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I'm sure you remember¹ you can create app folders by drag-and-drop when you enable the experimental chrome://flags/#enable-app-list-folder flag.

Unlike before though, we can also now drag easily an app out of its folder and reassign it to another one in the last Dev Update. It basically works as you would expect.

And if you've enabled the App Launcher Sync flag, app folders are also now synced. There are no reasons to not use them anymore and report feedback at http://crbug.com/new

¹ https://plus.google.com/+FrancoisBeaufort/posts/WaqNvaAJsaA

Source: https://codereview.chromium.org/136303008