Complete command-scoped authentication across update phases

docs/update-process.md

@@ -26,7 +26,7 @@ The design goal is:
 | `~/.local/state/omarchy/current/` | user | Generated active theme, selected theme name, and current background symlink. |
 | `~/.local/state/omarchy/migrations/` | user | Per-user migration markers. |
 | `~/.local/state/omarchy/reboot-required` | user | Optional reboot marker checked by `omarchy-update-restart`. |
-| `~/.local/state/omarchy/restart-*-required` | user | Optional allowlisted service/app restart markers checked by `omarchy-update-restart`. Marker names select fixed commands from the system-authorized Omarchy tree; they are not resolved through caller `PATH`. The shell needs no marker: it is restarted unconditionally after every update. |
+| `~/.local/state/omarchy/restart-*-required` | user | Optional service/app restart markers checked by `omarchy-update-restart`. The shell needs no marker: it is restarted unconditionally after every update. |
 
 ## Migration layout
 
@@ -56,12 +56,7 @@ privileged work should invoke the appropriate helper or privilege prompt.
 Migrations must be idempotent; if one user already applied a machine-wide repair,
 the migration should no-op for other users.
 
-The runner derives the migration source from root-owned `/etc/omarchy.conf`,
-starts from a cold sudo timestamp, and routes migration sudo calls through
-`sudo --no-update`. Historical migrations are strictly ordered and can mix
-user-controlled tools or theme hooks with later privileged repairs; no-update
-authentication lets those repairs run without publishing a credential a
-detached earlier process could reuse.
+When invoked by the update, migrations inherit its cold credential state and no-update sudo wrapper. The standalone migration runner has its own security changes in the migration-boundary PR; this update change does not establish that standalone boundary. Historical migrations remain strictly ordered.
 
 For watchers and diagnostics, `omarchy-migrate --pending` prints pending
 migration names and exits `0` when any are pending. When no migrations are
@@ -149,9 +144,9 @@ omarchy-update
 
 Important behavior:
 
-- `omarchy update` derives its source tree from root-owned `/etc/omarchy.conf`, or the root-owned `/usr/share/omarchy` default when that file is absent. It does not trust inherited `OMARCHY_PATH` or caller `PATH` for the privileged phase.
+- `omarchy update` uses the session’s `OMARCHY_PATH` and a fixed command search path for its system phases. User PATH is restored behind the sudo wrapper for hooks and mise.
 - Mixed-trust update entrypoints start Bash in privileged mode, discard `BASH_ENV`, `ENV`, and exported-function records before launching helpers, and reject an ordinary `bash path/to/command` invocation. Run them as executables (normally through the `omarchy` CLI); `/usr/bin/bash -p path/to/command` is the explicit interpreter form. This keeps shell startup injection from replacing the no-update sudo boundary.
-- In dev-link mode, the root-owned configuration is the explicit authorization for the user-writable checkout. `omarchy update` fast-forwards that authorized checkout from its configured upstream before changing system packages or running migrations.
+- In dev-link mode, `omarchy update` fast-forwards the active checkout from its configured upstream before changing system packages or running migrations.
 - Migrations remain in chronological order even though historical entries mix user-controlled code with later privileged repairs. Before entering that mixed-trust tail, Omarchy invalidates its timestamp and forces every later sudo call—including AUR's configurable sudo command—to use `--no-update`; prompts authorize one command without publishing a reusable timestamp. Yay's credential loop is disabled for the update.
 - User-controlled post-update hooks and mise tools run only after every sudo-capable update stage. Omarchy invalidates its sudo timestamp before each boundary and on every exit; detached children therefore have no later reusable update authorization to wait for.
 - `-y` exports `OMARCHY_UPDATE_UNATTENDED=1` — a promise not to ask anything.
@@ -292,7 +287,8 @@ scripts.
 | `omarchy-update-confirm` | Gum confirmation copy for `omarchy update`. | **Question.** Could be inlined into `omarchy-update`; separate file only helps keep copy isolated. |
 | `omarchy-update-dev` | Fast-forwards the active dev-linked checkout from its configured upstream; no-ops for package-backed installs. | **Keep.** Runs before package updates so a checkout conflict stops the update before system mutation. |
 | `omarchy-update-keyring` | Ensures Omarchy keyring and Arch keyring are current before the main transaction. | **Keep, but review.** It uses targeted `pacman -Sy` for keyring bootstrapping; acceptable for this special case but should remain tightly scoped. |
-| `omarchy-update-system-pkgs` | Runs the ordinary guarded `pacman -Syu --noconfirm`. Package-vs-package conflicts may be retried interactively with `pacman -Su`; filesystem conflicts fail closed without moving, restoring, quarantining, or broadly overwriting live paths. The production Quattro transition performs the sole explicit settings-package takeover with `--overwrite='*'`; all later production and developer package transactions obey Pacman's ownership checks. | **Keep.** Small leaf command with no generic privileged conflict handler. |
+| `omarchy-update-system-pkgs` | Runs `sudo env OMARCHY_UPDATE_PACMAN=1 pacman -Syu --noconfirm` with `--overwrite '/usr/share/omarchy/*'`, capturing stderr to a report file; on failure it execs `omarchy-update-system-pkgs-when-conflicted`. | **Keep for now.** Small leaf command, clear/testable. |
+| `omarchy-update-system-pkgs-when-conflicted` | Hidden conflict handler: quarantines unowned conflicting files under `/var/lib/omarchy/replaced`, retries the upgrade once, restores files the upgrade didn't claim, and hands package-vs-package conflicts to an interactive pacman run (never under `-y`). | **Keep internal/hidden.** Keeps conflict recovery out of the happy path. |
 | `omarchy-update-pkg-prune` | Trims the pacman cache to two versions per package (`paccache -rk2`) before the snapshot, keeping the offline downgrade path while capping snapshot growth. | **Keep internal/hidden.** |
 | `omarchy-update-requires-free-space` | Aborts the update below a 10 GiB free-space threshold on `/`; silently skipped when free space cannot be determined; `OMARCHY_UPDATE_FORCE=1` bypasses. | **Keep internal/hidden.** |
 | `omarchy-migrate` | Public migration command. Waits for pacman, then runs all pending migrations for the current user. Supports `--pending`. | **Keep.** This replaces the discarded `omarchy-update-user-finalize` name and no longer needs `--force`. |
@@ -304,7 +300,7 @@ scripts.
 | `omarchy-update-mise` | Runs `MISE_MINIMUM_RELEASE_AGE=0 mise up` for mise-managed tools — the override of mise's release-age cooldown is the point. | **Keep.** Mise-managed tools are intentionally part of the blessed update path. |
 | `omarchy-update-orphan-pkgs` | Lists orphans and prompts before removal; noninteractive mode never removes. | **Keep for now.** Safe because it is prompt-only. |
 | `omarchy-update-analyze-logs` | Scans `/tmp/omarchy-update.log` for known failure patterns, currently initramfs generation. | **Keep/expand.** Useful safety net; should grow only for high-signal checks. |
-| `omarchy-update-restart` | Restarts allowlisted components selected by `restart-*-required` markers, always restarts the shell, and prompts for reboot after kernel/Hyprland updates. Internal phase flags let the update finish sudo-capable restarts before user hooks and defer only the unprivileged reboot prompt. | **Keep.** Important final step; may eventually include service-restart checks. |
+| `omarchy-update-restart` | Restarts components selected by `restart-*-required` markers, always restarts the shell, and prompts for reboot after kernel/Hyprland updates. Internal phase flags let the update finish sudo-capable restarts before user hooks and defer only the unprivileged reboot prompt. | **Keep.** Important final step; may eventually include service-restart checks. |
 | `omarchy-update-firmware` | Manual firmware update command using fwupd. Not part of the normal update pipeline. | **Keep separate.** Firmware is not a routine system update step. |
 | `omarchy-update-time` | Restarts `systemd-timesyncd`. | **Question.** Not really an update command. Consider renaming/moving under system/time maintenance. |