Simple plugin to fix the plugins_url() and get_template_directory_uri() paths when WP installed in a subdirectory and wp-content not in ABSPATH

filter-examples.txt

add_filter(
	'subdirectory_fix_plugins_url',
	function() {
		return [ 'wpforms-lite', 'query-monitor' ];
	}
);

add_filter(
	'subdirectory_fix_template',
	function() {
		return 'twentytwentyone';
	}
);

subdirectory-content-uri-fix.php

<?php
/**
 * Plugin Name:          Subdirectory Plugin/Theme Directory URI Fix
 * Plugin URI:           https://gist.github.com/afragen/dcc77953ec95cdc1d06a2ed4aea67bf8
 * Description:          This plugin is used to fix plugins_url() and get_template_directory_uri() for WP subdirectory installation. Add plugin or theme slugs via filters in the plugin.
 * Version:              0.1
 * Author:               Andy Fragen
 * License:              MIT
 * Requires at least:    5.2
 * Requires PHP:         7.1
 * Gist Plugin URI:      https://gist.github.com/afragen/dcc77953ec95cdc1d06a2ed4aea67bf8
 *
 * @package Fragen\Subdirectory\Fix
 * @see https://wordpress.org/support/article/giving-wordpress-its-own-directory/
 */

namespace Fragen\Subdirectory;

/**
 * Class Fix
 */
class Fix {

	/**
	 * Site URL.
	 *
	 * @var string
	 */
	protected static $site_url;

	/**
	 * Home URL.
	 *
	 * @var string
	 */
	protected static $home_url;

	/**
	 * Array of slugs to test.
	 *
	 * @var array
	 */
	protected static $plugins = [ 'wp-dismiss-notice', 'debug-quick-look', 'query-monitor' ];

	/**
	 * Initialize variables and load hooks.
	 *
	 * @return void
	 */
	public function init() {
		static::$site_url = get_option( 'siteurl' );
		static::$home_url = get_option( 'home' );

		add_filter( 'plugins_url', [ $this, 'plugins_url' ], 10, 3 );
		add_filter( 'template_directory_uri', [ $this, 'template_directory_uri' ], 10, 3 );
	}

	/**
	 * Update plugins_url() for possible subdirectory install with wp-content outside of ABSPATH.
	 *
	 * Must have correctly set WordPress Address (URL) and Site Address (URL) in Settings.
	 * Must have correctly set WP_CONTENT_DIR in wp-config.php
	 *
	 * @param [type] $url    The complete URL to the plugins directory including scheme and path.
	 * @param [type] $path   Path relative to the URL to the plugins directory. Blank string
	 *                       if no path is specified.
	 * @param [type] $plugin The plugin file path to be relative to. Blank string if no plugin
	 *                       is specified.
	 *
	 * @return string
	 */
	public function plugins_url( $url, $path, $plugin ) {
		$slug = basename( dirname( $plugin ) );
		if ( static::$site_url !== static::$home_url ) {
			/**
			 * Filter the supplied plugin slugs.
			 *
			 * Accept a string or array as return value to be converted to an array.
			 *
			 * @param array Array of supplied plugin slugs.
			 */
			$plugin_slugs = (array) apply_filters( 'subdirectory_fix_plugins_url', static::$plugins );

			$plugin_slugs = array_unique( array_merge( static::$plugins, $plugin_slugs ) );
			foreach ( $plugin_slugs as $plugin_slug ) {
				if ( $plugin_slug === $slug ) {
					$url = str_replace( static::$site_url, static::$home_url, $url );
					break;
				}
			}
		}

		return $url;
	}

	/**
	 * Update get_template_directory_uri() for possible subdirectory install with wp-content
	 * outside of ABSPATH.
	 *
	 * Must have correctly set WordPress Address (URL) and Site Address (URL) in Settings.
	 * Must have correctly set WP_CONTENT_DIR in wp-config.php
	 *
	 * @param string $template_dir_uri The URI of the current theme directory.
	 * @param string $template         Directory name of the current theme.
	 * @param string $theme_root_uri   The themes root URI.
	 *
	 * @return string
	 */
	public function template_directory_uri( $template_dir_uri, $template, $theme_root_uri ) {
		if ( static::$site_url !== static::$home_url ) {
			/**
			 * Filter to add theme slug.
			 *
			 * @param string Default empty string.
			 */
			if ( apply_filters( 'subdirectory_fix_template', '' ) === $template ) {
				$template_dir_uri = str_replace( static::$site_url, static::$home_url, $template_dir_uri );
			}
		}

		return $template_dir_uri;
	}
}

( new Fix() )->init();