Nested tree shaking is not working at webpack@3.0.0

[navarroaxel]

Do you want to request a feature or report a bug?
bug

What is the current behavior?
The tree shaking at 2nd level is not working in webpack@3.0.0, but it's working with webpack@2.6.1.

If the current behavior is a bug, please provide the steps to reproduce.
Just use a code like this twice:

if (!module.hot || process.env.NODE_ENV === 'production') {
    module.exports = require('./index.prod');
} else {
    module.exports = require('./index.dev');
}

The 2nd tree shaking doesn't work. You can see the issue in this repo: https://github.com/navarroaxel/webpack-tree-shaking-bug

Just run this:

git clone https://github.com/navarroaxel/webpack-tree-shaking-bug.git
cd webpack-tree-shaking-bug
yarn install
yarn run webpack
# ctrl+c to stop the bundle analyzer server
yarn add --dev webpack
#the webpack should upgrade from 2.6.1 to 3.0.0
yarn run webpack #again

What is the expected behavior?
The tree shaking should works like webpack@2.6.1.

If this is a feature request, what is motivation or use case for changing the behavior?

Please mention other relevant information such as the browser version, Node.js version, webpack version and Operating System.
node@6.11.0
webpack@3.0.0

The issue affects this package react-hot-loader@3.0.0-beta.7 because the sourcemapped-stacktrace dependency is not removed in the production build.

[jakeNiemiec]

This also is a problem with builds by angular-cli imported via webpack.