A rewrite of the roots_add_rewrites function for the Roots Wordpress framework so that rewrites work when Wordpress is installed in a subdirectory. This function is found in roots/lib/htaccess.php. Once saved, go to the Settings->Permalinks page and things should work.

gistfile1.txt

function roots_add_rewrites($content) {
    global $wp_rewrite;
    $base = str_replace('/', '', WP_BASE);
    if($base != '') $base = $base.'/';
    $roots_new_non_wp_rules = array(
      $base .'assets/css/(.*)'      => $base . THEME_PATH . '/assets/css/$1',
      $base .'assets/js/(.*)'       => $base .  THEME_PATH . '/assets/js/$1',
      $base .'assets/img/(.*)'      => $base .  THEME_PATH . '/assets/img/$1',
      $base .'plugins/(.*)'         => $base .  RELATIVE_PLUGIN_PATH . '/$1'
    );
    $wp_rewrite->non_wp_rules = array_merge($wp_rewrite->non_wp_rules, $roots_new_non_wp_rules);
    return $content;
}