Webpack not including all our js and jsx file, even those in the same directory

We are trying to upgrade our React.js application which uses WebPack to build. In our upgrades we are moving from Webpack 1.0 to 2.0 and I have made the "necessary" changes for the upgrade. It is building, and compiling, however, when I look at the files included, it is a very smaller scale of the files it was including before.

For instance, we have 34 files in our React Flux Actions directory. Some files have .js extension some .jsx. However, of the 34 files, only 1 is showing up in the build. What happened to the other 33. This one has .js extension but there are more .js files in that directory too.

What am I missing?

This is our main config file.

var path = require('path');
var webpack = require('webpack');
var StringReplacePlugin = require("string-replace-webpack-plugin");
var Environment = require('./js/environment');

module.exports = {
  entry: [
    './js'
  ],
    output: {
    path: path.join(__dirname, 'build'),
    filename: 'bundle.js',
  },
  plugins: [
    new StringReplacePlugin(),
    new webpack.LoaderOptionsPlugin({
      options: {
        tslint: {
          emitErrors: true,
          failOnHint: true
        }
      }
    })
  ],
  resolve: {
    extensions: ['*', '.js', '.jsx'],
    modules: [
      path.join(__dirname, 'node_modules'),
      path.join(__dirname, 'js'),
      path.join(__dirname, 'jsx')
    ]
  },
  module: {
    loaders: [{
      test: /\.jsx?$/,
      exclude: /node_modules/,
      loaders: ['react-hot-loader/webpack', 'babel-loader' ]
    },
    {
      test: /js\/constants.js$/,
      loader: StringReplacePlugin.replace({
        replacements: [{
          pattern: /localhost/g,
          replacement: Environment.getBackendURL
        }]
      })
    }]
  }
};

This is our hot reload local version, I think both files are used, the one above and this one. But I am only doing "npm run build" command right now, then running "npm run local"

var path = require('path');
var webpack = require('webpack');

module.exports = {
  devtool: 'eval',
  entry: [
    'webpack-dev-server/client?http://localhost:3000',
    'webpack/hot/only-dev-server',
    './js/index'
  ],
  output: {
    path: path.join(__dirname, 'build-hot'),
    filename: 'bundle.js',
    publicPath: '/build/'
  },
  plugins: [
    new webpack.HotModuleReplacementPlugin(),
    // new webpack.NoErrorsPlugin()
    new webpack.LoaderOptionsPlugin({
      options: {
        tslint: {
          emitErrors: true,
          failOnHint: true
        }
      }
    })
  ],

  resolve: {
    extensions: ['*', '.js', '.jsx'],
    modules: [
      path.join(__dirname, 'node_modules'),
      path.join(__dirname, 'js'),
      path.join(__dirname, 'jsx')
    ]
  },
  module: {
    loaders: [{
      test: /\.jsx?$/,
      exclude: /node_modules/,
      loaders: ['react-hot-loader/webpack', 'babel-loader' ]
    }]
  }
};

via user1567291