Removed the modules submodule and added them correctly

modules/admin_ui_toggle/admin_ui_toggle.info.yml

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+name: Admin UI Toggle
+type: module
+description: 'Provides the Admin UI Toggle block'
+package: Sector
+core: 8.x
+dependencies:
+  - block

modules/admin_ui_toggle/admin_ui_toggle.libraries.yml

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+admin-ui-toggle:
+  version: VERSION
+  css:
+    component:
+      css/admin-ui-toggle.css: {}
+  js:
+    js/admin_ui_toggle.js: {}
+  dependencies:
+    - core/jquery
+    - core/jquery.once
+    - core/drupal

modules/admin_ui_toggle/admin_ui_toggle.module

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+<?php
+
+/**
+ * Implements hook_theme().
+ */
+function admin_ui_toggle_theme($existing, $type, $theme, $path) {
+  return [
+    'admin_ui_toggle' => [
+    ],
+  ];
+}

modules/admin_ui_toggle/css/admin-ui-toggle.css

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+body.admin-ui-hide {padding-top:0px!important;}
+.admin-ui-hide #toolbar-bar {display:none!important;}
+.admin-ui-hide .contextual-links-wrapper {display:none!important;}
+.admin-ui-hide .tabs--primary {display:none!important;}
+.admin-ui-hide .alert {display:none!important;}
+html body.admin-ui-hide.toolbar-bar {margin-top: 0!important;}
+.admin-ui-toggle p {
+    margin:0;padding:0;
+}
+.block-admin-ui-toggle {
+  display: flex;
+}
+.admin-ui-toggle button {
+    position: fixed;
+    top:0;
+    right:150px;
+    border: none;
+    outline:none;
+    z-index: 9999;
+}
+.admin-ui-toggle button:before {
+    content: 'Hide menu';
+    font-size: 12px;
+    line-height: 1;
+}
+.admin-ui-toggle.ui-is-hidden button:before {
+    content: 'Show menu';
+}
+.admin-ui-toggle button .fa-toggle-off {
+    display: none;
+}
+.admin-ui-toggle button .fa-toggle-on {
+    display: block;
+}
+.admin-ui-hide .admin-ui-toggle button .fa-toggle-off {
+    display: block;
+}
+.admin-ui-hide .admin-ui-toggle button .fa-toggle-on {
+    display: none;
+}

modules/admin_ui_toggle/js/admin_ui_toggle.js

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+(function ($, Drupal) {
+
+    'use strict';
+
+    Drupal.behaviors.admin_ui_toggle = {
+        attach: function (context, settings) {
+            $("button",".admin-ui-toggle").on('click', function(evt){
+                $("body").toggleClass("admin-ui-hide");
+                if ($("body").hasClass('admin-ui-hide')) {
+                    $('.admin-ui-toggle').addClass('ui-is-hidden');
+                } else {
+                    $('.admin-ui-toggle').removeClass('ui-is-hidden');
+                }
+                evt.preventDefault();
+            });
+        }
+    };
+})(jQuery, Drupal);

modules/admin_ui_toggle/src/Plugin/Block/AdminUiToggle.php

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+<?php
+
+namespace Drupal\admin_ui_toggle\Plugin\Block;
+
+use Drupal\Core\Block\BlockBase;
+
+/**
+ * Provides the admin ui toggle block.
+ *
+ * @Block(
+ *   id = "admin_ui_toggle",
+ *   admin_label = @Translation("Sector blocks - Admin UI toggle"),
+ * )
+ */
+class AdminUiToggle extends BlockBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function build() {
+    $items = array();
+
+    return array(
+      '#theme' => 'admin_ui_toggle',
+      '#attached' => [
+        'library' => [
+          'admin_ui_toggle/admin-ui-toggle'
+        ],
+      ],
+    );
+  }
+}

modules/admin_ui_toggle/templates/admin-ui-toggle.html.twig

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+{% block content %}
+    <div class="admin-ui-toggle">
+        <p>
+            <button></button>
+        </p>
+    </div>
+{% endblock %}

modules/composer.json

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+{
+  "name": "sparksi/sector_modules",
+  "description": "Project-specific modules for the Sector D8 project",
+  "type": "drupal-custom-module",
+  "license": "GPL-2.0+",
+  "minimum-stability": "dev",
+  "authors": [
+    {
+      "name": "Sparks Interactive",
+      "role": "Development"
+    }
+  ]
+}

modules/plain_text/README.md

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+Plain text module
+
+Probably needs a better name..
+
+This module creates a checkbox at  at /admin/config/content/formats/manage/{format}.
+If this checkbox is ticked then all text pasted in the ckeditor using this text
+format will have all formatting stripped.
+
+This retains the integrity of the Paste from word toolbar button.

modules/plain_text/js/plain_text.js

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+/**
+ * @file
+ *
+ * JS file for making sure that intercepts paste events from Ctrl/CMd+V and
+ * right click and strips the formatting from them using proper Jquery
+ * functions.
+ *
+ * @ignore
+ */
+
+(function ($, Drupal, drupalSettings, _) {
+
+  'use strict';
+
+  Drupal.ckeditor = Drupal.ckeditor || {};
+
+  Drupal.behaviors.plaintext = {
+    attach: function () {
+      // Checks if the CKEDITOR currently exists
+      if (typeof CKEDITOR !== 'undefined') {
+        CKEDITOR.on('instanceReady', function (i) {
+          // Gets the editor instance.
+          var editor = i.editor;
+          // The paste from word dialog shows up by default on any paste event.
+          // We don't want that, so this disables it.
+          editor.config.pasteFromWordPromptCleanup = false;
+          // Paste event.
+          editor.on('paste', function (e) {
+            // Checks if the PlainText config is true, if its false, don't apply
+            // the processing to the text.
+            if(editor.config.PlainText === true) {
+              console.log(e);
+              console.log(editor);
+              // Paste events that aren't the pastefromword paste dialog creates
+              // this $ object inside the editor. We check if it exists.
+              //
+              // If it exists it means the paste should be stripped.
+              if (e.data.dataTransfer.$) {
+                // Not 100% sure if this is needed. Will test.
+                e.data.type = 'text';
+
+                var text = '';
+                // Strip the tags using the jQuery.text function.
+                e.data.dataValue = jQuery(e.data.dataValue).text();
+              }
+            }
+          });
+        });
+      }
+    }
+  }
+})(jQuery, Drupal, drupalSettings, _);

modules/plain_text/plain_text.info.yml

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+name: Plain Text
+type: module
+description: 'Plain text plugin for ckeditor'
+package: Sector
+core: 8.x

modules/plain_text/plain_text.libraries.yml

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+plain-text:
+  version: VERSION
+  js:
+    js/plain_text.js: {}
+  dependencies:
+    - core/jquery
+    - core/drupal

modules/plain_text/plain_text.module

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+<?php
+
+/**
+ * Implements hook_page_attachments().
+ */
+function plain_text_page_attachments(array &$attachments) {
+  // Attach the library.
+  $attachments['#attached']['library'][] = 'plain_text/plain-text';
+}
+
+//TODO: MAKE THIS AND THE JS NICER
+
+function plain_text_editor_js_settings_alter(array &$settings) {
+  // Get all active formats.
+  $filters_list = filter_formats();
+
+  // For every text format, check if the Enable plain text filter is enabled,
+  // if it is, set the variable so it can be used later in the JS.
+  foreach (array_keys($settings['editor']['formats']) as $text_format_id) {
+    $format_filter = $filters_list[$text_format_id]->filters()->getAll();
+    $format_filter_config = $format_filter['plain_text_filter']->getConfiguration();
+    if($format_filter_config['status']) {
+      $settings['editor']['formats'][$text_format_id]['editorSettings']['PlainText'] = TRUE;
+    }
+  }
+}

modules/plain_text/src/Plugin/Filter/PlainTextFilter.php

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+<?php
+
+namespace Drupal\plain_text\Plugin\Filter;
+
+use Drupal\filter\Plugin\FilterBase;
+use Drupal\filter\FilterProcessResult;
+
+/**
+ * @Filter(
+ *   id = "plain_text_filter",
+ *   title = @Translation("Enforce plain text paste"),
+ *   description = @Translation("If enabled, all text pasted directly into the CKEditor will be stripped of all tags and pasted as plain text."),
+ *   type = Drupal\filter\Plugin\FilterInterface::TYPE_HTML_RESTRICTOR,
+ * )
+ */
+class PlainTextFilter extends FilterBase {
+
+  public function process($text, $langcode) {
+    // The text is processed using the JS that is loaded if this filter is
+    // enabled. Thus we only need to return the same text sent to this function.
+    $result = new FilterProcessResult($text);
+    return $result;
+  }
+}

modules/sector_blocks/sector_blocks.info.yml

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+name: Sector blocks
+description: Provides custom blocks for Sector
+package: Sector
+
+type: module
+core: 8.x

modules/sector_blocks/sector_blocks.module

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+<?php
+
+/**
+ * Implements hook_theme().
+ */
+function sector_blocks_theme($existing, $type, $theme, $path) {
+  return [
+    'responsive_menu_control_block' => [
+    ],
+    'search_desktop_fly_out_control_block' => [
+    ],
+    'search_api_box' => [
+    ],
+    'search_api_box_mobile' => [
+    ],
+  ];
+}

modules/sector_blocks/src/Plugin/Block/ResponsiveMenuControls.php

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+<?php
+
+namespace Drupal\sector_blocks\Plugin\Block;
+
+use Drupal\Core\Block\BlockBase;
+
+/**
+ * Provides the responsive menu controls block.
+ *
+ * @Block(
+ *   id = "responsive_menu_controls",
+ *   admin_label = @Translation("Sector blocks - Responsive menu controls"),
+ * )
+ */
+class ResponsiveMenuControls extends BlockBase {
+  /**
+   * {@inheritdoc}
+   */
+  public function build() {
+    $build = [];
+    $build['#theme'] = 'responsive_menu_control_block';
+
+    return $build;
+  }
+}

modules/sector_blocks/src/Plugin/Block/SearchApiBox.php

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+<?php
+
+namespace Drupal\sector_blocks\Plugin\Block;
+
+use Drupal\Core\Block\BlockBase;
+
+/**
+ * Provides the search api box block. Replicates the default search block design.
+ *
+ * @Block(
+ *   id = "search_api_box",
+ *   admin_label = @Translation("Sector blocks - Search API block"),
+ * )
+ */
+class SearchApiBox extends BlockBase {
+  /**
+   * {@inheritdoc}
+   */
+  public function build() {
+    $build = [];
+    $build['#theme'] = 'search_api_box';
+
+    return $build;
+  }
+}

modules/sector_blocks/src/Plugin/Block/SearchApiBoxMobile.php

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+<?php
+
+namespace Drupal\sector_blocks\Plugin\Block;
+
+use Drupal\Core\Block\BlockBase;
+
+/**
+ * Provides the search api box block. Replicates the default search block design.
+ * Mobile version.
+ *
+ * @Block(
+ *   id = "search_api_box_mobile",
+ *   admin_label = @Translation("Sector blocks - Search API block (mobile)"),
+ * )
+ */
+class SearchApiBoxMobile extends BlockBase {
+  /**
+   * {@inheritdoc}
+   */
+  public function build() {
+    $build = [];
+    $build['#theme'] = 'search_api_box_mobile';
+
+    return $build;
+  }
+}