How to individually set WP_DEBUG on a sub-directory multisite?

You can do this by adding some code to wp-config.php

$request_uri = $_SERVER['REQUEST_URI'];
$debug_dirs = array ('/debug-dir1/','/debug-dir2/'); // list of directories to turn on debugging
foreach ($debug_dirs as $debug_dir) {
    if (!strncmp($request_uri,$debug_dir,strlen($debug_dir))) {
        define('WP_DEBUG', true);
    } 
}
define('WP_DEBUG', false); // debug off by default