Esses dias navegando na net encontrei essa dica no blog Linux dicas e suporte.
Então para ficar registrado para posteridade, caso o site saia do ar, vou colocar aqui os passos.

No terminal do linux, digite os comandos abaixo:

Adicionando as Categorias

gsettings set org.gnome.desktop.app-folders folder-children "['accessories', 'chrome-apps', 'games', 'graphics', 'internet', 'office', 'programming', 'science', 'sound---video', 'system-tools', 'universal-access', 'wine', 'education']"

Adicionando Pastas

No terminal de o comando abaixo para o seu idioma, para adicionar a pasta Acessórios.

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/accessories/ name "Accessories" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/accessories/ categories "['Utility']"

Adicionando Games

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/games/ name "Games" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/games/ categories "['Game']"

Adicionando Gráficos

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/graphics/ name "Graphics" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/graphics/ categories "['Graphics']"

Adicionando Internet

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/internet/ name "Internet" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/internet/ categories "['Network', 'WebBrowser', 'Email']"

Adicionando Escritório

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/office/ name "Office" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/office/ categories "['Office']"

Adicionando Programação

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/programming/ name "Programming" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/programming/ categories "['Development']"

Adicionando Ciência

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/science/ name "Science" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/science/ categories "['Science']"

Adicionando Áudio e Vídeo

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/sound---video/ name "Sound & Video" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/sound---video/ categories "['AudioVideo', 'Audio', 'Video']"

Adicionando Ferramentas do sistema

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/system-tools/ name "System Tools" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/system-tools/ categories "['System', 'Settings']"

Adicionando Acessibilidade

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/universal-access/ name "Universal Access" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/universal-access/ categories "['Accessibility']"

Adicionando Wine (só aparece com o wine instalado)

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/wine/ name "Wine" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/wine/ categories "['Wine', 'X-Wine', 'Wine-Programs-Accessories']"

Adicionando Educação

gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/education/ name "Education" ; gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/education/ categories "['Education']"

No final, o seu menu do Gnome estará como o da imagem no inicio do post.

Caso queira voltar ao normal, basta digitar o código abaixo no seu terminal:

gsettings set org.gnome.desktop.app-folders folder-children “[]”