I love using Gnome as GUI, but the Applications folders never worked as they should, so I fixed them for myself. The following shell script will correct them and also sort some apps (mainly the ones I use) into categories that I consider more appropriate:

# Name (de)			desktop-directories file		dconf key-name		categories
#
# Büro				Office.directory			office			Office
# Grafik			Graphics.directory			graphics		Graphics
# Internet			Network.directory			internet		Network
# Multimedia			AudioVideo.directory			multimedia		AudioVideo
# Spiele			Game.directory				games			Game
# Zubehör			Utility.directory			accessories		Utility
# Hilfsprogramme		X-GNOME-Utilities.directory		utilities		X-GNOME-Utilities
# Systemwerkzeuge		System-Tools.directory			system-tools		System, Settings
# Sonstige			X-GNOME-Other.directory			other
#
# Entwicklung			Development.directory			programming		Development
# Bildung			Education.directory			education		Education
# Barrierefreiheit		Utility-Accessibility.directory		universal-access
# Internetanwendungen		X-GNOME-WebApplications.directory	web-applications
#
# Internet			webapps-webapps.directory		web
# Anwendungen			X-GNOME-Menu-Applications.directory	applications
# Diverses			X-GNOME-Sundry.directory		sundry
# Systemeinstellungen		X-GNOME-SystemSettings.directory	system-settings
#
########################################################################################################################

gsettings set org.gnome.desktop.app-folders folder-children "['office', 'graphics', 'internet', 'multimedia', 'games', 'accessories', 'utilities', 'system-tools', 'other', 'programming', 'education', 'universal-access', 'web-applications']"
# --------------------------------------------------
#	Deleting "YaST" and "Pardus" Folders if the exist in Gnome Vanilla
#--------------------------------------------------
gsettings reset org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/YaST/ name
gsettings reset org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/YaST/ translate
gsettings reset org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/YaST/ categories
gsettings reset org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/Pardus/ name
gsettings reset org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/Pardus/ translate
gsettings reset org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/Pardus/ categories
# --------------------------------------------------
#	Büro
#--------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/office/ name 'Office.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/office/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/office/ categories "['Office']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/office/ apps "['libreoffice-startcenter.desktop', 'libreoffice-base.desktop', 'libreoffice-calc.desktop', 'libreoffice-draw.desktop', 'libreoffice-impress.desktop', 'libreoffice-math.desktop', 'libreoffice-writer.desktop', 'org.gnome.Evolution.desktop', 'org.gnome.Contacts.desktop', 'org.gnome.Calendar.desktop', 'org.gnome.Evince.desktop', 'org.gnome.Papers.desktop', 'glabels-3.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/office/ excluded-apps "[]"
# --------------------------------------------------
#	Grafik
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/graphics/ name 'Graphics.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/graphics/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/graphics/ categories "['Graphics']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/graphics/ apps "['org.gnome.gThumb.desktop', 'org.gnome.Loupe.desktop', 'org.gnome.SimpleScan.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/graphics/ excluded-apps "['org.gnome.Evince.desktop', 'org.gnome.Papers.desktop', 'libreoffice-draw.desktop']"
# --------------------------------------------------
#	Internet
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/internet/ name 'Network.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/internet/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/internet/ categories "['Network']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/internet/ apps "['vivaldi-stable.desktop', 'signal-desktop.desktop', 'org.nickvision.tubeconverter.desktop', 'rustdesk.desktop', 'org.gnome.Geary.desktop', 'de.haeckerfelix.Fragments.desktop', 'org.gnome.Connections.desktop', 'org.gnome.Epiphany.desktop', 'vivaldi-snapshot.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/internet/ excluded-apps "['gwakeonlan.desktop', 'bvnc.desktop', 'bssh.desktop', 'steam.desktop']"
# --------------------------------------------------
#	Multimedia
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/multimedia/ name 'AudioVideo.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/multimedia/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/multimedia/ categories "['AudioVideo']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/multimedia/ apps "['vlc.desktop', 'io.github.celluloid_player.Celluloid.desktop', 'org.gnome.Totem.desktop', 'io.github.quodlibet.QuodLibet.desktop', 'brasero.desktop', 'com.obsproject.Studio.desktop', 'makemkv.desktop', 'org.bunkus.mkvtoolnix-gui.desktop', 'fr.handbrake.ghb.desktop', 'org.gnome.Snapshot.desktop', 'mpv.desktop', 'io.github.quodlibet.ExFalso.desktop', 'org.gnome.Showtime.desktop', 'org.gnome.Music.desktop', 'org.gnome.Decibels.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/multimedia/ excluded-apps "['qvidcap.desktop', 'qv4l2.desktop', 'org.nickvision.tubeconverter.desktop']"
# --------------------------------------------------
#	Spiele
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/games/ name 'Game.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/games/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/games/ categories "['Game']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/games/ apps "['steam.desktop', 'net.lutris.Lutris.desktop', 'Amiberry.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/games/ excluded-apps "[]"
# --------------------------------------------------
#	Zubehör
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/accessories/ name 'Utility.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/accessories/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/accessories/ categories "['Utility']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/accessories/ apps "['org.gnome.Nautilus.desktop', 'org.gnome.TextEditor.desktop', 'org.gnome.Calculator.desktop', 'org.gnome.Maps.desktop', 'org.gnome.clocks.desktop', 'org.gnome.Weather.desktop', 'org.gnome.Todo.desktop', 'org.gnome.Tour.desktop', 'org.gnome.Yelp.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/accessories/ excluded-apps "['com.mattjakeman.ExtensionManager.desktop', 'de.haeckerfelix.Fragments.desktop', 'vim.desktop', 'org.gnome.FileRoller.desktop', 'org.gnome.Extensions.desktop', 'dev.geopjr.Collision.desktop', 'org.gnome.Connections.desktop', 'org.gnome.Characters.desktop', 'org.gnome.Console.desktop', 'org.gnome.seahorse.Application.desktop', 'org.gnome.baobab.desktop', 'micro.desktop', 'org.gnome.font-viewer.desktop', 'ventoy.desktop', 'org.gnome.DiskUtility.desktop', 'org.gnome.tweaks.desktop', 'org.gnome.Logs.desktop', 'gnome-nettool.desktop']"
# --------------------------------------------------
#	Hilfsprogramme
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/utilities/ name 'X-GNOME-Utilities.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/utilities/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/utilities/ categories "['X-GNOME-Utilities']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/utilities/ apps "['org.gnome.DiskUtility.desktop', 'org.gnome.baobab.desktop', 'org.gnome.FileRoller.desktop', 'timeshift-gtk.desktop', 'grsync.desktop', 'org.gnome.seahorse.Application.desktop', 'gwakeonlan.desktop', 'dev.geopjr.Collision.desktop', 'ventoy.desktop', 'org.gnome.font-viewer.desktop', 'org.gnome.Characters.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/utilities/ excluded-apps "[]"
# --------------------------------------------------
#	Systemwerkzeuge
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/system-tools/ name 'System-Tools.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/system-tools/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/system-tools/ categories "['System', 'Settings']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/system-tools/ apps "['gparted.desktop', 'gufw.desktop', 'org.gnome.Console.desktop', 'org.gnome.Ptyxis.desktop', 'org.gnome.Boxes.desktop', 'ca.desrt.dconf-editor.desktop', 'virt-manager.desktop', 'org.manjaro.pamac.manager.desktop', 'com.mattjakeman.ExtensionManager.desktop', 'org.gnome.Extensions.desktop', 'org.gnome.tweaks.desktop', 'timeset.desktop', 'org.gnome.Firmware.desktop', 'org.gnome.SystemMonitor.desktop', 'org.gnome.Usage.desktop', 'gnome-nettool.desktop', 'org.gnome.Logs.desktop', 'btop.desktop', 'bssh.desktop', 'bvnc.desktop', 'avahi-discover.desktop', 'org.cachyos.KernelManager.desktop', 'cachyos-pi.desktop', 'org.cachyos.scx-manager.desktop', 'nvidia-settings.desktop', 'cups.desktop', 'system-config-printer.desktop', 'org.gnome.PowerStats.desktop', 'org.freedesktop.MalcontentControl.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/system-tools/ excluded-apps "['org.gnome.baobab.desktop', 'timeshift-gtk.desktop', 'grsync.desktop', 'cachyos-hello.desktop', 'org.gnome.Settings.desktop', 'dev.geopjr.Collision.desktop']"
# --------------------------------------------------
#	Entwicklung
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/programming/ name 'Development.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/programming/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/programming/ categories "['Development']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/programming/ apps "['cmake-gui.desktop', 'org.gnome.GHex.desktop', 'org.gnome.Meld.desktop', 'micro.desktop', 'vim.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/programming/ excluded-apps "['org.gnome.Boxes.desktop']"
# --------------------------------------------------
#	Bildung
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/education/ name 'Education.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/education/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/education/ categories "['Education']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/education/ apps "['anki.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/education/ excluded-apps "['libreoffice-math.desktop']"
# --------------------------------------------------
#	Sonstige
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/other/ name 'X-GNOME-Other.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/other/ translate true
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/other/ apps "['cachyos-hello.desktop', 'org.gnome.Settings.desktop', 'qvidcap.desktop', 'qv4l2.desktop']"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/other/ excluded-apps "[]"
# --------------------------------------------------
#	Barrierefreiheit
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/universal-access/ name 'Utility-Accessibility.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/universal-access/ translate true
# gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/universal-access/ apps "[]"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/universal-access/ excluded-apps "[]"
# --------------------------------------------------
#	Internetanwendungen
# --------------------------------------------------
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/web-applications/ name 'X-GNOME-WebApplications.directory'
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/web-applications/ translate true
# gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/web-applications/ apps "[]"
gsettings set org.gnome.desktop.app-folders.folder:/org/gnome/desktop/app-folders/folders/web-applications/ excluded-apps "[]"

Another important improvement would be the extension “gnome-shell-extension-legacy-theme-auto-switcher”, which is only available from the AUR. Would it be possible to add this extension to the official repositories as well? Together with the extension “adw-gtk-theme”, switching between dark and light themes would then work perfectly for older GNOME applications.

Since updating to Gnome 50, the Pamac update indicator icon no longer works. Simply adding the version number “50” to the following file fixes it:

/usr/share/gnome-shell/extensions/pamac-updates@manjaro.org/metadata.json