build.js

var Builder = require('systemjs-builder');

var b = (new Builder());
b.config({
  map: {
    app: 'src',
    'deep-assign': 'node_modules/deep-assign',
    'is-obj': 'node_modules/is-obj'
  },
  packages: {
    'deep-assign': {
      main: 'index.js',
      format: 'cjs'
    },
    'is-obj': {
      main: 'index.js'
    }
  }
});
b.buildStatic('app/index.js', 'out.js');

src-index.js

var deepAssign = require('deep-assign')
console.log(deepAssign);