Enables the loading of plugins not sitting in the mu-plugins directory to allow auto-updates and correct directory reads.

plugins-loader.php

<?php
/**
 * Plugin Name: Autoload Plugins
 * Plugin URI: https://gist.github.com/thefrosty/8303566
 * Description: Autoload non-MU plugins that live in the `wp-content/plugins` directory. This allows auto-updates to
 * work but have to plugin act like an must-use plugin.
 * Version: 0.2.1
 * Author: Austin Passy
 * Author URI: http://austin.passy.co/
 */

namespace TheFrosty;

use WP_Plugins_List_Table;

if ( ! defined( 'ABSPATH' ) ) {
	exit;
}

/**
 * These are default plugin that live in the `wp-content/plugins` directory that you want autoloaded.
 *      Add any plugins you wish to the $plugins array or filter in your own using the
 *      'mu_autoload_plugins_array' filter. Be sure to call that filter as early as possible.
 *
 * @return array
 */
function autoload_plugins() {

	$plugins   = array();
	$plugins[] = 'dev-debug-bar/debug-bar.php';
	$plugins[] = 'dev-debug-bar-actions-and-filters-addon/debug-bar-action-and-filters-addon.php';
	$plugins[] = 'query-monitor/query-monitor.php';

	apply_filters( 'mu_autoload_plugins_array', $plugins );

	foreach ( $plugins as $plugin_file ) {
		if ( ! file_exists( trailingslashit( WP_PLUGIN_DIR ) . $plugin_file ) ) {
			unset( $plugins[ $plugin_file ] );
		}
	}

	return $plugins;
}

add_filter( 'all_plugins', function( $plugins ) {

	foreach ( autoload_plugins() as $plugin_file ) {
		if ( isset( $plugins[ $plugin_file ] ) ) {
			unset( $plugins[ $plugin_file ] );
		}
	}

	return $plugins;
} );

add_action( 'muplugins_loaded', function() {

	$default_hook = current_action(); // muplugins_loaded
	$action_hook  = (string) apply_filters( 'mu_plugins_autoload_action_hook', $default_hook );

	add_action( $action_hook, function() {

		// `get_plugins` is not included by default
		if ( ! function_exists( 'get_plugins' ) ) {
			require_once ABSPATH . 'wp-admin/includes/plugin.php';
		}

		foreach ( autoload_plugins() as $plugin_file ) {
			if ( file_exists( trailingslashit( WP_PLUGIN_DIR ) . $plugin_file ) ) {
				if ( is_plugin_active( $plugin_file ) || is_plugin_active_for_network( $plugin_file ) ) {
					deactivate_plugins( $plugin_file );
				}
				require trailingslashit( WP_PLUGIN_DIR ) . $plugin_file;
			}
		}
	}, 8 );
}, 5 );

/**
 * Add rows for each plugin under this plugin when listing mu-plugins in wp-admin
 */
add_action( 'admin_init', function() {

	add_action( 'after_plugin_row_' . basename( __FILE__ ), function() {

		$table = new WP_Plugins_List_Table;

		foreach ( autoload_plugins() as $plugin_file ) {

			$data           = get_plugin_data( trailingslashit( WP_PLUGIN_DIR ) . $plugin_file, false );
			$name           = empty( $data[ 'Name' ] ) ? $plugin_file : $data[ 'Name' ];
			$data[ 'Name' ] = "&nbsp;&nbsp;&nbsp;&nbsp;+&nbsp;&nbsp;" . $name;

			$table->single_row( array( $plugin_file, $data ) );
		}
	} );
} );