postcss-loader: [2.0.5] `css-loader: modules` not working as needed after upgrade

css modules inside node_modules are working but css modules on my source are not added but loaded.

css is missed

require('babel-polyfill');
const fs = require('fs');
const path = require('path');
const webpack = require('webpack');
const FlowtypePlugin = require('flowtype-loader/plugin');
const assetsPath = path.resolve(__dirname, '../static/dist');
const host = (process.env.HOST || 'localhost');
const port = (+process.env.PORT + 1) || 4001;

const rootPath = path.join(__dirname, './..');
const nodeModulesPath = path.join(rootPath, 'node_modules');

// Isomorfic Tools
// https://github.com/halt-hammerzeit/webpack-isomorphic-tools
const WebpackIsomorphicToolsPlugin =
  require('webpack-isomorphic-tools/plugin');
const webpackIsomorphicToolsPlugin =
  new WebpackIsomorphicToolsPlugin(require('./webpack-isomorphic-tools'));

// Babel config update to for client

const babelrc = fs.readFileSync('./.babelrc');
let babelrcObject = {};

try {
  babelrcObject = JSON.parse(babelrc);
} catch (err) {
  console.error('==>     ERROR: Error parsing your .babelrc.');
  console.error(err);
}

const babelrcObjectDevelopment =
  babelrcObject.env && babelrcObject.env.development || {};

// merge global and dev-only plugins
let combinedPlugins = babelrcObject.plugins || [];
combinedPlugins = combinedPlugins.concat(babelrcObjectDevelopment.plugins);

const babelLoaderQuery = Object.assign(
  {},
  babelrcObjectDevelopment,
  babelrcObject,
  { plugins: combinedPlugins }
);

delete babelLoaderQuery.env;

// Since we use .babelrc for client and server, and we don't want HMR enabled
// on the server, we have to add the babel plugin react-transform-hmr manually
// here.

// make sure react-transform is enabled
babelLoaderQuery.plugins = babelLoaderQuery.plugins || [];
let reactTransform = null;
for (let i = 0; i < babelLoaderQuery.plugins.length; ++i) {
  let plugin = babelLoaderQuery.plugins[i];
  if (Array.isArray(plugin) && plugin[0] === 'react-transform') {
    reactTransform = plugin;
  }
}

babelLoaderQuery.presets =
  babelLoaderQuery.presets.map(function (item) {
    if (item === 'es2015') {
      return ['es2015', { modules: false }];
    }
    return item;
  });

if (!reactTransform) {
  reactTransform = ['react-transform', {transforms: []}];
  babelLoaderQuery.plugins.push(reactTransform);
}

if (!reactTransform[1] || !reactTransform[1].transforms) {
  reactTransform[1] = Object.assign({}, reactTransform[1], {transforms: []});
}

module.exports = {
  entry: {
    vendor: require('./vendorList'),
    main: [
      'react-hot-loader/patch',
      //activate HMR for React

      'webpack-hot-middleware/client?path=http://' + host + ':' + port + '/__webpack_hmr',

      './src/client.js'
      //the entry point of our app
    ],
  },

  output: {
    path: assetsPath,
    filename: '[hash]-[id].js',
    chunkFilename: '[name]-[chunkhash].js',
    publicPath: 'http://' + host + ':' + port + '/assets/',
  },

  context: path.resolve(__dirname, '..'),

  devtool: 'inline-source-map',

  performance: { hints: false },

  module: {
    rules: [{
      test: /\.jsx?$/,
      exclude: /node_modules/,
      use: [
        'react-hot-loader/webpack',
        'babel-loader?' + JSON.stringify(babelLoaderQuery),
        'eslint-loader',
        // 'flowtype-loader',
      ],
    }, {
      test: /\.json$/,
      loader: 'json-loader',
    }, {
      test: /\.css$/,
      use: [
        'style-loader',
        {
          loader: 'css-loader',
          options: {
            sourceMap: true,
            localIdentName: '[local]___[hash:base64:5]',
            importLoaders: 2,
            modules: true,
          }
        },
        {
          loader: 'postcss-loader',
          options: {
            plugins: (loader) => [
              require('postcss-import')({
                root: loader.resourcePath,
              }),
              require('postcss-mixins')(),
              require('postcss-each')(),
              require('postcss-cssnext')({
                features: {
                  customProperties: {
                    variables: require('../src/theme/variables.js'),
                  }
                }
              }),
            ],
          } ,
        },
      ]
    }, {
      test: /\.(graphql|gql)$/,
      exclude: /node_modules/,
      loader: 'graphql-tag/loader',
    }, {
      test: /\.woff(\?v=\d+\.\d+\.\d+)?$/,
      loader: 'url-loader?limit=10000&mimetype=application/font-woff',
    }, {
      test: /\.woff2(\?v=\d+\.\d+\.\d+)?$/,
      loader: 'url-loader?limit=10000&mimetype=application/font-woff',
    }, {
      test: /\.ttf(\?v=\d+\.\d+\.\d+)?$/,
      loader: 'url-loader?limit=10000&mimetype=application/octet-stream',
    }, {
      test: /\.eot(\?v=\d+\.\d+\.\d+)?$/,
      loader: 'file-loader',
    }, {
      test: /\.svg(\?v=\d+\.\d+\.\d+)?$/,
      loader: 'url-loader?limit=10000&mimetype=image/svg+xml',
    }, {
      test: webpackIsomorphicToolsPlugin.regular_expression('images'),
      loader: 'url-loader?limit=10',
    }],
  },

  resolve: {
    modules: [
      'src',
      'node_modules'
    ],
    extensions: ['.json', '.js', '.jsx', '*'],
  },

  plugins: [
    // new FlowtypePlugin(),

    new webpack.LoaderOptionsPlugin({
      options: {
        context: path.resolve(__dirname, '..'),
      }
    }),

    new webpack.optimize.CommonsChunkPlugin({
      names: ['vendor', 'manifest'], // Specify the common bundle's name.
    }),

    new webpack.HotModuleReplacementPlugin(),
    //activates HMR

    new webpack.NamedModulesPlugin(),
    //prints more readable module names in the browser console on HMR updates
    //
    new webpack.IgnorePlugin(/webpack-stats\.json$/),

    new webpack.DefinePlugin({
      __CLIENT__: true,
      __SERVER__: false,
      __DEVELOPMENT__: true,
      __DEVTOOLS__: true  // <-------- DISABLE redux-devtools HERE
    }),

    webpackIsomorphicToolsPlugin.development()
  ],
};