Custom Post type and Taxonomy using same slug with rewrite

After working on this for a week I finally solved the issue. I kept the post types exactly as they were. I replaced the generate_rewrite_rules function with the following.

add_filter('request', 'setTermRequest', 1, 1 );function setTermRequest($query){    $tax_name = 'services';    if( $query['attachment'] ) :        $include_children = true;        $name = $query['attachment'];    else:        $include_children = false;        $name = $query['name'];    endif;    $term = get_term_by('slug', $name, $tax_name); // get the current term to make sure it exists    if (isset($name) && $term && !is_wp_error($term)): // check it here        if( $include_children ) {            unset($query['attachment']);            $parent = $term->parent;            while( $parent ) {                $parent_term = get_term( $parent, $tax_name);                $name = $parent_term->slug . '/' . $name;                $parent = $parent_term->parent;            }        } else { unset($query['name']); }        switch( $tax_name ):            case 'category':{                $query['category_name'] = $name; // for categories                break;            }            case 'post_tag':{                $query['tag'] = $name; // for post tags                break;            }            default:{                $query[$tax_name] = $name; // for another taxonomies                break;            }        endswitch;    endif;    return $query;}add_filter( 'term_link', 'writeTermPerm', 10, 3 );function writeTermPerm( $url, $term, $taxonomy ){    $taxonomy_name = 'services';    $taxonomy_slug = 'services';    if ( strpos($url, $taxonomy_slug) === FALSE || $taxonomy != $taxonomy_name ) return $url;    $url = str_replace('/'.$taxonomy_slug, '/portfolio', $url);    return $url;}

After that fixed the url structure I added the following code to my taxonomy-services.php document in order to control the entire system in one file.

locate_template( 'archive-portfolio.php', true );