeObj);
+              }
+              var select = this.parts.contents.$.getElementsByTagName('select');
+              var selectBox = select.item(0);
+              // Remove all but the default 'None' item from teh list.
+              var i;
+              for (i = selectBox.options.length - 1; i >= 1; i--) {
+                selectBox.remove(i)
+              }
+
+              // Re-add buttons from the current state of Settings.
+              if (typeof (drupalSettings.bibcite_footnotes) !== 'undefined') {
+
+                drupalSettings.bibcite_footnotes.references.forEach(function (reference) {
+                  var newReference = document.createElement('option');
+                  newReference.text = reference[0];
+                  newReference.setAttribute("value", reference[1]);
+                  selectBox.add(newReference);
+                });
+              }
+              this.setupContent( this.realObj );
             },
             onOk : function() {
                 var referenceNote = this.getValueOf('info', 'reference');
@@ -84,4 +113,4 @@
     CKEDITOR.dialog.add( 'editreferencefootnotes', function( editor ) {
         return referenceFootnotesDialog( editor, 1 );
     });
-})();
+})();

js/plugins/reference_footnotes/plugin.js

@@ -26,8 +26,22 @@
 
                 );
             },
+            beforeInit: function( editor )
+            {
+                // Adapt some critical editor configuration for better support
+                // of BBCode environment.
+                var config = editor.config;
+                CKEDITOR.tools.extend( config,
+                    {
+                        enterMode : CKEDITOR.ENTER_BR,
+                        basicEntities: false,
+                        entities : false,
+                        fillEmptyBlocks : false
+                    }, true );
+            },
             init: function( editor )
             {
+
                 editor.addCommand('createreferencefootnotes', new CKEDITOR.dialogCommand('createreferencefootnotes', {
                     allowedContent: 'fn[value]'
                 }));
@@ -103,7 +117,7 @@ CKEDITOR.plugins.reference_footnotes = {
         }
 
         if (text && text.length > 0 ) {
-            realElement.setText(text);
+            realElement.setHtml(text);
         }
         realElement.setAttribute('value',value);
         if (page && page.length > 0) {

js/replace_citations.js

@@ -0,0 +1,28 @@
+/**
+ * @file
+ * Provides JavaScript additions to entity embed dialog.
+ *
+ * This file provides popup windows for previewing embedded entities from the
+ * embed dialog.
+ */
+
+(function ($, Drupal) {
+
+  "use strict";
+
+  Drupal.behaviors.bibciteFootnotesReplaceCitations = {
+    attach: function attach(context, settings) {
+      /*
+      if (CKEDITOR.instances) {
+        for (var instance in CKEDITOR.instances) {
+          var editor = CKEDITOR.instances[instance];
+          var config = editor.config;
+          var name = editor.name;
+          editor.destroy();
+          CKEDITOR.replace(name, config);
+        }
+      }
+      */
+    }
+  }
+})(jQuery, Drupal);

src/CitationTools.php

@@ -11,12 +11,14 @@ namespace Drupal\bibcite_footnotes;
 
 class CitationTools {
 
-  public function getRenderableReference($reference_entity_id) {
-    $reference_storage = \Drupal::entityTypeManager()
-      ->getStorage('bibcite_reference')
-      ->load($reference_entity_id);
+  public function getRenderableReference($reference_entity) {
+    if (is_numeric($reference_entity)) {
+      $reference_entity = \Drupal::entityTypeManager()
+        ->getStorage('bibcite_reference')
+        ->load($reference_entity);
+    }
     $serializer = \Drupal::service('serializer');
-    $data = $serializer->normalize($reference_storage, 'csl');
+    $data = $serializer->normalize($reference_entity, 'csl');
     return ['#theme' => 'bibcite_citation', '#data' => $data];
   }
 }

src/Plugin/BibCiteProcessor/CiteprocPhpInline.php

@@ -0,0 +1,73 @@
+<?php
+
+namespace Drupal\bibcite_footnotes\Plugin\BibCiteProcessor;
+
+use AcademicPuma\CiteProc\CiteProc;
+use Drupal\Core\Config\ConfigFactoryInterface;
+use Drupal\Core\Plugin\ContainerFactoryPluginInterface;
+use Drupal\bibcite\Plugin\BibCiteProcessorBase;
+use Drupal\bibcite\Plugin\BibCiteProcessorInterface;
+use Symfony\Component\DependencyInjection\ContainerInterface;
+
+/**
+ * Defines a style provider based on citeproc-php library.
+ *
+ * Extended to support inline citation links based on the CSL.
+ *
+ * @BibCiteProcessor(
+ *   id = "citeproc-php",
+ *   label = @Translation("Citeproc PHP"),
+ * )
+ */
+class CiteprocPhpInline extends BibCiteProcessorBase implements BibCiteProcessorInterface, ContainerFactoryPluginInterface {
+
+  /**
+   * Config factory service.
+   *
+   * @var \Drupal\Core\Config\ConfigFactoryInterface
+   */
+  protected $configFactory;
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function create(ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition) {
+    return new static(
+      $configuration,
+      $plugin_id,
+      $plugin_definition,
+      $container->get('config.factory')
+    );
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public function __construct(array $configuration, $plugin_id, $plugin_definition, ConfigFactoryInterface $config_factory) {
+    parent::__construct($configuration, $plugin_id, $plugin_definition);
+
+    $this->configFactory = $config_factory;
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public function getDescription() {
+    return $this->t('Render citation by citeproc-php library');
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public function render($data, $csl, $lang) {
+    $cite_proc = new CiteProc($csl, $lang);
+    $mode = !empty($data['mode']) ? $data['mode'] : NULL;
+
+    if (!$data instanceof \stdClass) {
+      $data = json_decode(json_encode($data));
+    }
+
+    return $cite_proc->render($data, $mode);
+  }
+
+}

src/Plugin/CKEditorPlugin/ReferenceFootnotes.php

@@ -33,7 +33,8 @@ class ReferenceFootnotes extends CKEditorPluginBase {
     return [
       'reference_footnotes' => [
         'label' => t('Reference Footnotes'),
-        'image' => drupal_get_path('module', 'bibcite_footnotes') . '/js/plugins/reference_footnotes/images/icon.png',
+        'image' => \Drupal::service('extension.list.module')->getPath('bibcite_footnotes') .
+          '/js/plugins/reference_footnotes/images/icon.png',
       ],
     ];
   }
@@ -44,7 +45,7 @@ class ReferenceFootnotes extends CKEditorPluginBase {
   public function getFile() {
     // Make sure that the path to the plugin.js matches the file structure of
     // the CKEditor plugin you are implementing.
-    return drupal_get_path('module', 'bibcite_footnotes') . '/js/plugins/reference_footnotes/plugin.js';
+    return \Drupal::service('extension.list.module')->getPath('bibcite_footnotes') . '/js/plugins/reference_footnotes/plugin.js';
   }
 
   /**
@@ -72,27 +73,6 @@ class ReferenceFootnotes extends CKEditorPluginBase {
    * {@inheritdoc}
    */
   public function getConfig(Editor $editor) {
-    $uid = \Drupal::currentUser()->id();
-
-    $query = \Drupal::service('entity.query');
-
-    $ref_ids = $query
-      ->get('bibcite_reference')
-      ->condition('uid', $uid)
-      ->execute();
-
-    $reference_storage = \Drupal::entityTypeManager()->getStorage('bibcite_reference')->loadMultiple($ref_ids);
-    $view_builder = \Drupal::entityTypeManager()->getViewBuilder('bibcite_reference');
-    $options = [];
-    foreach($reference_storage as $ref_id => $ref_item) {
-      $build = $view_builder->view($ref_item, 'citation');
-      $render = render($build);
-      $output = trim(strip_tags($render));
-      //$options[] = [$output, $ref_id];
-      $options[] = [$output, $ref_id];
-    }
-
-    return ['referenceFootnotes_list' => $options];
+    return [];
   }
-
 }

src/Plugin/Filter/ReferenceFootnotesFilter.php

@@ -4,7 +4,9 @@ namespace Drupal\bibcite_footnotes\Plugin\Filter;
 
 use Drupal\Component\Utility\Xss;
 use Drupal\Core\Form\FormStateInterface;
-use Drupal\footnotes\Plugin\Filter\FootnotesFilter;
+use Drupal\filter\FilterProcessResult;
+use Drupal\filter\Plugin\FilterBase;
+
 
 /**
  * Reference Footnotes filter.
@@ -20,14 +22,11 @@ use Drupal\footnotes\Plugin\Filter\FootnotesFilter;
  *     "footnotes_footnotefootnote_linkcollapse" = FALSE,
  *     "footnotes_ibid" = FALSE,
  *     "notes_section_label" = "Notes",
- *     "references_section_label" = "References"
  *   },
  *   weight = 0
  * )
  */
-class ReferenceFootnotesFilter extends FootnotesFilter {
-  const ENDNOTE = 0;
-  const REFERENCE = 1;
+class ReferenceFootnotesFilter extends FilterBase {
 
   /**
    * Object with configuration for reference footnotes.
@@ -49,6 +48,7 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
   public function __construct(array $configuration, $plugin_id, array $plugin_definition) {
     parent::__construct($configuration, $plugin_id, $plugin_definition);
 
+    $this->renderer = \Drupal::service('renderer');
     $this->config = \Drupal::config('reference_footnotes.settings');
     $this->configEditable = \Drupal::configFactory()
       ->getEditable('reference_footnotes.settings');
@@ -80,34 +80,27 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
     ];
     $settings['notes_section_label'] = [
       '#type' => 'textfield',
-      '#title' => t('Notes section label'),
+      '#title' => t('Notes section heading label'),
       '#default_value' => $this->settings['notes_section_label'],
     ];
-    $settings['references_section_label'] = [
-      '#type' => 'textfield',
-      '#title' => $this->t('References section label'),
-      '#description' => $this->t('E.g., "Works Cited" for MLA style.'),
-      '#default_value' => $this->settings['references_section_label'],
-    ];
     $settings['reference_dont_show_backlink_text'] = [
       '#type' => 'checkbox',
       '#title' => $this->t("Don't show note 'value' text in reference list."),
       '#description' => $this->t("Suitable for MLA-style citations, like (Smith, 33-22)"),
       '#default_value' => $this->settings['reference_dont_show_backlink_text'],
     ];
-    $settings['reference_sort_by'] = [
+    $settings['works_cited_sort_by'] = [
       '#type' => 'select',
-      '#title' => $this->t("Sort references list by"),
+      '#title' => $this->t("Sort Workd Cited list by"),
       '#options' => [
-        'order' => $this->t("Order in text"),
-        'alphabetical' => $this->t("Alphabetical"),
+        'weight' => $this->t("Manually"),
+        'alphabetical' => $this->t("Alphabetically"),
       ],
-      '#default_value' => $this->settings['reference_sort_by'],
+      '#default_value' => $this->settings['works_cited_sort_by'],
     ];
     return $settings;
   }
 
-
   /**
    * Helper function called from preg_replace_callback() above.
    *
@@ -136,7 +129,7 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
     if ($op == 'prepare') {
       // In the 'prepare' case, the first argument contains the options to use.
       // The name 'matches' is incorrect, we just use the variable anyway.
-      $opt_collapse = $matches;
+      $opt_collapse = isset($matches['footnotes_collapse']) && $matches['footnotes_collapse'];
       return 0;
     }
 
@@ -145,8 +138,6 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
 
       if (count($store_matches) > 0) {
         // Separate out endontes and reference notes.
-        $notes = $this->extractNotesByType(self::ENDNOTE, $store_matches);
-        $references = $this->extractNotesByType(self::REFERENCE, $store_matches);
 
         if ($this->settings['footnotes_ibid']) {
           $this->ibidemify($references);
@@ -155,19 +146,10 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
         // themed as a list
         $markup = [
           '#theme' => 'bibcite_footnote_list',
-          '#notes' => $notes,
-          '#note_type' => self::ENDNOTE,
+          '#notes' => $store_matches,
           '#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;
@@ -184,6 +166,8 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
     $randstr = $this->randstr();
 
     $value = $this->extractAttribute($matches, 'value');
+    $page = $this->extractAttribute($matches, 'page');
+    $reference = $this->extractAttribute($matches, 'reference');
 
     if ($value) {
       // A value label was found. If it is numeric, record it in $n so further
@@ -195,7 +179,7 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
         $n = $value;
       }
     }
-    elseif ($opt_collapse and $value_existing = $this->findFootnote($matches[2], $store_matches)) {
+    elseif ($opt_collapse and $value_existing = $this->findFootnote($matches[2], $reference, $store_matches)) {
       // An identical footnote already exists. Set value to the previously
       // existing value.
       $value = $value_existing;
@@ -211,8 +195,6 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
     // attribute.
     $value_id = preg_replace('|[^\w\-]|', '', $value);
 
-    $page = $this->extractAttribute($matches, 'page');
-    $reference = $this->extractAttribute($matches, 'reference');
 
     // Create a sanitized version of $text that is suitable for using as HTML
     // attribute value. (In particular, as the title attribute to the footnote
@@ -279,10 +261,10 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
   /**
    * @inheritdoc
    */
-  private function findFootnote($text, &$store_matches) {
+  private function findFootnote($text, $reference, &$store_matches) {
     if (!empty($store_matches)) {
       foreach ($store_matches as &$fn) {
-        if ($fn['text'] == $text) {
+        if ($fn['text'] == $text && $fn['reference'] == $reference) {
           return $fn['value'];
         }
       }
@@ -332,22 +314,88 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
     }
   }
 
-  protected function extractNotesByType($type, $footnotes) {
-    $notes = [];
-    foreach ($footnotes as $fn) {
-      switch ($type) {
-        case self::ENDNOTE:
-          if (!empty($fn['text'])) {
-            $notes[] = $fn;
-          }
-          break;
-        case self::REFERENCE:
-          if (!empty($fn['reference'])) {
-            $notes[] = $fn;
-          }
-          break;
-      }
+  /**
+   * {@inheritdoc}
+   */
+  public function process($text, $langcode) {
+    // Supporting both [fn] and <fn> now. Thanks to fletchgqc
+    // http://drupal.org/node/268026.
+    // Convert all square brackets to angle brackets. This way all further code
+    // just manipulates angle brackets. (Angle brackets are preferred here for
+    // the simple reason that square brackets are more tedious to use in
+    // regexps).
+    if (is_array($text)) {
+      implode($text);
+    }
+    $text = preg_replace('|\[fn([^\]]*)\]|', '<fn$1>', $text);
+    $text = preg_replace('|\[/fn\]|', '</fn>', $text);
+    $text = preg_replace('|\[footnotes([^\]]*)\]|', '<footnotes$1>', $text);
+
+    // Check that there are an even number of open and closing tags.
+    // If there is one closing tag missing, append this to the end.
+    // If there is more disparity, throw a warning and continue.
+    // A closing tag may sometimes be missing when we are processing a teaser
+    // and it has been cut in the middle of the footnote.
+    // See http://drupal.org/node/253326
+    $foo = [];
+    $open_tags = preg_match_all("|<fn([^>]*)>|", $text, $foo);
+    $close_tags = preg_match_all("|</fn>|", $text, $foo);
+
+    if ($open_tags == $close_tags + 1) {
+      $text = $text . '</fn>';
+    }
+    elseif ($open_tags > $close_tags + 1) {
+      trigger_error($this->t("You have unclosed fn tags. This is invalid and will
+        produce unpredictable results."));
+    }
+
+    // Before doing the replacement, the callback function needs to know which
+    // options to use.
+    $this->replaceCallback($this->settings, 'prepare');
+
+    $pattern = '|<fn([^>]*)>(.*?)</fn>|s';
+    $text = preg_replace_callback($pattern, [
+      $this,
+      'replaceCallback',
+    ], $text);
+
+    // Replace tag <footnotes> with the list of footnotes.
+    // If tag is not present, by default add the footnotes at the end.
+    // Thanks to acp on drupal.org for this idea. see
+    // http://drupal.org/node/87226.
+    $footer = $this->replaceCallback(NULL, 'output footer');
+    $pattern = '|(<footnotes([^\]]*)>)|';
+    if (preg_match($pattern, $text) > 0) {
+      $text = preg_replace($pattern, $footer, $text, 1);
+    }
+    elseif (!empty($footer)) {
+      $text .= "\n\n" . $footer;
+    }
+    $result = new FilterProcessResult($text);
+    $result->setAttachments([
+      'library' => [
+        'footnotes/footnotes',
+      ],
+    ]);
+    return $result;
+  }
+
+
+  /**
+   * Helper function to return a random text string.
+   *
+   * @return string
+   *   Random (lowercase) alphanumeric string.
+   */
+  public function randstr() {
+    $chars = "abcdefghijklmnopqrstuwxyz1234567890";
+    $str = "";
+
+    // Seeding with srand() not necessary in modern PHP versions.
+    for ($i = 0; $i < 7; $i++) {
+      $n = rand(0, strlen($chars) - 1);
+      $str .= substr($chars, $n, 1);
     }
-    return $notes;
+    return $str;
   }
 }