webpack + babel + typescript + es6 - total solutions!

.babelrc

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

install.sh

npm install babel-core@6 --save-dev
npm install babel-loader@6 --save-dev
npm install babel-runtime@6 --save-dev
npm install babel-preset-es2015@6 --save-dev
npm install babel-preset-react@6 --save-dev
npm install babel-plugin-transform-runtime@6 --save-dev
npm install babel-plugin-transform-es2015-modules-commonjs@6 --save-dev
npm install babel-plugin-transform-object-assign@6 --save-dev
npm install babel-polyfill --save-dev
sudo npm install typings -g 
typings install

package.json

{
  "devDependencies": {
    "async": "^1.2.0",
    "babel-core": "^6.9.0",
    "babel-loader": "^6.2.4",
    "babel-plugin-transform-es2015-modules-commonjs": "^6.8.0",
    "babel-plugin-transform-object-assign": "^6.8.0",
    "babel-plugin-transform-runtime": "^6.9.0",
    "babel-polyfill": "^6.9.0",
    "babel-preset-es2015": "^6.9.0",
    "babel-preset-es2015-native-modules": "^6.6.0",
    "babel-preset-react": "^6.5.0",
    "babel-preset-stage-0": "^6.5.0",
    "babel-runtime": "^6.9.0",
    "file-loader": "^0.8.1",
    "object-assign": "^4.0.1",
    "uglify-loader": "^1.3.0",
    "webpack": "^1.13.1",
    "webpack-closure-compiler": "^2.0.2",
    "webpack-dev-server": "^1.14.1",
    "webpack-stream": "^3.2.0",
    "ts-loader": "^0.8.2"
  }
}

tsconfig.json

{
  "compilerOptions": {
    "target": "es6",
    "allowSyntheticDefaultImports": true,
    "sourceMap": true,
    "allowJs": true,
    "outDir": "build"
  },
  "exclude": ["node_modules"],
  "files": ["typings/index.d.ts", "entry.ts"]
}

typings

{
  "globalDependencies": {
    "d3": "registry:dt/d3#0.0.0+20160514171929",
    "jquery": "registry:dt/jquery#1.10.0+20160417213236",
    "mocha": "registry:dt/mocha#2.2.5+20160317120654"
  }
}

webpack.config.js

var path = require('path');
var nodeModulesPath = path.resolve(__dirname, 'node_modules');
var webpack = require('webpack');
module.exports = {
  'entry': {
    // your entry file file (entry.ts or entry.js)
    'd3metric': ['./entry'],
    'd3metric.demo': ['./demo/demo.entry'],
  },
  'output': {
    'path': __dirname,
    'filename': '[name].js'
  },
  'module': {
    'loaders': [
      // ts-loader: convert typescript (es6) to javascript (es6),
      // babel-loader: converts javascript (es6) to javascript (es5)
      {
        'test': /\.tsx?$/,
        'loaders': ['babel-loader','ts-loader'],
        'exclude': [/node_modules/,nodeModulesPath]
      },
      // babel-loader for pure javascript (es6) => javascript (es5)
      {
        'test': /\.(jsx?)$/,
        'loaders': ['babel'],
        'exclude': [/node_modules/,nodeModulesPath]
      }
    ]
  },
  'externals': {
    // don't bundle the 'react' npm package with our bundle.js
    // but get it from a global 'React' variable
    'react': 'React'
  },
  'plugins': [],
  'resolve': {
    'root': [path.resolve('./src')],
    'extensions': ['', '.js', '.jsx', '.ts', '.tsx'],

    // this is only required when we "import 'jquery'"
    // 'alias': { 'jquery': path.join(__dirname, "vendor", "jquery-2.2.0.min.js") }
  }
};