If you're looking to use compiled a Webpack application with chunks in your gh-pages repository, you'll need to make sure your output.publicPath is set properly in your webpack.config.js (or similar) file, otherwise your chunks will probably have the wrong URL!

Simply set up your output.publicPath to point to the output directory, prefixed with the name of your GitHub project. For example my durandal-webpack compiles to a dist/ directory, and it's publicPath points to...

output: {  
    // ...other config here
    publicPath: '/durandal-webpack/dist/'

You'll also need to update your index.html to make sure the <script> referencing your compiled file reflects this change!

Took me a few tries to understand why my chunks weren't loading, so hope this saves you some of that debugging pain!

Hint: This also works well with webpack-dev-server. Awesome.