My current somewhat hacky solution for uninstalling items from a Brewfile involves using the trash utility to delete the MAS apps, so there will be a prompt for password. (Perhaps my implementation is a bit strange… learning Bash.)

trash_file () {
  local item=$1
  if [[ -d $item || -f $item ]]; then
    echo "Trashing $item"
    if test ! $(which trash); then
      brew install trash
      trash "$item"
      brew uninstall trash
    else
      trash "$item"
    fi
  fi
}

# Uninstall packages from manifests, named Brewfile
local manifest=Brewfile #local, because this is excerpt from a function
if [[ -f $manifest ]]; then
  echo "Checking for manifest packages to remove."
  cat "$manifest" | tr -s " " | # squash spaces and pass to loop
  {
    while read -r line; do
      line=${line%,*} # keep up to first comma
      line=${line//\'/} # hope package names don't contain single quotes
      line=${line//\"/} # hope package names don't contain double quotes
      case $line in
        '#'* ) ;; # ignore comments
        'brew '* ) brew uninstall "${line#brew }" ;;
        'cask '* ) brew cask uninstall "${line#cask }" ;;
        'mas '*  ) trash_file "/Applications/${line#mas }.app" ;;
        * ) echo "Unsure how to handle line: $line" ;;
      esac
    done
  }
fi

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Add `uninstall` #81