Installing and updating system packages and applications is much easier under macOS using the CLI if you use homebrew and the Mac App Store Command Line Interface, then you can just:

update all the system components,

$ softwareupdate -i

update all the apps installed via the App Store and

$ mas upgrade

update everything installed via brew and cleans up the otherwise always growing cache folder

$ brew upgrade --cleanup

Now you have a completely up-to-date machine. I added this with some additional upgrade commands to my .zshrc to have a shell function for it, so I can just type $ upgrade:

upgrade() {
	# updates system updates, mac app store, homebrew packages and ruby gems
	softwareupdate -i
	mas upgrade
	brew upgrade
	brew cleanup -s
	for app in `brew cask outdated --quiet`; do brew cask install --force $app; done
	brew cask cleanup
	gem update --no-document
	gem cleanup
outdated() {
	softwareupdate -l
	mas outdated
	brew outdated
	brew cask outdated
	gem outdated