engine.js

import World from "./World";
import Physics from "./Physics";

// expose all the things
window.ENGINE = { World: World, Physics: Physics };

Physics.js

const Physics = {
  applyForce: function(x, y) { ... },
  processEntity: function(entity) { ... }
};
export default Physics;

World.js

const World = {
  the_answer_to_everything: 42
};
export default World;

ES6 destructuring makes this nice too - you can pull out bits only when you need them

import Engine from './Engine';
const {Lander, Astronaut, WaveCharge} = Engine;
const {Encouter, Mission, Junkyard} = Engine;

Etc... not sure why Junkyard is part of your engine though ;)