I chose to install Homebrew and let it due the heavy lifting for adding packages.
Following the Homebrew installation run:
And possibly fix the items mentioned in brew doctor. Some do not need fixing and are only warnings.
After that simply run:
brew update && brew upgrade
But see the add-on below.
The next suggested addition is Cask. Cask extends Homebrew to allow managing the installation of graphical applications using the command line.
To get the add-on Cask run:
brew tap caskroom/cask
Then the way to update is to simply run:
brew update; brew cleanup; brew cask cleanup