I use Homebrew to install allmost all of my macOS apps, both CLI tools and applications ending up in
/Applications
.
I keep track of what I have installed using a Brewfile. This allows me to reinstall a machine very fast.
Please submit MuteDeck to Homebrew as a Cask in https://github.com/homebrew/homebrew-cask or create a separate cask repository in your own Github organization.