#1371 make upgrade

• refactor: reorganize Makefile targets and add nix-daemon-upgrade
• refactor: reorganize test and development targets in Makefile
• refactor: consolidate update target and sync commands in Makefile
• refactor: remove redundant target from upgrade command in Makefile
• refactor: rename upgrade targets in Makefile for consistency
• refactor: rename update and upgrade targets in Makefile for clarity
• refactor: add upgrade-dev target for Nix dev shell upgrades

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Summary by cubic

Standardized Makefile targets and streamlined the upgrade flow. make upgrade now runs sync then update, adds a bun-update target, improves macOS Nix daemon checks, and bumps JS deps.

• Refactors

  • sync includes dotagents-sync, codex-security-sync, rtk-rewrite-sync. update runs nix-update, overlays-update, neovim-update, llm-update, gitalias-update; bun-update is available separately.
  • Renamed targets for consistency (nix-flake-update, overlays-update, neovim-update, llm-update, gitalias-update); neovim-sync depends on neovim-update; added devenv-cli; renamed launchctl agent to brew-updater.
  • nix-update now runs nix-connect + nix-daemon-update + nix-flake-update; macOS nix-connect skips restarts when reachable and supports Determinate/NixOS plists.
  • CI: checkout submodules in upgrade.yml; tmux-bridge.sh adds shellcheck-disable hints; updated package.json and regenerated bun.lock.

• Migration

  • Use the new *-update target names; old *-upgrade targets are replaced.
  • Use make upgrade-dev when upgrading inside the Nix dev shell.
  • update-local-binaries was removed; run ./scripts/update-local-binaries.sh directly if needed.