// If you want to change the path, you will also have to change:
// - index.php, src to main.js and config.js
// - All the css: urls to images
var CONFIG = new function(){
  this.scriptList = [
    "libs/jquery.min.js",
    "libs/event-manager.js",
    "libs/utils.js",
    "controller/naut-controller.js",
    "controller/build-controller.js",
    "model/build.js",
    "model/effect.js",
    "model/info-box.js",
    "model/naut.js",
    "model/skill.js",
    "model/upgrade.js",
    "view/info-box-view.js",
    "view/naut-view.js",
    "view/shop-view.js"
  ];

  this.styleList = [
    "main.css",
    "naut-info.css",
    "shop.css",
    "tooltip.css",
    "upgrade.css"
  ];

  this.apiURL = "https://orikaru.net/resources/logic/php/ajax/awesomenauts.php";

  var path = {};
  path["base"] = "/nautsbuilder/";
  path["scripts"] = path["base"] + "scripts/";
  path["images"] = path["base"] + "images/";
  path["styles"] = path["base"] + "styles/";

  this.path = path;
};

@@ -781,24 +781,21 @@
 ;%0A  path
-%5B%22
+.
 base
-%22%5D
  = %22/nau
@@ -817,34 +817,28 @@
 path
-%5B%22
+.
 scripts
-%22%5D
  = path
-%5B%22
+.
 base
-%22%5D
  + %22
@@ -858,33 +858,27 @@
 path
-%5B%22
+.
 images
-%22%5D
  = path
-%5B%22
+.
 base
-%22%5D
  + %22
@@ -897,33 +897,27 @@
 path
-%5B%22
+.
 styles
-%22%5D
  = path
-%5B%22
+.
 base
-%22%5D
  + %22

Replaced the [""] notation by the "." notation