babel having trouble with import statement

I don't think you need to exclude the node_modules in your loader config. However, you might want to let webpack know what to resolve. Try adding something like this:

resolve: {    root: path.join(__dirname),    fallback: path.join(__dirname, 'node_modules'),    modulesDirectories: ['node_modules'],    extensions: ['', '.json', '.js', '.jsx', '.scss', '.png', '.jpg', '.jpeg', '.gif']},

The modulesDirectories key should keep webpack from running down every single require / import in your working directory.

Also, adding target to the top of your config should resolve issues with builtins like fs

target: 'node'

Ok I figured it out thanks to other answers and 4m1r' answer. I post the example code.

var path = require('path');var fs = require('fs');var nodeModules = {};fs.readdirSync('node_modules')  .filter(function (x) {    return ['.bin'].indexOf(x) === -1;  })  .forEach(function (mod) {    nodeModules[mod] = 'commonjs ' + mod;  });module.exports = {  name: 'server',  target: 'node',  context: path.join(__dirname, 'src', 'cloud'),  entry: {    server: './main.js'  },  output: {    path: path.join(__dirname),    filename: '[name].js'  },  externals: nodeModules,  module: {    loaders: [      {test: /\.js$/, exclude: /node_modules/, loaders: ['babel-loader?presets[]=es2015']}    ]  },  resolve: {    root: path.join(__dirname),    fallback: path.join(__dirname, 'node_modules'),    modulesDirectories: ['node_modules'],  }};

What was really important too was the externals key which prevented it fro leaking to the node_modules through requires and specifying for some reason ?presets[]=2015 in the babel-loader. I'm accepting 4m1r because it was what finally fixed the code.