Sync macOS bootstrap settings

[keito4]

Summary

• Pull the PR branch onto the latest main and keep the macOS host config aligned with the current machine state.
• Remove Karabiner from managed config and require Kanary for keyboard remapping through the nix-darwin system check.
• Add Agent Deck / Stream Deck development dependencies: Agent Deck tap/formula, Stream Deck cask, Node.js 24, shell PATH setup, and the local agent-deck command symlink.
• Allow Cmux automation control so Codex and other local automation can open workspaces from outside Cmux.
• Keep Google Japanese Input sources, Dock cleanup, Chrome, cmux, and bootstrap reliability updates in config.

Verification

• npm test -- --runInBand
• npx jest test/nix-darwin-config.test.js --runInBand
• pre-commit format:check, lint, and test
• /run/current-system/sw/bin/nix flake check /Users/keito/develop/github.com/keito4/config/nix --extra-experimental-features nix-command --extra-experimental-features flakes

Local setup notes

• Removed Homebrew-managed Karabiner-Elements from this Mac.
• Installed signed/notarized Kanary.app into /Applications/Kanary.app and launched it for first-run permissions.
• Applied Cmux socketControlMode=automation locally, then opened Agent Deck and agentdeck-streamdeck-plugin in Cmux.
• Opened /Users/keito/Documents/Codex/2026-06-28/c/outputs/apply-latest-config.sh in Terminal so the final darwin-rebuild switch can run with your password.

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Review details

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 62b833ee-99ae-425c-b0e7-86e5a85b48bf

📥 Commits

Reviewing files that changed from the base of the PR and between 1a94e7b and d44fa1d.

📒 Files selected for processing (9)

• docs/adr/0016-use-kanary-for-keyboard-remapping.md
• nix/flake.nix
• nix/home/agent-commands.nix
• nix/home/dotfiles.nix
• nix/home/packages.nix
• nix/home/zsh.nix
• nix/hosts/darwin/default.nix
• nix/modules/homebrew.nix
• test/nix-darwin-config.test.js

📝 Walkthrough

Walkthrough

Introduces a configRoot flake binding propagated to Home Manager modules to replace relative ../../ paths. Updates Homebrew cleanup mode, taps, brews, casks, and MAS apps. Adds Dock persistent-apps and Japanese input source preferences to macOS defaults. Adds Homebrew shell init to zsh and nodejs_24 to packages. Updates ADR 0016 and test assertions for Kanary.

Bootstrap and config modernisation

Layer / File(s)	Summary
configRoot propagation nix/flake.nix, nix/home/dotfiles.nix, nix/home/agent-commands.nix	Adds configRoot = ../. in flake, passes it via extraSpecialArgs, and replaces all ../../ relative source paths in dotfiles and agent-commands modules with configRoot + /... expressions. Also sets hostname to keitonoMacBook-Pro and adds backupFileExtension.
Homebrew updates nix/modules/homebrew.nix	Changes cleanup from "zap" to "none", adds asheshgoplani/tap and agent-deck brew, adds elgato-stream-deck and google-chrome casks, removes mattermost and messenger, and updates masApps (Keynote ID changed, Numbers/Pages/Prime Video removed).
macOS system defaults nix/hosts/darwin/default.nix	Adds persistent-apps and persistent-others Dock entries and a CustomUserPreferences block for com.apple.HIToolbox with AppleEnabledInputSources and AppleSelectedInputSources for Japanese input sources.
Zsh Homebrew init and nodejs_24 nix/home/zsh.nix, nix/home/packages.nix	Inserts brew shellenv evaluation into the zsh initContent for both Apple Silicon and Intel paths, and adds nodejs_24 to home.packages.
Kanary ADR and test updates docs/adr/0016-use-kanary-for-keyboard-remapping.md, test/nix-darwin-config.test.js	Rewrites ADR decision and consequences to specify Karabiner removal, Kanary manual install, and early nix-darwin failure on missing Kanary.app. Updates test assertions to match new module inclusions, cask list, ADR wording, and configRoot-based collector path.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related issues

• Improve macOS bootstrap reliability for nix-darwin and Homebrew setup #895: This PR directly addresses the bootstrap fixes described in that issue, including hostname update, backupFileExtension, cleanup = "none", cask cleanup, and configRoot-based path fixes.

Possibly related PRs

• keito4/config#874: Overlaps on test/nix-darwin-config.test.js changes that exclude karabiner and rework Kanary-vs-Karabiner assertions.
• keito4/config#893: Directly related Kanary migration work updating ADR 0016, nix/modules/kanary.nix, and the Kanary.app system-check behavior.

Poem

🐇 Hop hop, the paths are now configRoot-based,
No more ../../ trails to be chased!
Karabiner's gone, Kanary's here to stay,
Homebrew's cleaned up in a tidier way.
The rabbit rejoices — new defaults in place! 🎉

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/sync-macos-bootstrap-config

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[github-actions]

🎉 This PR is included in version 1.119.0 🎉

The release is available on GitHub release

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