Version 1.4.1: Add FAQ about keeping plugin installed

.distignore

@@ -8,10 +8,14 @@
 .distignore
 build.sh
 build
+.drone.yml
+.woodpecker.yml
 
 # Documentation
 CONTRIBUTING.md
 CODE_OF_CONDUCT.md
+CHANGELOG.md
+assets/README.md
 
 # Development files
 node_modules
@@ -31,6 +35,9 @@ package-lock.json
 composer.json
 composer.lock
 
+# WordPress.org specific
+.wordpress-org
+
 # Miscellaneous
 .DS_Store
 Thumbs.db
@@ -40,3 +47,5 @@ Thumbs.db
 *.bak
 *.tmp
 *.zip
+*~
+._* 

.github/workflows/assets.yml

@@ -0,0 +1,24 @@
+name: Plugin Asset Update
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - '.wordpress-org/**'
+      - 'assets/**'
+
+jobs:
+  assets:
+    name: Push assets to WordPress.org
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        
+      - name: WordPress.org plugin asset/readme update
+        uses: 10up/action-wordpress-plugin-asset-update@stable
+        env:
+          SVN_PASSWORD: ${{ secrets.SVN_PASSWORD }}
+          SVN_USERNAME: ${{ secrets.SVN_USERNAME }}
+          SLUG: fix-plugin-does-not-exist-notices 

.github/workflows/release.yml

@@ -20,19 +20,19 @@ jobs:
         run: echo "VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT
 
       - name: Create build directory
-        run: mkdir -p build/plugin-reference-cleaner
+        run: mkdir -p build/fix-plugin-does-not-exist-notices
 
       - name: Copy plugin files
         run: |
-          cp plugin-reference-cleaner.php build/plugin-reference-cleaner/
+          cp fix-plugin-does-not-exist-notices.php build/fix-plugin-does-not-exist-notices/
-          cp readme.txt build/plugin-reference-cleaner/
+          cp readme.txt build/fix-plugin-does-not-exist-notices/
-          cp LICENSE build/plugin-reference-cleaner/
+          cp LICENSE build/fix-plugin-does-not-exist-notices/
-          cp README.md build/plugin-reference-cleaner/
+          cp README.md build/fix-plugin-does-not-exist-notices/
 
       - name: Create ZIP file
         run: |
           cd build
-          zip -r ../plugin-reference-cleaner-${{ steps.get_version.outputs.VERSION }}.zip plugin-reference-cleaner
+          zip -r ../fix-plugin-does-not-exist-notices-${{ steps.get_version.outputs.VERSION }}.zip fix-plugin-does-not-exist-notices
 
       - name: Create Release
         id: create_release
@@ -42,8 +42,27 @@ jobs:
           draft: false
           prerelease: false
           files: |
-            plugin-reference-cleaner-${{ steps.get_version.outputs.VERSION }}.zip
+            fix-plugin-does-not-exist-notices-${{ steps.get_version.outputs.VERSION }}.zip
           body: |
-            Plugin Reference Cleaner v${{ steps.get_version.outputs.VERSION }}
+            Fix 'Plugin file does not exist.' Notices v${{ steps.get_version.outputs.VERSION }}
             
-            See [CHANGELOG.md](https://github.com/wpallstars/plugin-reference-cleaner/blob/main/CHANGELOG.md) for details. 
+            See [CHANGELOG.md](https://github.com/wpallstars/fix-plugin-does-not-exist-notices/blob/main/CHANGELOG.md) for details.
+
+  # Deploy to WordPress.org
+  wordpress:
+    name: Deploy to WordPress.org
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      
+      - name: WordPress Plugin Deploy
+        id: deploy
+        uses: 10up/action-wordpress-plugin-deploy@stable
+        with:
+          generate-zip: true
+        env:
+          SVN_USERNAME: ${{ secrets.SVN_USERNAME }}
+          SVN_PASSWORD: ${{ secrets.SVN_PASSWORD }}
+          SLUG: fix-plugin-does-not-exist-notices 

.gitignore

@@ -3,6 +3,9 @@
 Thumbs.db
 ehthumbs.db
 Desktop.ini
+._*
+.Spotlight-V100
+.Trashes
 
 # Editor files
 *.swp
@@ -12,11 +15,19 @@ Desktop.ini
 .vscode/
 *.sublime-project
 *.sublime-workspace
+*.komodoproject
+.komodotools
+*.tmproj
+*.tmproject
+.project
+.settings/
 
 # Dependency directories
 node_modules/
 vendor/
 bower_components/
+composer.lock
+package-lock.json
 
 # Build files
 build/
@@ -39,3 +50,30 @@ debug.log
 .env
 .env.*
 !.env.example
+
+# WordPress testing
+.phpunit.result.cache
+.phpcs.cache
+phpunit.xml
+phpcs.xml
+
+# Development tools
+.git/
+.github/
+.gitlab/
+.gitattributes
+.travis.yml
+.drone.yml
+.woodpecker.yml
+codecov.yml
+.babelrc
+.browserslistrc
+.editorconfig
+.eslintignore
+.eslintrc
+.prettierrc
+.stylelintrc
+webpack.config.js
+gulpfile.js
+Gruntfile.js
+*.zip 

.wordpress-org/README.md

@@ -0,0 +1,20 @@
+# WordPress.org Plugin Repository Assets
+
+This directory contains assets specific to the WordPress.org plugin repository and is used for automatic deployment via GitHub Actions.
+
+## Directory Contents
+
+- `icon.svg` - Plugin icon displayed in the WordPress.org plugin directory
+- `banner-772x250.png` - Standard banner for plugin header
+- `banner-1544x500.png` - Retina banner for plugin header
+- `screenshot-1.png` - First screenshot displayed on plugin page
+- `screenshot-2.png` - Second screenshot displayed on plugin page
+- `screenshot-3.png` - Third screenshot displayed on plugin page
+
+## Purpose
+
+When using GitHub Actions for WordPress.org plugin deployments (via the 10up WordPress GitHub Actions), this directory is used to automatically update plugin assets in the WordPress.org repository.
+
+## Naming Conventions
+
+Files must be named exactly as shown above to be properly recognized by the WordPress.org system during the deployment process. 

CHANGELOG.md

@@ -2,6 +2,81 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.4.1] - 2023-11-30
+### Added
+- FAQ about keeping the plugin installed after notices are cleared
+
+## [1.4.0] - 2023-11-30
+### Changed
+- Updated plugin name and text domain
+- Repository rename from plugin-reference-cleaner to fix-plugin-does-not-exist-notices
+
+## [1.3.3] - 2023-10-05
+### Added
+- "Click here to scroll" button to automatically find missing plugins
+- Visual arrow pointing from notification to error message
+- Smooth scrolling with highlighting of missing plugin rows
+
+### Improved
+- Notification reliability using multiple injection methods
+- Earlier placement in page load cycle for better visibility
+- Enhanced error detection for all WordPress error message formats
+
+## [1.3.2] - 2023-10-05
+### Added
+- Prominent notification that appears directly below WordPress error messages
+- Visual styling to help users connect error message with solution
+- Direction arrows and highlighted text to improve user guidance
+
+## [1.3.1] - 2023-10-05
+### Added
+- Instructional notification explaining how to use the plugin
+- Step-by-step guidance for removing plugin references
+- Clear visual indicators for missing plugins
+
+## [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
+- Specific targeting for admin notices in various themes
+
+### Added
+- Advanced DOM traversal using TreeWalker API
+- Multiple fallback approaches to ensure button appears
+- Enhanced console logging for troubleshooting
+
+## [1.2.3] - 2023-10-05
+### Fixed
+- Button not appearing in some WordPress admin themes
+- Error message detection for greater theme compatibility
+
+### Improved
+- DOM traversal to find notification elements in various themes
+- Added console logging for troubleshooting
+
+## [1.2.2] - 2023-10-05
+### Fixed
+- Timeout issue during plugin activation
+- Potential infinite recursion in admin notices handling
+
+### Improved
+- Hook management to prevent performance issues
+- Optimized by only loading on plugins page
+
 ## [1.2.1] - 2025-04-07
 ### Improved
 - Fixed typos in documentation

README.md

@@ -1,70 +1,151 @@
-# Plugin Reference Cleaner
+# Fix 'Plugin file does not exist.' Notices
-Author: Marcus Quinn
+
-Author URI: https://wpallstars.com
+[![WordPress Plugin Version](https://img.shields.io/wordpress/plugin/v/fix-plugin-does-not-exist-notices)](https://wordpress.org/plugins/fix-plugin-does-not-exist-notices/)
-Version: 1.2.1
+[![WordPress Plugin Rating](https://img.shields.io/wordpress/plugin/rating/fix-plugin-does-not-exist-notices)](https://wordpress.org/plugins/fix-plugin-does-not-exist-notices/)
-License: GPL-2.0+
+[![WordPress Plugin Downloads](https://img.shields.io/wordpress/plugin/dt/fix-plugin-does-not-exist-notices)](https://wordpress.org/plugins/fix-plugin-does-not-exist-notices/)
+[![License](https://img.shields.io/badge/license-GPL--2.0%2B-blue.svg)](https://www.gnu.org/licenses/gpl-2.0.html)
+
+Easily remove references to deleted plugins that cause "Plugin file does not exist" errors in your WordPress admin.
 
 ## Description
 
-Have you ever deleted a plugin some other way than through the /wp-admin/plugins.php page? If so, you've probably been stuck with this annoying notification that can't be cleared:
+Have you ever deleted a plugin directly from the server or database and then been stuck with annoying error notifications that can't be cleared?
 
 "The plugin folder-name/file-name.php has been deactivated due to an error: Plugin file does not exist."
 
-This small WordPress utility plugin adds a "Remove Reference" button to these plugin deactivation error notices, allowing you to clean up the invalid plugin entries in the database.
+This small utility plugin adds missing plugins to your WordPress plugins list and provides a "Remove Reference" link, allowing you to safely clean up invalid plugin entries with one click.
 
-When WordPress detects a plugin file that no longer exists but is still referenced in the database as active, it displays an error notice. This plugin enhances those notices with a button that allows you to safely remove the invalid reference with a single click.
+### Key Features
 
-You can find these with `SELECT * FROM wp_options WHERE option_name = 'active_plugins';` — but the cleanup involves removing the rogue entry, and renumbering all others. This plugin can simply do that for you at the click of a button added to that WP standard notification.
+* Adds missing plugins directly to your plugins list
+* Provides a simple "Remove Reference" action link
+* Works with both single site and multisite WordPress installations
+* Includes helpful notifications explaining how to fix plugin errors
+* One-click auto-scroll to find missing plugins in large sites
+* Clean, user-friendly interface following WordPress design patterns
 
-It's probably something that should be added to WP core. If anyone from the core team wants to adopt this solution, it's GPL, so feel free.
+### How It Works
 
-Note: This plugin only needs to be installed and active if you have an error notification showing at /wp-admin/plugins.php, like this:
+When WordPress detects a plugin file that no longer exists but is still referenced in the database as active, it displays an error notice. This plugin:
-"The plugin folder-name/file-name.php has been deactivated due to an error: Plugin file does not exist."
 
-If you don't have this notification perpetually showing on your /wp-admin/plugins.php page, then you don't need this, but you might like to save or bookmark it for if ever you do.
+1. Detects all missing plugin references in your database
+2. Adds them to your plugins list with "(File Missing)" indicators
+3. Provides a "Remove Reference" link to safely remove them
+4. Shows clear notifications guiding you through the cleanup process
 
-## Features
+### Use Cases
 
-* Adds a "Remove Reference" button to plugin error notices
+* You've accidentally deleted a plugin via FTP
-* Works for both single site and multisite WordPress installations
+* A plugin was removed by another admin but references remain
-* Confirms before removing any plugin references
+* You've migrated from another site and have leftover plugin references
-* Simple, lightweight solution with no settings page required
+* Your hosting provider removed a plugin but didn't clean the database
-* Secure implementation with proper permissions checking
-* Compatible with WordPress 5.0+
 
 ## Installation
 
-1. Upload the plugin-reference-cleaner.php file to your /wp-content/plugins/ directory
+### From WordPress.org:
-2. Activate the plugin through the 'Plugins' menu in WordPress
+
-3. No configuration needed - the plugin works automatically
+1. Visit Plugins > Add New in your WordPress admin
+2. Search for "Fix 'Plugin file does not exist.' Notices"
+3. Click "Install Now" and then "Activate"
+
+### Manual Installation:
+
+1. Download the plugin ZIP file
+2. Go to Plugins > Add New > Upload Plugin
+3. Upload the ZIP file
+4. Activate the plugin
 
 ## Usage
 
-1. Navigate to Plugins > Installed Plugins
+1. After activation, navigate to Plugins > Installed Plugins
-2. If any "Plugin file does not exist" error notices appear, a "Remove Reference" button will be displayed
+2. If you have missing plugin errors, you'll see them in your plugins list with "(File Missing)" markers
-3. Click the button and confirm to remove the invalid plugin reference
+3. Click the "Remove Reference" link next to any missing plugin
-4. The page will refresh with the error notice removed
+4. The reference will be removed, and the error notification will disappear
+
+## Frequently Asked Questions
+
+### Is it safe to remove plugin references?
+
+Yes, this plugin only removes entries from the WordPress active_plugins option, which is safe to modify when a plugin no longer exists. It doesn't modify any other database tables or settings.
+
+### What happens after I remove a reference?
+
+The plugin entry will be removed from your active plugins list, and the corresponding error notification will no longer appear after you refresh the page.
+
+### Can I use this plugin on a multisite installation?
+
+Yes, the plugin works on both single sites and multisite installations. It properly handles network-activated plugins as well.
+
+## Screenshots
+
+1. Error message with explanation notification
+2. Missing plugin shown in the plugins list with "Remove Reference" link
+3. Auto-scroll feature that highlights the missing plugin
+
+## FAQ
+
+### Do I need to keep this plugin installed and active after notices are cleared?
+
+Although this plugin consumes minimal disk space, and doesn't run unless you are on the /wp-admin/plugins.php page, you don't need to keep it active or installed if you don't have this notice to clear — but it is safe to, if you just want it as a part of your overall WordPress stack of enhancements and conveniences.
+
+## Developers
+
+### Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.
+
+1. Fork the repository
+2. Create your feature branch: `git checkout -b feature/amazing-feature`
+3. Commit your changes: `git commit -m 'Add some amazing feature'`
+4. Push to the branch: `git push origin feature/amazing-feature`
+5. Submit a pull request
+
+### Technical Details
+
+The plugin works by:
+1. Filtering the `all_plugins` array to add missing plugins
+2. Adding a custom "Remove Reference" action link via `plugin_action_links`
+3. Adding helpful notifications near error messages
+4. Providing a secure method to remove plugin references from the database
 
 ## Changelog
 
-### 1.2.1
+### 1.4.1
-* Fixed typos in documentation
+- Added FAQ about keeping the plugin installed after notices are cleared
-* Improved text clarity
-* Added question mark to first sentence for better readability
 
-### 1.2
+### 1.4.0
-* Improved documentation with detailed explanation
+- Updated plugin name and text domain
-* Added SQL reference for technical users
+- Repository rename from plugin-reference-cleaner to fix-plugin-does-not-exist-notices
-* Suggested potential inclusion in WordPress core
 
-### 1.1
+### 1.3.3
-* Improved error handling
+* Improved notification placement next to WordPress error messages
-* Added support for multisite installations
+* Added "Click here to scroll" button that automatically locates missing plugins
-* Enhanced security with proper capability checks
+* Enhanced reliability with multiple injection methods
+* Added visual arrow pointing from notification to error message
 
-### 1.0
+### 1.3.2
-* Initial release
+* Added prominent notification directly below WordPress error messages
+* Improved user guidance with visual cues to connect error and solution
+* Added eye-catching styling to help users understand how to fix errors
+
+### 1.3.1
+* Added instructional notification explaining how to use the plugin
+* Improved user guidance with step-by-step instructions
+* Enhanced visual identification of missing plugins
+
+### 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
+
+[View full changelog](CHANGELOG.md)
+
+## License
+
+This project is licensed under the GPL-2.0+ License - see the [LICENSE](LICENSE) file for details.
 
 ## Support
 
-For support, please visit https://wpallstars.com 
+For support, please visit [WP All Stars](https://www.wpallstars.com). 

assets/README.md

@@ -0,0 +1,53 @@
+# Plugin Assets for WordPress.org
+
+This directory contains assets for the WordPress.org plugin repository.
+
+## Directory Structure
+
+- `banner/` - Banner images for the plugin page header
+  - `banner-772x250.jpg` - Standard banner (772x250px)
+  - `banner-1544x500.jpg` - Retina banner (1544x500px)
+  
+- `icon/` - Plugin icon images
+  - `icon-128x128.jpg` - Standard icon (128x128px)
+  - `icon-256x256.jpg` - Retina icon (256x256px)
+
+- `screenshots/` - Screenshots shown on the plugin page
+  - `screenshot-1.jpg` - Error message with explanation notification
+  - `screenshot-2.jpg` - Missing plugin shown in the plugins list with "Remove Reference" link
+  - `screenshot-3.jpg` - Auto-scroll feature that highlights the missing plugin
+
+## WordPress.org Requirements
+
+### Required Image Dimensions
+
+- **Banner**: 772x250px with 2x retina version at 1544x500px
+- **Icon**: 128x128px with 2x retina version at 256x256px
+- **Screenshots**: No specific size requirements, but they should be clear and readable
+
+### Image Formats
+
+- All images should be in JPG or PNG format
+- Images should be optimized for web (compressed without losing quality)
+
+### Additional Notes
+
+- Screenshots should be numbered sequentially starting with 1
+- They should match the descriptions in the `readme.txt` file
+- Dark theme versions of banners and icons can be provided by appending `-rtl` to the filename
+
+## Example Filenames
+
+```
+assets/
+├── banner/
+│   ├── banner-772x250.jpg
+│   └── banner-1544x500.jpg
+├── icon/
+│   ├── icon-128x128.jpg
+│   └── icon-256x256.jpg
+└── screenshots/
+    ├── screenshot-1.jpg
+    ├── screenshot-2.jpg
+    └── screenshot-3.jpg
+``` 

build.sh

@@ -10,7 +10,7 @@ if [ -z "$1" ]; then
 fi
 
 VERSION=$1
-PLUGIN_SLUG="plugin-reference-cleaner"
+PLUGIN_SLUG="fix-plugin-does-not-exist-notices"
 BUILD_DIR="build/$PLUGIN_SLUG"
 ZIP_FILE="${PLUGIN_SLUG}-${VERSION}.zip"
 
@@ -20,7 +20,7 @@ mkdir -p $BUILD_DIR
 
 # Copy required files
 echo "Copying plugin files..."
-cp plugin-reference-cleaner.php $BUILD_DIR/
+cp fix-plugin-does-not-exist-notices.php $BUILD_DIR/
 cp readme.txt $BUILD_DIR/
 cp LICENSE $BUILD_DIR/
 cp README.md $BUILD_DIR/

fix-plugin-does-not-exist-notices.php

@@ -0,0 +1,343 @@
+<?php
+/**
+ * Fix 'Plugin file does not exist.' Notices
+ *
+ * @package           FixPluginDoesNotExistNotices
+ * @author            Marcus Quinn
+ * @copyright         2023 WP All Stars
+ * @license           GPL-2.0+
+ *
+ * @wordpress-plugin
+ * Plugin Name: Fix 'Plugin file does not exist.' Notices
+ * Description: Adds missing plugins to the plugins list with a "Remove Reference" link so you can clean up invalid plugin entries.
+ * Version: 1.4.1
+ * Author: Marcus Quinn
+ * Author URI: https://www.wpallstars.com
+ * License: GPL-2.0+
+ * License URI: https://www.gnu.org/licenses/gpl-2.0.html
+ * Text Domain: fix-plugin-does-not-exist-notices
+ * Domain Path: /languages
+ * Requires at least: 5.0
+ * Requires PHP: 7.0
+ *
+ * This plugin is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 2 of the License, or
+ * any later version.
+ *
+ * This plugin is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this plugin. If not, see https://www.gnu.org/licenses/gpl-2.0.html.
+ */
+
+// Exit if accessed directly
+if (!defined('ABSPATH')) {
+    exit;
+}
+
+class Fix_Plugin_Does_Not_Exist_Notices {
+    public function __construct() {
+        // Add our plugin to the plugins list
+        add_filter('all_plugins', array($this, 'add_missing_plugins_references'));
+        
+        // Add our action link to the plugins list
+        add_filter('plugin_action_links', array($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;
+        }
+
+        // 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' => ''
+                );
+            }
+        }
+        
+        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', 'fix-plugin-does-not-exist-notices') . '">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;
+        }
+        
+        // Verify permissions
+        if (!current_user_can('activate_plugins')) {
+            wp_die(__('You do not have sufficient permissions to perform this action.', 'fix-plugin-does-not-exist-notices'));
+        }
+        
+        // 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
+        if (is_multisite() && is_network_admin()) {
+            $active_plugins = get_site_option('active_sitewide_plugins', array());
+            if (isset($active_plugins[$plugin_file])) {
+                unset($active_plugins[$plugin_file]);
+                $success = update_site_option('active_sitewide_plugins', $active_plugins);
+            }
+        } 
+        // Handle single site or multisite subsite
+        else {
+            $active_plugins = get_option('active_plugins', array());
+            $key = array_search($plugin_file, $active_plugins);
+            if ($key !== false) {
+                unset($active_plugins[$key]);
+                $active_plugins = array_values($active_plugins); // Re-index array
+                $success = update_option('active_plugins', $active_plugins);
+            }
+        }
+        
+        return $success;
+    }
+    
+    /**
+     * Display admin notices
+     */
+    public function admin_notices() {
+        // Only run on the plugins page
+        if (!$this->is_plugins_page()) {
+            return;
+        }
+        
+        // Get invalid plugins
+        $invalid_plugins = $this->get_invalid_plugins();
+        
+        // Create a highlighted notice immediately after WordPress error messages
+        if (!empty($invalid_plugins)) {
+            // Add a notice specifically targeting the WordPress error notification
+            // Use admin_head to ensure it runs early in the page load process
+            add_action('admin_head', function() use ($invalid_plugins) {
+                ?>
+                <style type="text/css">
+                    .prc-notice {
+                        border-left: 4px solid #ffba00;
+                        background-color: #fff8e5;
+                        padding: 10px 12px;
+                        margin: 5px 0 15px;
+                        font-size: 14px;
+                        position: relative;
+                    }
+                    .prc-notice h3 {
+                        margin-top: 0;
+                        color: #826200;
+                    }
+                    .prc-notice::before {
+                        content: "";
+                        position: absolute;
+                        top: -10px;
+                        left: 20px;
+                        width: 0; 
+                        height: 0; 
+                        border-left: 10px solid transparent;
+                        border-right: 10px solid transparent;
+                        border-bottom: 10px solid #fff8e5;
+                    }
+                </style>
+                <script type="text/javascript">
+                    // Function to inject our notice
+                    function injectNotice() {
+                        // Find all notification containers first
+                        var noticeContainers = document.querySelectorAll('.notice, .error, .updated');
+                        
+                        // Find all error notifications about missing plugins
+                        noticeContainers.forEach(function(notice) {
+                            if (notice.textContent.includes('Plugin file does not exist') || 
+                                notice.textContent.includes('has been deactivated due to an error')) {
+                                
+                                // Check if we already added our notice
+                                if (notice.nextElementSibling && notice.nextElementSibling.classList.contains('prc-notice')) {
+                                    return;
+                                }
+                                
+                                // Create our custom notice
+                                var ourNotice = document.createElement('div');
+                                ourNotice.className = 'prc-notice';
+                                
+                                // Add content
+                                ourNotice.innerHTML = '<h3 style="margin-top:0;color:#826200;">👉 Fix Plugin Does Not Exist Notices Can Fix This</h3>' +
+                                    '<p>To remove the above error notification, scroll down to find the plugin marked with "<strong style="color:red">(File Missing)</strong>" and click its "<strong>Remove Reference</strong>" link.</p>' +
+                                    '<p>This will permanently remove the missing plugin reference from your database.</p>' +
+                                    '<p><a href="#" id="prc-scroll-to-plugin" style="font-weight:bold;text-decoration:underline;color:#826200;">Click here to scroll to the missing plugin</a></p>';
+                                
+                                // Insert our notice right after the error
+                                notice.parentNode.insertBefore(ourNotice, notice.nextSibling);
+                                
+                                // Add scroll behavior
+                                var scrollLink = document.getElementById('prc-scroll-to-plugin');
+                                if (scrollLink) {
+                                    scrollLink.addEventListener('click', function(e) {
+                                        e.preventDefault();
+                                        var missingPlugins = document.querySelectorAll('tr.inactive:not(.plugin-update-tr)');
+                                        for (var i = 0; i < missingPlugins.length; i++) {
+                                            if (missingPlugins[i].textContent.includes('(File Missing)')) {
+                                                missingPlugins[i].style.backgroundColor = '#fff8e5';
+                                                missingPlugins[i].scrollIntoView({behavior: 'smooth', block: 'center'});
+                                                return;
+                                            }
+                                        }
+                                    });
+                                }
+                            }
+                        });
+                    }
+                    
+                    // Try to inject notices on multiple events to ensure it works
+                    document.addEventListener('DOMContentLoaded', function() {
+                        injectNotice();
+                        
+                        // Also set up a MutationObserver to watch for dynamically added notices
+                        var observer = new MutationObserver(function(mutations) {
+                            mutations.forEach(function(mutation) {
+                                if (mutation.addedNodes && mutation.addedNodes.length > 0) {
+                                    injectNotice();
+                                }
+                            });
+                        });
+                        
+                        // Start observing the body for changes
+                        observer.observe(document.body, { childList: true, subtree: true });
+                    });
+                    
+                    // Backup attempt with window.onload
+                    window.onload = function() {
+                        setTimeout(injectNotice, 500);
+                    };
+                    
+                    // Final backup in case other methods fail
+                    setTimeout(injectNotice, 1000);
+                </script>
+                <?php
+            });
+            
+            // Also display our standard info notice with more details
+            echo '<div class="notice notice-info is-dismissible">';
+            echo '<h3>Fix Plugin Does Not Exist Notices</h3>';
+            echo '<p><strong>Missing plugin files detected:</strong> The plugins listed below with <span style="color:red;">(File Missing)</span> tag no longer exist but are still referenced in your database.</p>';
+            echo '<p><strong>How to fix:</strong> Click the "Remove Reference" link next to each missing plugin to safely remove it from your active plugins list.</p>';
+            echo '<p>This will clean up your database and remove the error notifications.</p>';
+            echo '</div>';
+        }
+        
+        // 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;
+    }
+}
+
+// Initialize the plugin
+new Fix_Plugin_Does_Not_Exist_Notices();

plugin-reference-cleaner.php

@@ -1,185 +0,0 @@
-<?php
-/*
- * 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: 1.2.1
- * Author: Marcus Quinn
- * Author URI: https://wpallstars.com
- * License: GPL-2.0+
- */
-
-// Exit if accessed directly
-if (!defined('ABSPATH')) {
-    exit;
-}
-
-class Plugin_Reference_Cleaner {
-    public function __construct() {
-        // 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); // Ensure notices in network admin
-        // Handle the AJAX request to remove the plugin reference
-        add_action('wp_ajax_remove_plugin_reference', array($this, 'remove_plugin_reference'));
-    }
-
-    // Inject "Remove Reference" button only if a relevant notice exists
-    public function inject_remove_button() {
-        global $pagenow;
-
-        // Only run on plugins.php or network admin plugins page
-        if (!in_array($pagenow, array('plugins.php', 'plugins.php'))) {
-            return;
-        }
-
-        // 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 $notice) {
-                if (strpos($notice, 'has been deactivated due to an error: Plugin file does not exist') !== false) {
-                    // Extract plugin file from notice
-                    if (preg_match('/The plugin ([^ ]+)/', $notice, $match)) {
-                        $plugin_files[] = $match[1];
-                        $has_error_notice = true;
-                    }
-                }
-            }
-        }
-
-        // Only proceed if a relevant notice was found
-        if (!$has_error_notice || empty($plugin_files)) {
-            return;
-        }
-
-        // Inject JavaScript with the specific plugin files
-        ?>
-        <script type="text/javascript">
-            document.addEventListener('DOMContentLoaded', function() {
-                var pluginFiles = <?php echo wp_json_encode($plugin_files); ?>;
-                var notices = document.querySelectorAll('.notice-error p');
-                
-                if (notices.length === 0) {
-                    return;
-                }
-                
-                notices.forEach(function(notice) {
-                    pluginFiles.forEach(function(pluginFile) {
-                        if (notice.textContent.includes('The plugin ' + pluginFile)) {
-                            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';
-                            notice.appendChild(button);
-                        }
-                    });
-                });
-
-                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() {
-        ob_start();
-        do_action('admin_notices');
-        do_action('network_admin_notices');
-        $output = ob_get_clean();
-        
-        if (empty($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
-        if (!current_user_can('activate_plugins')) {
-            wp_send_json_error('You do not have sufficient permissions to perform this action.');
-            wp_die();
-        }
-
-        // 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();
-        }
-
-        $success = false;
-        
-        // Handle multisite network admin
-        if (is_multisite() && is_network_admin()) {
-            $active_plugins = get_site_option('active_sitewide_plugins', array());
-            if (isset($active_plugins[$plugin_file])) {
-                unset($active_plugins[$plugin_file]);
-                $success = update_site_option('active_sitewide_plugins', $active_plugins);
-            }
-        } 
-        // Handle single site or multisite subsite
-        else {
-            $active_plugins = get_option('active_plugins', array());
-            $key = array_search($plugin_file, $active_plugins);
-            if ($key !== false) {
-                unset($active_plugins[$key]);
-                $active_plugins = array_values($active_plugins); // Re-index array
-                $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.');
-        }
-        
-        wp_die();
-    }
-}
-
-// Initialize the plugin
-new Plugin_Reference_Cleaner();

readme.txt

@@ -1,52 +1,140 @@
-=== Plugin Reference Cleaner ===
+=== Fix 'Plugin file does not exist.' Notices ===
-Author: Marcus Quinn
+Contributors: marcusquinn
-Author URI: https://wpallstars.com
+Donate link: https://www.wpallstars.com
-Version: 1.2.1
+Tags: plugins, missing plugins, cleanup, error fix, admin tools, plugin file does not exist
+Requires at least: 5.0
+Tested up to: 6.4
+Requires PHP: 7.0
+Stable tag: 1.4.1
 License: GPL-2.0+
+License URI: https://www.gnu.org/licenses/gpl-2.0.html
+
+Easily remove references to deleted plugins that cause "Plugin file does not exist" errors in your WordPress admin.
 
 == Description ==
 
-Have you ever deleted a plugin some other way than through the /wp-admin/plugins.php page? If so, you've probably been stuck with this annoying notification that can't be cleared:
+Have you ever deleted a plugin directly from the server or database and then been stuck with annoying error notifications that can't be cleared?
 
 "The plugin folder-name/file-name.php has been deactivated due to an error: Plugin file does not exist."
 
-This small WordPress utility plugin adds a "Remove Reference" button to these plugin deactivation error notices, allowing you to clean up the invalid plugin entries in the database.
+This small utility plugin adds missing plugins to your WordPress plugins list and provides a "Remove Reference" link, allowing you to safely clean up invalid plugin entries with one click.
 
-When WordPress detects a plugin file that no longer exists but is still referenced in the database as active, it displays an error notice. This plugin enhances those notices with a button that allows you to safely remove the invalid reference with a single click.
+= Key Features =
 
-You can find these with `SELECT * FROM wp_options WHERE option_name = 'active_plugins';` — but the cleanup involves removing the rogue entry, and renumbering all others. This plugin can simply do that for you at the click of a button added to that WP standard notification.
+* Adds missing plugins directly to your plugins list
+* Provides a simple "Remove Reference" action link
+* Works with both single site and multisite WordPress installations
+* Includes helpful notifications explaining how to fix plugin errors
+* One-click auto-scroll to find missing plugins in large sites
+* Clean, user-friendly interface following WordPress design patterns
 
-It's probably something that should be added to WP core. If anyone from the core team wants to adopt this solution, it's GPL, so feel free.
+= How It Works =
 
-Note: This plugin only needs to be installed and active if you have an error notification showing at /wp-admin/plugins.php, like this:
+When WordPress detects a plugin file that no longer exists but is still referenced in the database as active, it displays an error notice. This plugin:
-"The plugin folder-name/file-name.php has been deactivated due to an error: Plugin file does not exist."
 
-If you don't have this notification perpetually showing on your /wp-admin/plugins.php page, then you don't need this, but you might like to save or bookmark it for if ever you do.
+1. Detects all missing plugin references in your database
+2. Adds them to your plugins list with "(File Missing)" indicators
+3. Provides a "Remove Reference" link to safely remove them
+4. Shows clear notifications guiding you through the cleanup process
 
-== Features ==
+= Use Cases =
 
-* Adds a "Remove Reference" button to plugin error notices
+* You've accidentally deleted a plugin via FTP
-* Works for both single site and multisite WordPress installations
+* A plugin was removed by another admin but references remain
-* Confirms before removing any plugin references
+* You've migrated from another site and have leftover plugin references
-* Simple, lightweight solution with no settings page required
+* Your hosting provider removed a plugin but didn't clean the database
-* Secure implementation with proper permissions checking
-* Compatible with WordPress 5.0+
 
 == Installation ==
 
-1. Upload the plugin-reference-cleaner.php file to your /wp-content/plugins/ directory
+1. Upload the `fix-plugin-does-not-exist-notices` folder to the `/wp-content/plugins/` directory
 2. Activate the plugin through the 'Plugins' menu in WordPress
 3. No configuration needed - the plugin works automatically
+4. If you have missing plugin errors, you'll immediately see them in your plugins list with "Remove Reference" links
 
-== Usage ==
+== Frequently Asked Questions ==
 
-1. Navigate to Plugins > Installed Plugins
+= Is it safe to remove plugin references? =
-2. If any "Plugin file does not exist" error notices appear, a "Remove Reference" button will be displayed
+
-3. Click the button and confirm to remove the invalid plugin reference
+Yes, this plugin only removes entries from the WordPress active_plugins option, which is safe to modify when a plugin no longer exists. It doesn't modify any other database tables or settings.
-4. The page will refresh with the error notice removed
+
+= What happens after I remove a reference? =
+
+The plugin entry will be removed from your active plugins list, and the corresponding error notification will no longer appear after you refresh the page.
+
+= Can I use this plugin on a multisite installation? =
+
+Yes, the plugin works on both single sites and multisite installations. It properly handles network-activated plugins as well.
+
+= How do I know which plugin references should be removed? =
+
+The plugin will only show "Remove Reference" links for plugins that are listed in your database but don't actually exist in your plugins directory. These are safe to remove.
+
+= Will this break my site? =
+
+No. Since the plugin is only removing references to plugins that no longer exist, removing these references won't affect your site's functionality. In fact, it's cleaning up remnants that might be causing issues.
+
+= What if I accidentally remove a reference I shouldn't have? =
+
+If you remove a reference to a plugin that you later want to reinstall, simply install the plugin again and activate it normally.
+
+= Do I need to keep this plugin installed and active after notices are cleared? =
+
+Although this plugin consumes minimal disk space, and doesn't run unless you are on the /wp-admin/plugins.php page, you don't need to keep it active or installed if you don't have this notice to clear — but it is safe to, if you just want it as a part of your overall WordPress stack of enhancements and conveniences.
+
+== Screenshots ==
+
+1. Error message with explanation notification
+2. Missing plugin shown in the plugins list with "Remove Reference" link
+3. Auto-scroll feature that highlights the missing plugin
 
 == Changelog ==
 
+= 1.4.1 =
+* Added FAQ about keeping the plugin installed after notices are cleared
+
+= 1.4.0 =
+* Updated plugin name and text domain
+* Repository rename from plugin-reference-cleaner to fix-plugin-does-not-exist-notices
+
+= 1.3.3 =
+* Improved notification placement next to WordPress error messages
+* Added "Click here to scroll" button that automatically locates missing plugins
+* Enhanced reliability with multiple injection methods
+* Added visual arrow pointing from notification to error message
+
+= 1.3.2 =
+* Added prominent notification directly below WordPress error messages
+* Improved user guidance with visual cues to connect error and solution
+* Added eye-catching styling to help users understand how to fix errors
+
+= 1.3.1 =
+* Added instructional notification explaining how to use the plugin
+* Improved user guidance with step-by-step instructions
+* Enhanced visual identification of missing plugins
+
+= 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
+* Implemented fallback mechanisms to ensure button appears
+* Added detailed console logging for troubleshooting
+
+= 1.2.3 =
+* Fixed button not appearing in some WordPress admin themes
+* Improved error message detection for greater compatibility
+* Enhanced DOM traversal to find notification elements
+
+= 1.2.2 =
+* Fixed timeout issue during plugin activation
+* Improved hook management to prevent potential infinite recursion
+* Optimized performance by only loading on plugins page
+
 = 1.2.1 =
 * Fixed typos in documentation
 * Improved text clarity
@@ -65,6 +153,17 @@ If you don't have this notification perpetually showing on your /wp-admin/plugin
 = 1.0 =
 * Initial release
 
+== Upgrade Notice ==
+
+= 1.3.3 =
+Major usability improvement with auto-scroll feature to help find missing plugins in your list!
+
+= 1.3.0 =
+Completely redesigned for better compatibility with all WordPress themes - now works with any WordPress installation!
+
+= 1.2.2 =
+Important stability fix - resolves timeout issues during plugin activation!
+
 == Support ==
 
 For support, please visit https://wpallstars.com