brunch.config.js

module.exports = {
  server: {
    base: '/public',
    stripSlashes: true,
    command: 'php -S 0.0.0.0:3000 -t public'
  }, 
  paths: {
    watched: ['resources'],
    public: './public/build'
  },

  files: {
    javascripts: {
      joinTo: 'js/app.js'
    },
    stylesheets: {
      joinTo:'css/app.css'
    },
    templates: {joinTo: 'js/app.js'}        
  }, 
  plugins: {
	 postcss: {}
  }
};

initialize.js

document.addEventListener('DOMContentLoaded', function() {
  // do your setup here
});

package.json

{
  "name": "brunch-app",
  "description": "Description",
  "author": "Your Name",
  "version": "0.1.0",
  "repository": {
    "type": "git",
    "url": ""
  },
  "scripts": {
    "start": "brunch watch --server",
    "build": "brunch build --production"
  },
  "dependencies": {},
  "devDependencies": {
    "auto-reload-brunch": "^2.0.0",
    "brunch": "^2.0.0",
    "clean-css-brunch": "^2.0.0",
    "css-brunch": "^2.0.0",
    "javascript-brunch": "^2.0.0",
    "postcss-brunch": "^2.0.3",
    "uglify-js-brunch": "^2.0.0"
  }
}

tree.md

/my-project/
  node_modules
  public/
    build/
      README.md
      css/
        app.css
        app.css.map
      js
        app.js
        app.js.map
    index.php

  
  resources/
    assets/
      README.md
    css/
      styles.css
    js/
      test.js
    initialize.js
    README.md