Brew Doctor and Linking, and In-App Software Updater

[yordis]

Output of brew config

HOMEBREW_VERSION: 4.3.24
ORIGIN: https://github.com/Homebrew/brew
HEAD: 916044581862c32fc2365e8e9ff0b1507a98925e
Last commit: 4 days ago
Core tap JSON: 26 Sep 17:33 UTC
Core cask tap JSON: 26 Sep 17:33 UTC
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: code --wait
HOMEBREW_MAKE_JOBS: 12
Homebrew Ruby: 3.3.4 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.4_1/bin/ruby
CPU: dodeca-core 64-bit kabylake
Clang: 15.0.0 build 1500
Git: 2.46.2 => /usr/local/bin/git
Curl: 8.6.0 => /usr/bin/curl
macOS: 14.5-x86_64
CLT: 15.3.0.0.1.1708646388
Xcode: 15.4

Output of brew doctor

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  zed
  gnupg

Description of issue

How do I deal with the situation where some apps get updated using the In-App Software Updater?

brew Doctor asked me to link it. Ideally, Brew would play more in a friendly manner with the In-App Software Updater.

[p-linnane]

brew Doctor asked me to link it. Ideally, Brew would play more in a friendly manner with the In-App Software Updater.

That's not what that message is saying. It's saying you have 2 things installed that are not correctly linked.

brew only knows about the things it does. If you want to use in-app updates, then you should expect brew will not know about them. If you want to update via Homebrew, you can run brew upgrade --greedy to upgrade casks that have in-app updaters.

[yordis]

I was not aware of --greedy flag, thank you so much!