Shield Omarchy pacman transactions from desktop session teardown

Upgrading systemd runs its post_upgrade scriptlet mid-transaction, which
reexecs both the system manager and every user manager. When pacman runs
inside a user-session scope (the floating update terminal), that reexec
can SIGKILL it and abandon the transaction halfway, with packages
upgraded but none of the post-transaction hooks run.

Route every Omarchy-owned system mutation through a new hidden
omarchy-update-pacman helper that registers the transaction as a PID 1
scope via systemd-run, keeping it out of the user manager's cgroups.
System scopes survive the system manager's own reexec, and as a bonus the
transaction now also survives its terminal window closing. On unbooted
systems (the installer chroot) the helper runs pacman directly.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

bin/omarchy-channel-set

@@ -85,7 +85,7 @@ fi
 
 omarchy-refresh-pacman "$pacman_channel"
 # --ask 4 accepts omarchy <-> omarchy-dev replacement prompts without file overwrites.
-sudo env OMARCHY_UPDATE_PACMAN=1 pacman -S --needed --noconfirm --ask 4 "${packages[@]}"
+omarchy-update-pacman -S --needed --noconfirm --ask 4 "${packages[@]}"
 
 if [[ -z $dev_checkout ]]; then
   omarchy-dev-unlink --no-reboot

bin/omarchy-refresh-pacman

@@ -23,4 +23,4 @@ sudo cp -f "$OMARCHY_PATH/default/pacman/mirrorlist-$channel" /etc/pacman.d/mirr
 omarchy-hook pre-refresh-pacman
 
 # Reset all package DBs and then update
-sudo env OMARCHY_UPDATE_PACMAN=1 pacman -Syyuu --noconfirm
+omarchy-update-pacman -Syyuu --noconfirm

bin/omarchy-reinstall-pkgs

@@ -11,8 +11,8 @@ set -e
 omarchy-refresh-pacman
 
 # Downgrade any packages to the stable setup
-sudo env OMARCHY_UPDATE_PACMAN=1 pacman -Suu --noconfirm
+omarchy-update-pacman -Suu --noconfirm
 
 # Ensure all packages are installed
 mapfile -t packages < <(grep -v '^#' "$OMARCHY_PATH/install/omarchy-base.packages" | grep -v '^$')
-sudo env OMARCHY_UPDATE_PACMAN=1 pacman -Syu --noconfirm --needed "${packages[@]}"
+omarchy-update-pacman -Syu --noconfirm --needed "${packages[@]}"

bin/omarchy-update-pacman

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# omarchy:summary=Run a pacman transaction for the Omarchy update flow, shielded from desktop session teardown.
+# omarchy:args=<pacman-args>
+# omarchy:hidden=true
+# omarchy:requires-sudo=true
+
+# Upgrading systemd runs its post_upgrade scriptlet mid-transaction, which
+# reexecs both the system manager and every user manager. A pacman running
+# inside a user-session scope can be SIGKILLed by that reexec, abandoning the
+# transaction halfway. Registering the transaction as a PID 1 scope keeps it
+# out of the user manager's cgroups entirely, and system scopes survive the
+# system manager's own reexec.
+scope=()
+if [[ -d /run/systemd/system && ! -L /run/systemd/system ]]; then
+  scope=(systemd-run --scope --quiet --collect)
+fi
+
+# LC_ALL passes through so callers that parse pacman's stderr can pin the locale.
+env_args=(OMARCHY_UPDATE_PACMAN=1)
+if [[ -n ${LC_ALL:-} ]]; then
+  env_args+=(LC_ALL="$LC_ALL")
+fi
+
+exec sudo env "${env_args[@]}" "${scope[@]}" pacman "$@"

bin/omarchy-update-system-pkgs

@@ -10,7 +10,7 @@ set -e
 # a stream, because an upgrade without --noconfirm prompts on stderr. The
 # handler has already said why, so no heading here either.
 if [[ ${OMARCHY_UPDATE_CONFLICT:-} == 1 && ${OMARCHY_UPDATE_INTERACTIVE:-} == 1 ]]; then
-  exec sudo env OMARCHY_UPDATE_PACMAN=1 pacman -Syu --overwrite '/usr/share/omarchy/*'
+  exec omarchy-update-pacman -Syu --overwrite '/usr/share/omarchy/*'
 fi
 
 echo -e "\e[32m\nUpdate system packages\e[0m"
@@ -23,7 +23,7 @@ trap 'rm -f "$errors"' EXIT
 #
 # Progress bars stay on stdout. Errors are on stderr, kept for the conflict
 # handler below; LC_ALL=C is what keeps them parseable in any locale.
-if sudo env LC_ALL=C OMARCHY_UPDATE_PACMAN=1 pacman -Syu --noconfirm \
+if LC_ALL=C omarchy-update-pacman -Syu --noconfirm \
   --overwrite '/usr/share/omarchy/*' 2>"$errors"; then
   cat "$errors" >&2
   exit 0

docs/update-process.md

@@ -82,13 +82,18 @@ Omarchy update command, the hook exits non-zero with `AbortOnFail`, which stops
 the transaction before packages are changed.
 
 `omarchy-update-system-pkgs`, `omarchy-refresh-pacman`, `omarchy-reinstall-pkgs`,
-`omarchy-channel-set`, and the v4 upgrader run pacman through:
+and `omarchy-channel-set` run pacman through the hidden `omarchy-update-pacman`
+helper (the v4 upgrader sets `OMARCHY_UPDATE_PACMAN=1` directly):
 
 ```bash
-env OMARCHY_UPDATE_PACMAN=1 pacman ...
+sudo env OMARCHY_UPDATE_PACMAN=1 systemd-run --scope --quiet --collect pacman ...
 ```
 
-so the guard allows Omarchy-owned update flows. A user can intentionally bypass
+so the guard allows Omarchy-owned update flows. The `systemd-run --scope`
+wrapper registers the transaction as a PID 1 scope: upgrading systemd reexecs
+the system and user managers mid-transaction, and a pacman left inside a
+user-session scope can be SIGKILLed by that reexec. On unbooted systems (such
+as the installer chroot) the helper runs pacman directly. A user can intentionally bypass
 the guard with:
 
 ```bash
@@ -272,12 +277,13 @@ 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 `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` | Runs `omarchy-update-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`. |
 | `omarchy-update-pacman-guard` | ALPM pre-transaction guard that aborts direct `pacman -Syu` style upgrades unless Omarchy set `OMARCHY_UPDATE_PACMAN=1` or the user explicitly set `OMARCHY_ALLOW_DIRECT_PACMAN=1`. | **Keep internal/hidden.** This is what nudges users back to `omarchy update`. |
+| `omarchy-update-pacman` | Hidden helper that runs a guard-approved pacman transaction as a PID 1 scope (`systemd-run --scope`) so a mid-transaction systemd reexec cannot kill it; runs pacman directly when not booted under systemd. | **Keep internal/hidden.** Single place that owns how Omarchy invokes pacman for system mutation. |
 | `omarchy-migrate-notify` | Internal login-time notification helper. Uses `omarchy-migrate --pending` and shows a notification only when this user has pending migrations. | **Keep internal/hidden.** Clear name now that the public command is `omarchy-migrate`. |
 | `omarchy-update-user-notify` | Hidden compatibility wrapper for `omarchy-migrate-notify`. | **Temporary.** Keep only for old callers. |
 | `omarchy-update-available` | Update checker for shell widget and post-update refresh. | **Keep.** Could eventually be renamed `omarchy-update-check`, but current name matches widget semantics. |

test/shell.d/channel-test.sh

@@ -31,6 +31,12 @@ for arg in "$@"; do printf "\t%s" "$arg" >>"$OMARCHY_CHANNEL_TEST_LOG"; done
 printf "\n" >>"$OMARCHY_CHANNEL_TEST_LOG"
 '
 
+write_stub omarchy-update-pacman '#!/bin/bash
+printf "update-pacman" >>"$OMARCHY_CHANNEL_TEST_LOG"
+for arg in "$@"; do printf "\t%s" "$arg" >>"$OMARCHY_CHANNEL_TEST_LOG"; done
+printf "\n" >>"$OMARCHY_CHANNEL_TEST_LOG"
+'
+
 write_stub omarchy-dev-unlink '#!/bin/bash
 printf "unlink" >>"$OMARCHY_CHANNEL_TEST_LOG"
 for arg in "$@"; do printf "\t%s" "$arg" >>"$OMARCHY_CHANNEL_TEST_LOG"; done
@@ -106,7 +112,7 @@ assert_log_line() {
 
 run_channel stable
 assert_log_line $'refresh\tstable' "stable refreshes the stable pacman channel"
-assert_log_line $'sudo\tenv\tOMARCHY_UPDATE_PACMAN=1\tpacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy\tomarchy-settings' "stable installs stable Omarchy packages"
+assert_log_line $'update-pacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy\tomarchy-settings' "stable installs stable Omarchy packages"
 assert_log_line $'unlink\t--no-reboot' "stable restores the package-backed Omarchy path without an early reboot prompt"
 assert_log_line $'update\t-y\tOMARCHY_PATH=/usr/share/omarchy' "stable runs the normal update pipeline from the package-backed path"
 if grep -q $'^state\tset\treboot-required$' "$log_file"; then
@@ -116,17 +122,17 @@ pass "stable does not require reboot when already package-backed"
 
 run_channel rc
 assert_log_line $'refresh\trc' "rc refreshes the rc pacman channel"
-assert_log_line $'sudo\tenv\tOMARCHY_UPDATE_PACMAN=1\tpacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy\tomarchy-settings' "rc installs rc Omarchy packages"
+assert_log_line $'update-pacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy\tomarchy-settings' "rc installs rc Omarchy packages"
 assert_log_line $'unlink\t--no-reboot' "rc restores the package-backed Omarchy path without an early reboot prompt"
 assert_log_line $'update\t-y\tOMARCHY_PATH=/usr/share/omarchy' "rc runs the normal update pipeline from the package-backed path"
 
 OMARCHY_TEST_PATH="$ROOT" run_channel edge
 assert_log_line $'refresh\tedge' "edge refreshes the edge pacman channel"
-assert_log_line $'sudo\tenv\tOMARCHY_UPDATE_PACMAN=1\tpacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy-dev\tomarchy-settings-dev' "edge installs development Omarchy packages"
+assert_log_line $'update-pacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy-dev\tomarchy-settings-dev' "edge installs development Omarchy packages"
 assert_log_line $'unlink\t--no-reboot' "edge unlinks dev without an early reboot prompt"
 assert_log_line $'state\tset\treboot-required' "edge marks reboot required when leaving dev"
 assert_log_line $'update\t-y\tOMARCHY_PATH=/usr/share/omarchy' "edge runs the normal update pipeline from the package-backed path"
-[[ $(grep -E '^(unlink|state|update)' "$log_file") == $'unlink\t--no-reboot\nstate\tset\treboot-required\nupdate\t-y\tOMARCHY_PATH=/usr/share/omarchy' ]] ||
+[[ $(grep -E $'^(unlink|state|update)\t' "$log_file") == $'unlink\t--no-reboot\nstate\tset\treboot-required\nupdate\t-y\tOMARCHY_PATH=/usr/share/omarchy' ]] ||
   fail "edge defers the reboot prompt until the update restart stage" "$(cat "$log_file")"
 pass "edge defers the reboot prompt until the update restart stage"
 
@@ -146,12 +152,12 @@ rmdir "$checkout"
 run_channel dev
 assert_log_line $'gum\tconfirm\t--default=false\tSwitch to dev channel?' "dev asks for confirmation"
 assert_log_line $'refresh\tedge' "dev refreshes the edge pacman channel"
-assert_log_line $'sudo\tenv\tOMARCHY_UPDATE_PACMAN=1\tpacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy-dev\tomarchy-settings-dev' "dev installs development Omarchy packages"
+assert_log_line $'update-pacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy-dev\tomarchy-settings-dev' "dev installs development Omarchy packages"
 assert_log_line $'git\tclone\thttps://github.com/basecamp/omarchy.git\t'"$checkout" "dev clones the source checkout to ~/omarchy"
 assert_log_line $'link\t'"$checkout"$'\t--no-reboot' "dev links ~/omarchy without an early reboot prompt"
 assert_log_line $'state\tset\treboot-required' "dev defers the reboot prompt to the update pipeline"
 assert_log_line $'update\t-y\tOMARCHY_PATH='"$checkout" "dev runs the normal update pipeline from the source checkout"
-[[ $(grep -E '^(git|link|state|refresh|sudo|update)' "$log_file") == $'git\tclone\thttps://github.com/basecamp/omarchy.git\t'"$checkout"$'\nlink\t'"$checkout"$'\t--no-reboot\nstate\tset\treboot-required\nrefresh\tedge\nsudo\tenv\tOMARCHY_UPDATE_PACMAN=1\tpacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy-dev\tomarchy-settings-dev\nupdate\t-y\tOMARCHY_PATH='"$checkout" ]] ||
+[[ $(grep -E '^(git|link|state|refresh|sudo|update)' "$log_file") == $'git\tclone\thttps://github.com/basecamp/omarchy.git\t'"$checkout"$'\nlink\t'"$checkout"$'\t--no-reboot\nstate\tset\treboot-required\nrefresh\tedge\nupdate-pacman\t-S\t--needed\t--noconfirm\t--ask\t4\tomarchy-dev\tomarchy-settings-dev\nupdate\t-y\tOMARCHY_PATH='"$checkout" ]] ||
   fail "dev activates the checkout before changing or updating packages" "$(cat "$log_file")"
 pass "dev activates the checkout before changing or updating packages"