PHP: Adjust the rewrite of a registered post type.

gs_projects_rewrite.php

<?php

add_action( 'registered_post_type', 'gs_projects_rewrite', 10, 2 );
 /**
 * Modify registered post type menu label
 *
 * @param string $post_type Registered post type name.
 * @param array $args Array of post type parameters.
 */
 function gs_projects_rewrite( $post_type, $args ) {
  if ( 'project' === $post_type ) {
	global $wp_post_types;
    	$permastruct_args         = $args->rewrite;
	$permastruct_args['feed'] = $permastruct_args['feeds'];
	add_permastruct( $post_type, "{$args->rewrite['slug']}/%$post_type%/%project_category%", $permastruct_args );
  }
 } 

For a further explanation, see the tutorial here: http://wpsmith.net/2013/wp/use-registered_post_type-hook-to-modify-post-type-registration/