a.js

let config = {
  supercalifragilisticexpialidocious: true
};

module.exports = config;

b.js

let config = {
  superlongpropertyname: true
};

module.exports = config;

config.js

import _ from 'lodash';

let config = require('./a.js');
config = _.assign(config, require('./b.js'));

module.exports = config;

index.js

import config from './config/config.js';

console.log(config);

webpack.config.js

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

var nodeModules = {};
fs.readdirSync('node_modules').filter(function(x) {
  return ['.bin'].indexOf(x) === -1;
}).forEach(function(mod) {
  nodeModules[mod] = 'commonjs ' + mod;
});

module.exports = {
  context: path.join(__dirname, ''),
  target: 'node',
  node: {
    fs: 'empty'
  },
  externals: nodeModules,
  plugins: [
  ],
  resolve: {
    extensions: ['', '.js', '.jsx', '.json']
  },
  module: {
    loaders: [{
      test: require.resolve('./config/config.js'),
      exclude: /node_modules/,
      loader: 'json!val!to-string!babel'
    }, {
      test: /\.js$/,
      exclude: /node_modules/,
      loader: 'babel'
    }]
  },
  entry: './index.js',
  output: {
    path: __dirname,
    filename: 'bundle.js'
  }
};