.babelrc

{
  "presets": ["es2015"],
  "plugins": ["transform-runtime"]
}

build-babel.js

"use strict";

var mv = {};

build-webpack.js

/******/ (function(modules) { // webpackBootstrap
/******/ 	// The module cache
/******/ 	var installedModules = {};

/******/ 	// The require function
/******/ 	function __webpack_require__(moduleId) {

/******/ 		// Check if module is in cache
/******/ 		if(installedModules[moduleId])
/******/ 			return installedModules[moduleId].exports;

/******/ 		// Create a new module (and put it into the cache)
/******/ 		var module = installedModules[moduleId] = {
/******/ 			exports: {},
/******/ 			id: moduleId,
/******/ 			loaded: false
/******/ 		};

/******/ 		// Execute the module function
/******/ 		modules[moduleId].call(module.exports, module, module.exports, __webpack_require__);

/******/ 		// Flag the module as loaded
/******/ 		module.loaded = true;

/******/ 		// Return the exports of the module
/******/ 		return module.exports;
/******/ 	}


/******/ 	// expose the modules object (__webpack_modules__)
/******/ 	__webpack_require__.m = modules;

/******/ 	// expose the module cache
/******/ 	__webpack_require__.c = installedModules;

/******/ 	// __webpack_public_path__
/******/ 	__webpack_require__.p = "";

/******/ 	// Load entry module and return exports
/******/ 	return __webpack_require__(0);
/******/ })
/************************************************************************/
/******/ ([
/* 0 */
/***/ function(module, exports) {

	let mv = {};


/***/ }
/******/ ]);

command

# Test with node 6.2.0 and 4.4.4

$ nodebrew use 6.2.0
$ node --version  # v6.2.0
$ npm --version  # 3.8.9
$ npm install
$ npm run babel
$ npm run webpack
$ rm -R node_modules
$ nodebrew use 4.4.4
$ node --version  # v4.4.4
$ npm --version  # 2.15.1
$ npm install
$ npm run babel
$ npm run webpack

index.js

let mv = {};

package.json

{
  "name": "foo",
  "version": "1.0.0",
  "description": "",
  "main": "aap/index.js",
  "scripts": {
    "test": "echo \"Error: no test specified\" && exit 1",
    "webpack": "webpack",
    "babel": "babel index.js > build-babel.js"
  },
  "author": "",
  "license": "ISC",
  "devDependencies": {
    "babel-cli": "^6.9.0",
    "babel-core": "^6.9.0",
    "babel-loader": "^6.2.4",
    "babel-plugin-transform-runtime": "^6.9.0",
    "babel-preset-es2015": "^6.9.0",
    "babel-register": "^6.9.0",
    "babel-runtime": "^6.9.0",
    "webpack": "^1.13.1"
  },
  "dependencies": {}
}

webpack.config.babel.js

import path from 'path';
import webpack from 'webpack';

module.exports = {
  entry: {
    'index': './index.js',
  },
  externals: {
  },
  resolve: {
    modulesDirectories: ['node_modules', 'bower_components'],
  },
  plugins: [
    new webpack.optimize.DedupePlugin(),
    new webpack.optimize.AggressiveMergingPlugin(),
    // new webpack.optimize.UglifyJsPlugin(),
  ],
  output: {
    path: path.join(__dirname),
    filename: 'build-webpack.js',
  },
  loaders: [{
    test: /\.js$/,
    exclude: /node_modules/,
    loader: 'babel-loader',
    query: {
      preset: ['es2015'],
      plugins: ['transform-runtime']
    }
  }]
};