If you have a number of files that you'd like to add to IPFS and end up with a hash representing the directory containing your files, you can invoke ipfs.files.add with an array of objects.
But what if you don't know how many there will be in advance? You can add multiple files to a directory in IPFS over time by using ipfs.files.addReadableStream.
See index.js for a working example and open index.html in your browser to see it run.