Как обновить все пакеты, установленные через Homebrew, после большого обновления операционной системы

У меня была рабочая конфигурация со старой версией Mac, и я сделал несколько резервных копий в облаке. Недавно я приобрел новый компьютер и восстановил всё, что смог, из облака. Думаю, это включало некоторые настройки homebrew. Теперь моя установка homebrew не работает. Когда я пытаюсь обновить что-то, сталкиваюсь с отказом доступа, например, Error: Permission denied @ apply2files - /usr/local/lib/docker/cli-plugins. Как лучше всего это исправить? Я полностью готов удалить все пакеты, установленные с помощью старого подхода (sudo).

Пример вывода:

brew upgrade python3

Error: python3 not installed
==> `brew cleanup` has not been run in the last 30 days, running now...
Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/aom--3.10.0... (4.4MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/c-ares--1.34.3... (298.5KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/ca-certificates--2024-09-24... (132.6KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/ca-certificates--2024-11-26... (133.8KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/cfitsio--4.4.1... (1.1MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/cmake--3.31.0... (17.9MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/doxygen--1.12.0... (5.6MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/gettext--0.22.5... (8.8MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/gettext--0.23... (9.0MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/gh--2.61.0... (12.3MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/git-gui--2.47.0_1... (480.8KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/glib--2.82.2... (8.2MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/gnupg--2.4.6... (5.2MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/imagemagick--7.1.1-40... (10.6MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/ipfs--0.31.0... (40.0MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/libheif--1.19.3... (2.0MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/libomp--19.1.3... (573KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/libtool--2.5.3... (1MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/libxau--1.0.11... (28.2KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/libxrender--0.9.11... (51.7KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/neovim--0.10.2_1... (8.7MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/nss--3.106... (6.0MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/open-mpi--5.0.5... (16.1MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/openjpeg--2.5.2... (2.1MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/pango--1.54.0... (786.3KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/pixman--0.44.0... (238KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/pkgconf--2.3.0.tar.xz... (308.8KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/pkgconf--2.3.0_1... (105KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/poppler--24.11.0... (8.9MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/[email protected]... (18.7MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/[email protected]_2... (121.4MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/sqlite--3.47.0... (2.3MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/[email protected]... (8.5MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/webp--1.4.0... (995.7KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/x265--4.0_1... (5.2MB)
==> Автоудаление 4 ненужных формул:
adns
assimp
brotli
dbus
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/luajit--2.1.1727870382... (856.7KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/jpeg-xl--0.11.0_1... (17.0MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/libdeflate--1.22... (120.6KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/make--4.4.1... (422.4KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/tree-sitter--0.24.4... (5.5MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/jpeg-turbo--3.0.4... (1.3MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/[email protected]_1... (15.4MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/gpgme--1.24.0_1... (1.3MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/pmix--5.0.3... (4MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/Cask/font-fira-code-nerd-font--3.2.1.zip... (23.8MB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/api-source/Homebrew/homebrew-core/c18289230a6c0135711d027339ef1a1a8a8f5296/Formula/pkgconf.rb... (4KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/api-source/Homebrew/homebrew-core/e6ff20365349a90c5c4e05fccfe8631ce6f39491/Formula/gcc.rb... (10.8KB)
Removing: /Users/dzenan.zukic/Library/Caches/Homebrew/api-source/Homebrew/homebrew-core/e6ff20365349a90c5c4e05fccfe8631ce6f39491/Formula/[email protected]... (22.4KB)
Removing: /Users/dzenan.zukic/Library/Logs/Homebrew/openssl@3... (64B)
Removing: /Users/dzenan.zukic/Library/Logs/Homebrew/ca-certificates... (64B)
Error: Permission denied @ apply2files - /usr/local/lib/docker/cli-plugins

sudo brew upgrade python3

Error: Running Homebrew as root is extremely dangerous and no longer supported.
As Homebrew does not drop privileges on installation you would be giving all
build scripts full access to your system.