From cd593f68d3f259ef39d93c63c8d8ed2eb235ecff Mon Sep 17 00:00:00 2001
From: Marcus Quinn <6428977+marcusquinn@users.noreply.github.com>
Date: Thu, 10 Apr 2025 00:06:07 +0100
Subject: [PATCH] Complete redesign to use WordPress plugins list directly
 (v1.3.0)

---
 CHANGELOG.md                 |  15 ++
 README.md                    |   9 +-
 plugin-reference-cleaner.php | 386 +++++++++++++----------------------
 readme.txt                   |   9 +-
 4 files changed, 175 insertions(+), 244 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 91cbe45..0e5ae4b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,21 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.3.0] - 2023-10-05
+### Changed
+- Complete redesign for maximum compatibility with all WordPress themes
+- Now uses the plugins list table for missing plugin references
+- Uses standard WordPress admin UI patterns and hooks
+
+### Added
+- Missing plugins now appear directly in the plugins list
+- "Remove Reference" action link in the plugins list
+- Success/error notices after removing references
+
+### Fixed
+- Compatibility issues with various WordPress admin themes
+- Reliability issues with notification detection
+
 ## [1.2.4] - 2023-10-05
 ### Fixed
 - Compatibility with more WordPress admin UI variations
diff --git a/README.md b/README.md
index f97182a..95a758f 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Plugin Reference Cleaner
 Author: Marcus Quinn
 Author URI: https://www.wpallstars.com
-Version: 1.2.4
+Version: 1.3.0
 License: GPL-2.0+
 
 ## Description
@@ -47,6 +47,13 @@ If you don't have this notification perpetually showing on your /wp-admin/plugin
 
 ## Changelog
 
+### 1.3.0
+* Complete redesign for maximum compatibility with all WordPress themes
+* Now adds missing plugins directly to the plugins list table
+* Uses standard WordPress admin UI patterns instead of DOM manipulation
+* Added "Remove Reference" action link in the plugins list
+* Significantly improved reliability across all WordPress configurations
+
 ### 1.2.4
 * Fixed compatibility with more WordPress admin themes
 * Added advanced DOM traversal to find error messages
diff --git a/plugin-reference-cleaner.php b/plugin-reference-cleaner.php
index 3ec1d35..8de4c7a 100644
--- a/plugin-reference-cleaner.php
+++ b/plugin-reference-cleaner.php
@@ -2,7 +2,7 @@
 /*
  * Plugin Name: Plugin Reference Cleaner
  * Description: Adds a "Remove Reference" button to plugin deactivation error notices, allowing users to clean up invalid plugin entries.
- * Version: 1.2.4
+ * Version: 1.3.0
  * Author: Marcus Quinn
  * Author URI: https://www.wpallstars.com
  * License: GPL-2.0+
@@ -15,252 +15,108 @@ if (!defined('ABSPATH')) {
 
 class Plugin_Reference_Cleaner {
     public function __construct() {
-        // Only hook into admin actions when on the plugins page
-        add_action('current_screen', function($screen) {
-            if (isset($screen->id) && ($screen->id === 'plugins' || $screen->id === 'plugins-network')) {
-                // Hook into admin notices to modify plugin error messages
-                add_action('admin_notices', array($this, 'inject_remove_button'), 100);
-                add_action('network_admin_notices', array($this, 'inject_remove_button'), 100);
-            }
-        });
+        // Add our plugin to the plugins list
+        add_filter('all_plugins', array($this, 'add_missing_plugins_references'));
         
-        // Handle the AJAX request to remove the plugin reference
-        add_action('wp_ajax_remove_plugin_reference', array($this, 'remove_plugin_reference'));
+        // Add our action link to the plugins list
+        add_filter('plugin_action_links', array($this, 'add_remove_reference_action'), 20, 4);
+        
+        // Handle the remove reference action
+        add_action('admin_init', array($this, 'handle_remove_reference'));
+        
+        // Add admin notices for operation feedback
+        add_action('admin_notices', array($this, 'admin_notices'));
     }
+    
+    /**
+     * Find and add invalid plugin references to the plugins list
+     */
+    public function add_missing_plugins_references($plugins) {
+        // Only run on the plugins page
+        if (!$this->is_plugins_page()) {
+            return $plugins;
+        }
 
-    // Inject "Remove Reference" button only if a relevant notice exists
-    public function inject_remove_button() {
-        // Check if a "Plugin file does not exist" notice exists
-        $notices = $this->get_admin_notices();
-        $has_error_notice = false;
-        $plugin_files = array();
-
-        if (!empty($notices)) {
-            foreach ($notices as $notice) {
-                // Look for both variations of the error message
-                if (strpos($notice, 'has been deactivated due to an error: Plugin file does not exist') !== false || 
-                    strpos($notice, 'deactivated due to an error: Plugin file does not exist') !== false) {
-                    // Extract plugin file from notice using various patterns
-                    if (preg_match('/The plugin ([^ ]+)/', $notice, $match)) {
-                        $plugin_files[] = $match[1];
-                        $has_error_notice = true;
-                    }
-                }
+        // Get active plugins that don't exist
+        $invalid_plugins = $this->get_invalid_plugins();
+        
+        // Add each invalid plugin to the plugin list
+        foreach ($invalid_plugins as $plugin_path) {
+            if (!isset($plugins[$plugin_path])) {
+                $plugin_name = basename($plugin_path);
+                $plugins[$plugin_path] = array(
+                    'Name' => $plugin_name . ' <span class="error">(File Missing)</span>',
+                    'Description' => 'This plugin file does not exist. You can safely remove this reference.',
+                    'Version' => 'N/A',
+                    'Author' => '',
+                    'PluginURI' => '',
+                    'AuthorURI' => '',
+                    'Title' => $plugin_name . ' (Missing)',
+                    'AuthorName' => ''
+                );
             }
         }
         
-        // Only proceed if a relevant notice was found
-        if (!$has_error_notice || empty($plugin_files)) {
+        return $plugins;
+    }
+    
+    /**
+     * Add the Remove Reference action link to invalid plugins
+     */
+    public function add_remove_reference_action($actions, $plugin_file, $plugin_data, $context) {
+        // Only run on the plugins page
+        if (!$this->is_plugins_page()) {
+            return $actions;
+        }
+        
+        // Check if this is a missing plugin
+        if (isset($plugin_data['Name']) && strpos($plugin_data['Name'], '<span class="error">(File Missing)</span>') !== false) {
+            // Clear existing actions
+            $actions = array();
+            
+            // Add our action
+            $nonce = wp_create_nonce('remove_plugin_reference_' . $plugin_file);
+            $remove_url = admin_url('plugins.php?action=remove_reference&plugin=' . urlencode($plugin_file) . '&_wpnonce=' . $nonce);
+            $actions['remove_reference'] = '<a href="' . esc_url($remove_url) . '" class="delete" aria-label="' . esc_attr__('Remove Reference', 'plugin-reference-cleaner') . '">Remove Reference</a>';
+        }
+        
+        return $actions;
+    }
+    
+    /**
+     * Handle the remove reference action
+     */
+    public function handle_remove_reference() {
+        // Check if we're removing a reference
+        if (!isset($_GET['action']) || $_GET['action'] !== 'remove_reference' || !isset($_GET['plugin'])) {
             return;
         }
-
-        // Inject JavaScript with the specific plugin files
-        ?>
-        <script type="text/javascript">
-            document.addEventListener('DOMContentLoaded', function() {
-                var pluginFiles = <?php echo wp_json_encode($plugin_files); ?>;
-                console.log('Plugin Reference Cleaner: Detected plugin files:', pluginFiles);
-                
-                // Get all notifications directly in the plugins page
-                var pluginsPage = document.querySelector('.wrap');
-                if (!pluginsPage) {
-                    console.log('Plugin Reference Cleaner: Could not find the plugins page wrapper');
-                    return;
-                }
-                
-                // Look specifically for elements containing the error message
-                // Use direct DOM traversal to find all text nodes
-                function findTextNodesWithText(element, searchText) {
-                    var result = [];
-                    var walk = document.createTreeWalker(element, NodeFilter.SHOW_TEXT, null, false);
-                    var node;
-                    
-                    while (node = walk.nextNode()) {
-                        if (node.nodeValue.indexOf(searchText) > -1) {
-                            result.push(node);
-                        }
-                    }
-                    
-                    return result;
-                }
-                
-                // Find paragraphs containing error messages
-                var errorTexts = findTextNodesWithText(pluginsPage, 'Plugin file does not exist');
-                console.log('Plugin Reference Cleaner: Found error nodes:', errorTexts.length);
-                
-                if (errorTexts.length === 0) {
-                    // Try another approach - find direct error messages
-                    var allElements = pluginsPage.querySelectorAll('*');
-                    for (var i = 0; i < allElements.length; i++) {
-                        var el = allElements[i];
-                        var text = el.textContent;
-                        if (text && text.includes('has been deactivated due to an error: Plugin file does not exist')) {
-                            errorTexts.push(el);
-                        }
-                    }
-                }
-                
-                // Handle each error message
-                errorTexts.forEach(function(textNode) {
-                    console.log('Plugin Reference Cleaner: Processing error node:', textNode);
-                    
-                    // Get the parent element of the text node
-                    var errorElement = textNode.parentNode || textNode;
-                    
-                    // Check if a button already exists to avoid duplicates
-                    if (errorElement.querySelector('.remove-plugin-ref')) {
-                        console.log('Plugin Reference Cleaner: Button already exists for this element');
-                        return;
-                    }
-                    
-                    // Find which plugin file this error refers to
-                    var matchingPluginFile = null;
-                    pluginFiles.forEach(function(pluginFile) {
-                        if (textNode.nodeValue && textNode.nodeValue.includes(pluginFile) || 
-                            (textNode.textContent && textNode.textContent.includes(pluginFile))) {
-                            matchingPluginFile = pluginFile;
-                        }
-                    });
-                    
-                    // If we couldn't match a specific plugin, use the first one as fallback
-                    if (!matchingPluginFile && pluginFiles.length > 0) {
-                        matchingPluginFile = pluginFiles[0];
-                        console.log('Plugin Reference Cleaner: Using fallback plugin file:', matchingPluginFile);
-                    }
-                    
-                    if (matchingPluginFile) {
-                        // Create button
-                        var button = document.createElement('button');
-                        button.textContent = 'Remove Reference';
-                        button.className = 'button button-secondary remove-plugin-ref';
-                        button.dataset.plugin = matchingPluginFile;
-                        button.style.marginLeft = '10px';
-                        
-                        // Append the button to the error message
-                        errorElement.appendChild(button);
-                        console.log('Plugin Reference Cleaner: Added button for ' + matchingPluginFile + ' to', errorElement);
-                    } else {
-                        console.log('Plugin Reference Cleaner: Could not determine plugin file for this error');
-                    }
-                });
-                
-                // Inject a more direct approach if the above fails
-                if (errorTexts.length === 0) {
-                    // Target the specific format in the screenshot
-                    var errorMessages = document.querySelectorAll('.wrap > .notice, .wrap > div > .notice');
-                    console.log('Plugin Reference Cleaner: Trying direct approach, found notices:', errorMessages.length);
-                    
-                    errorMessages.forEach(function(notice) {
-                        var text = notice.textContent;
-                        if (text && text.includes('Plugin file does not exist')) {
-                            // Extract the plugin path
-                            var pluginMatch = /The plugin ([^ ]+) has been deactivated/.exec(text);
-                            var pluginFile = pluginMatch ? pluginMatch[1] : (pluginFiles.length > 0 ? pluginFiles[0] : null);
-                            
-                            if (pluginFile) {
-                                // Get container to add button
-                                var container = notice.querySelector('p') || notice;
-                                
-                                if (!container.querySelector('.remove-plugin-ref')) {
-                                    var button = document.createElement('button');
-                                    button.textContent = 'Remove Reference';
-                                    button.className = 'button button-secondary remove-plugin-ref';
-                                    button.dataset.plugin = pluginFile;
-                                    button.style.marginLeft = '10px';
-                                    container.appendChild(button);
-                                    console.log('Plugin Reference Cleaner: Direct approach - added button for ' + pluginFile);
-                                }
-                            }
-                        }
-                    });
-                }
-
-                // Add click event listeners to all created buttons
-                document.querySelectorAll('.remove-plugin-ref').forEach(function(button) {
-                    button.addEventListener('click', function(e) {
-                        e.preventDefault();
-                        var pluginFile = this.dataset.plugin;
-                        if (confirm('Are you sure you want to remove the reference to ' + pluginFile + '?')) {
-                            var xhr = new XMLHttpRequest();
-                            xhr.open('POST', '<?php echo esc_url(admin_url('admin-ajax.php')); ?>', true);
-                            xhr.setRequestHeader('Content-Type', 'application/x-www-form-urlencoded');
-                            xhr.onload = function() {
-                                if (xhr.status === 200) {
-                                    try {
-                                        var response = JSON.parse(xhr.responseText);
-                                        if (response.success) {
-                                            alert('Plugin reference removed successfully.');
-                                            location.reload();
-                                        } else {
-                                            alert('Failed to remove plugin reference: ' + (response.data || 'Unknown error'));
-                                        }
-                                    } catch (e) {
-                                        alert('Failed to parse server response.');
-                                        console.error(e);
-                                    }
-                                } else {
-                                    alert('Failed to remove plugin reference. Server returned status ' + xhr.status);
-                                }
-                            };
-                            xhr.onerror = function() {
-                                alert('Network error occurred while trying to remove plugin reference.');
-                            };
-                            xhr.send('action=remove_plugin_reference&plugin=' + encodeURIComponent(pluginFile) + '&nonce=<?php echo wp_create_nonce('remove_plugin_reference'); ?>');
-                        }
-                    });
-                });
-            });
-        </script>
-        <?php
-    }
-
-    // Helper function to capture admin notices
-    private function get_admin_notices() {
-        // Static flag to prevent infinite recursion
-        static $is_capturing = false;
         
-        // If already capturing, return empty to break potential loops
-        if ($is_capturing) {
-            return array();
-        }
-        
-        $is_capturing = true;
-        
-        ob_start();
-        do_action('admin_notices');
-        do_action('network_admin_notices');
-        $output = ob_get_clean();
-        
-        $is_capturing = false;
-        
-        if (empty($output)) {
-            return array();
-        }
-        
-        return array_filter(explode("\n", $output));
-    }
-
-    // Handle the AJAX request to remove the plugin reference
-    public function remove_plugin_reference() {
-        // Verify nonce
-        if (!isset($_POST['nonce']) || !wp_verify_nonce($_POST['nonce'], 'remove_plugin_reference')) {
-            wp_send_json_error('Invalid security token. Please refresh the page and try again.');
-            wp_die();
-        }
-
-        // Check user permissions
+        // Verify permissions
         if (!current_user_can('activate_plugins')) {
-            wp_send_json_error('You do not have sufficient permissions to perform this action.');
-            wp_die();
+            wp_die(__('You do not have sufficient permissions to perform this action.', 'plugin-reference-cleaner'));
         }
-
-        // Get and validate plugin file parameter
-        $plugin_file = isset($_POST['plugin']) ? sanitize_text_field($_POST['plugin']) : '';
-        if (empty($plugin_file)) {
-            wp_send_json_error('No plugin specified.');
-            wp_die();
-        }
-
+        
+        // Get the plugin file
+        $plugin_file = isset($_GET['plugin']) ? $_GET['plugin'] : '';
+        
+        // Verify nonce
+        check_admin_referer('remove_plugin_reference_' . $plugin_file);
+        
+        // Remove the plugin reference
+        $success = $this->remove_plugin_reference($plugin_file);
+        
+        // Redirect back to plugins page with a message
+        $redirect = admin_url('plugins.php');
+        $redirect = add_query_arg($success ? 'reference_removed' : 'reference_removal_failed', '1', $redirect);
+        wp_redirect($redirect);
+        exit;
+    }
+    
+    /**
+     * Remove a plugin reference from the active plugins
+     */
+    public function remove_plugin_reference($plugin_file) {
         $success = false;
         
         // Handle multisite network admin
@@ -281,14 +137,60 @@ class Plugin_Reference_Cleaner {
                 $success = update_option('active_plugins', $active_plugins);
             }
         }
-
-        if ($success) {
-            wp_send_json_success('Plugin reference removed successfully.');
-        } else {
-            wp_send_json_error('Plugin reference not found or could not be removed.');
+        
+        return $success;
+    }
+    
+    /**
+     * Display admin notices
+     */
+    public function admin_notices() {
+        // Only run on the plugins page
+        if (!$this->is_plugins_page()) {
+            return;
         }
         
-        wp_die();
+        // Show success message
+        if (isset($_GET['reference_removed']) && $_GET['reference_removed'] === '1') {
+            echo '<div class="notice notice-success is-dismissible"><p>Plugin reference removed successfully.</p></div>';
+        }
+        
+        // Show error message
+        if (isset($_GET['reference_removal_failed']) && $_GET['reference_removal_failed'] === '1') {
+            echo '<div class="notice notice-error is-dismissible"><p>Failed to remove plugin reference. The plugin may already have been removed.</p></div>';
+        }
+    }
+    
+    /**
+     * Check if we're on the plugins page
+     */
+    private function is_plugins_page() {
+        global $pagenow;
+        return is_admin() && $pagenow === 'plugins.php';
+    }
+    
+    /**
+     * Get a list of invalid plugin references
+     */
+    private function get_invalid_plugins() {
+        $invalid_plugins = array();
+        
+        // Get all active plugins
+        if (is_multisite() && is_network_admin()) {
+            $active_plugins = array_keys(get_site_option('active_sitewide_plugins', array()));
+        } else {
+            $active_plugins = get_option('active_plugins', array());
+        }
+        
+        // Check if each plugin exists
+        foreach ($active_plugins as $plugin) {
+            $plugin_path = WP_PLUGIN_DIR . '/' . $plugin;
+            if (!file_exists($plugin_path)) {
+                $invalid_plugins[] = $plugin;
+            }
+        }
+        
+        return $invalid_plugins;
     }
 }
 
diff --git a/readme.txt b/readme.txt
index f84b76d..4179909 100644
--- a/readme.txt
+++ b/readme.txt
@@ -1,7 +1,7 @@
 === Plugin Reference Cleaner ===
 Author: Marcus Quinn
 Author URI: https://www.wpallstars.com
-Version: 1.2.4
+Version: 1.3.0
 License: GPL-2.0+
 
 == Description ==
@@ -47,6 +47,13 @@ If you don't have this notification perpetually showing on your /wp-admin/plugin
 
 == Changelog ==
 
+= 1.3.0 =
+* Complete redesign for maximum compatibility with all WordPress themes
+* Now adds missing plugins directly to the plugins list table
+* Uses standard WordPress admin UI patterns instead of DOM manipulation
+* Added "Remove Reference" action link in the plugins list
+* Significantly improved reliability across all WordPress configurations
+
 = 1.2.4 =
 * Fixed compatibility with more WordPress admin themes
 * Added advanced DOM traversal to find error messages