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By default, the GNOME (Shell) overview displays applications in two views: "all", where all the applications are listed in alphabetic order, and "frequent", in which the frequently used applications are displayed.

GNOME Shell supports grouping applications in app folders, and there are two such predefined folders, "Utilities" and "Sundry". Some might not know how to create custom app folders, so here are two ways of achieving this.

Create and edit GNOME Shell app folders with GNOME AppFolders Manager

GNOME Appfolders Manager

GNOME AppFolders Manager is a tool to create and edit app folders in GNOME Shell.

The application is fairly easy to use - in the left section, you can create, delete or edit app folders, while in the right section you can add (or remove) applications to app folders.

Once you've added the applications you want to an app folder, click the save button. That's it! Here's a custom GNOME application folder I created using GNOME AppFolders Manager:

GNOME Appfolders

To install GNOME AppFolders Manager in Ubuntu GNOME 16.04, 15.10 or 15.04 (the app requires GNOME 3.12+, while Ubuntu 14.04 uses GNOME 3.10), you can use the main WebUpd8 PPA. Add the PPA and install the app using the following commands:
sudo add-apt-repository ppa:nilarimogard/webupd8
sudo apt update
sudo apt install gnome-appfolders-manager

Arch Linux users can install GNOME AppFolders Manager via AUR.

For other Linux distributions, see the application installation page.

Report any bugs you may find @ GitHub.

Add applications to app folders using GNOME Software

Note that in my test, the instructions below did not work in Ubuntu 16.04 with GNOME 3.18 and GNOME Software 3.20 (no error was displayed, the appfolder simply wasn't created). It didn't work in Fedora 24 with GNOME 3.20 either, but it did work in Fedora 22 with GNOME 3.16.

Also, GNOME Software is not available in the official repositories for Ubuntu versions older than 16.04. So for Ubuntu and for GNOME versions in which this functionality is broken, use GNOME AppFolders Manager.

If you're using GNOME Software, you can easily add applications to app folders and create new app folders. To do this, launch GNOME Software, switch to the "Installed" tab and click the select button (top right):

GNOME Appfolders

Then, select the applications you want to add to a folder and click "Add to Folder":

GNOME Appfolders

And finally, simply select the app folder you want to add the applications to, or click "+" to add a new app folder, and click "Add":

GNOME Appfolders

In the same way, you can also remove or move applications from app folders.

Here's the result:

GNOME Appfolders