pacnew and pacsave files after an Omarchy update

Checked on 4.0.4 (2026-09-15), with the 3.x behaviour taken from the v3.8.4 tree.

A .pacnew file is pacman telling you that a package shipped a new version of a config file you had edited, so it kept yours and saved the new one alongside. A .pacsave is the mirror case: a package was removed and pacman preserved the config you had. Neither is an error. Pacman prints a one line warning as it happens, but that scrolls past in the update transcript, and as of 4.0.4 nothing in the update pipeline goes back to look for them.

The fix

1. List what you have. pacman-contrib is in install/omarchy-base.packages, so pacdiff is already installed:

   sudo find /etc /boot /usr/share -name '*.pacnew' -o -name '*.pacsave' 2>/dev/null

   For an interactive pass, use pacdiff, which walks each pair and lets you view, merge, skip, or remove:

   sudo DIFFPROG='nvim -d' pacdiff

2. Handle /etc/pacman.conf.pacnew first, and do not blindly copy it over. Omarchy replaces this file with its own, which carries the [omarchy] repo pointing at https://pkgs.omarchy.org/<channel>/$arch. The .pacnew comes from upstream Arch and has none of that. Merge only the new [options] lines you want, or reset the whole file to Omarchy’s version for your channel:

   omarchy-refresh-pacman stable   # or rc, or edge

   That backs up your current file to /etc/pacman.conf.bak, swaps in both pacman.conf and /etc/pacman.d/mirrorlist for the channel, then runs a full pacman -Syyuu.

3. Handle /etc/mkinitcpio.conf.d/omarchy_hooks.conf.pacnew next. This is the one that can cost you a boot. The file is owned by omarchy-settings and it reassigns HOOKS wholesale rather than extending it, which is why people on LVM, mdraid, hibernation, or a systemd initramfs chain end up editing it (issue #6876). Merge the new hook list by hand, keep the hooks your root layout needs, then rebuild and inspect before rebooting:

   sudo limine-mkinitcpio
   sudo lsinitcpio -a /boot/EFI/Linux/omarchy_linux-omarchy.efi | grep -A1 'Hook run order'

   Omarchy enables unified kernel images by default through /etc/limine-entry-tool.d/omarchy-uki.conf, so the initramfs lives inside the .efi file rather than as a standalone image. The file is named omarchy_<kernel>.efi, so check omarchy_linux.efi or omarchy_linux-lts.efi too if you still boot those. Reading the hook list straight out of the .efi is how the thread on #6876 proved the lvm2 and sd-encrypt hooks had vanished.

4. Handle /etc/limine-entry-tool.d/omarchy-defaults.conf.pacnew. Leaving this one is fine. Migration 1789325478 in 4.0.4 writes BOOT_ORDER into /etc/default/limine, which has priority over every drop-in, and Omarchy’s own test asserts that the .pacnew is left untouched for the administrator to merge. Merge any non-BOOT_ORDER settings you care about, or delete it.

5. Handle the rest. For anything else, diff it, take what you want, and remove the leftover:

   sudo rm /etc/some/file.pacnew

6. Delete .pacsave files once you have read them. They belong to packages that are gone. Migration 1788009111 removes cups-browsed, for example, and Omarchy’s acceptance test asserts that neither /etc/cups/cups-browsed.conf.pacsave nor the matching .pacnew is left behind.

Verify it worked

• The find command above returns nothing.
• pacman -Sl omarchy | head -n 1 prints a package, which proves you did not lose the [omarchy] repo while merging pacman.conf.
• If you touched anything under /etc/mkinitcpio.conf.d/, the Hook run order line lists every hook your root needs, especially encrypt or sd-encrypt, and lvm2, mdadm_udev, or resume if you use them. A short list missing the one your root layout depends on is the signature of issue #6876.
• Reboot once after merging any boot path file, before you forget you changed it.

Why it happens

Pacman only writes a .pacnew when three things are true: the file is listed as a backup file by its package, the package shipped a new version, and your copy differs from the one the package previously installed. Unmodified files are simply replaced and you never see a .pacnew.

What changed in Omarchy 4 is who owns the files. In 3.x Omarchy was a git checkout under your home directory, so Omarchy’s own defaults were never pacman managed and could never produce a .pacnew. Only plain Arch packages did. There is no mention of pacnew anywhere in the v3.8.4 tree. Quattro made Omarchy package backed: omarchy and omarchy-settings now install real files into /etc, so your edits to them can now collide with a package upgrade the way any other Arch config does.

Omarchy has not caught up with that yet. docs/update-process.md closes with a section called Remaining concerns, and the second entry says pacnew and pacsave handling is still missing, noting that package backed Omarchy should warn about or help process these files. omarchy-update-analyze-logs, the only step that reads the update transcript, currently checks for one thing: failed initramfs generation.

There is a second, quieter category worth knowing about. docs/file-layout.md explains that a few files owned by upstream Arch packages, including /etc/nsswitch.conf, /etc/security/faillock.conf, /etc/cups/cups-browsed.conf, /etc/plymouth/plymouthd.conf, /etc/os-release, and /etc/skel/.bashrc, ship at /usr/share/omarchy/etc-overrides/ and are copied into place by the omarchy-settings scriptlet. The doc states the tradeoff plainly: user edits to those files get clobbered on every omarchy-settings upgrade. No .pacnew is written, because pacman is not the one doing the copying.

A .pacnew also has a knock on effect on migrations. Migration 1786605598 rebuilds the initramfs to drop unused nouveau firmware, and its comment notes that a user edited omarchy_hooks.conf, whose update landed in a .pacnew, keeps the old hook list and correctly skips the rebuild. Merging your .pacnew files is therefore also how you stop silently opting out of repairs.

Asking for better handling is not new. Issue #619, opened by dhh, proposed locking configs so Omarchy would not auto update them, and was closed as not planned in November 2025. PR #887 by mfontcada proposed a pacnew style baseline with safe diffs for Omarchy’s own configs, and was closed without merging.

If that did not work

• The machine will not boot after you merged a hooks file. Pick the pre update snapshot in the Limine menu and start over. See /upgrade/rollback-with-snapper-and-limine/ and /fix/you-are-in-emergency-mode-after-update/.
• The same .pacnew returns after every update. That is the expected outcome of editing a package owned file. Where the directory supports it, move your change into a separate drop in that sorts after Omarchy’s, rather than editing Omarchy’s file. This works for mkinitcpio.conf.d, sysctl.d, and systemd drop in directories, since the last assignment wins.
• You cannot remember what you changed. Compare the installed file against the package’s copy with pacman -Qkk <package>, or extract the original from /var/cache/pacman/pkg/.
• You want a warning next time. omarchy update runs omarchy-hook post-update after migrations, so a script at ~/.config/omarchy/hooks/post-update.d/pacnew-check that runs the find command above will print leftovers at the end of every update. Install it with omarchy hook install post-update <file>.
• The update itself failed rather than leaving a .pacnew. That is a different problem. See /fix/errors-occurred-no-packages-were-upgraded/.

Related

• /upgrade/what-migrations-do/
• /upgrade/before-you-update-checklist/
• /upgrade/3-to-4-quattro/
• /fix/migration-failed-mid-update/
• /fix/kernel-panic-after-update-limine/
• /reference/commands/omarchy-refresh-pacman/
• Official manual chapter: Updates