**System details:** Apple MacBookPro16,1 (T2, `106b:1801`/`106b:1802`), Intel i7-9750H + AMD Navi 14, Omarchy 4.0.2-1, kernel `linux-t2` 7.1.8.arch1-3, Hyprland 0.56.2, bootloader Limine (UKI).

## Summary

`omarchy-refresh-pacman` overwrites `/etc/pacman.conf` from the channel template but never re-applies the hardware-specific repository additions that `install/hardware/pacman.sh` is responsible for. On Apple T2 Macs this silently drops the `[arch-mact2]` repository, orphaning `linux-t2` and the other T2 packages so they can no longer receive updates — including the kernel.

The install path does this correctly; the refresh/upgrade path does not.

## Impact

After upgrading to 4.x on a T2 Mac, these packages remain installed but have no update source:

- `linux-t2` — **the running kernel**
- `t2fanrd`
- `apple-t2-audio-config`
- `apple-bcm-firmware`

The machine keeps booting and working, so there is no visible symptom. The failure is silent: the kernel simply stops receiving security and bugfix updates, and the user has no indication anything is wrong. `pacman -Syu` reports nothing missing because the packages resolve locally.

## Root cause

`bin/omarchy-refresh-pacman` overwrites the config and then only runs the user hook:

```bash
sudo cp -f "$OMARCHY_PATH/default/pacman/pacman-$channel.conf" /etc/pacman.conf
sudo cp -f "$OMARCHY_PATH/default/pacman/mirrorlist-$channel" /etc/pacman.d/mirrorlist

# Allow user customization of /etc/pacman.conf before the upgrade runs
omarchy-hook pre-refresh-pacman

sudo env OMARCHY_UPDATE_PACMAN=1 pacman -Syyuu --noconfirm
```

`install/post-install/pacman.sh` does the same overwrite but *does* re-apply hardware repos:

```bash
cp -f "$OMARCHY_PATH/default/pacman/pacman-${OMARCHY_MIRROR:-stable}.conf" /etc/pacman.conf
...
source "$OMARCHY_INSTALL/hardware/pacman.sh"
```

And `install/hardware/pacman.sh` states the intent explicitly:

```bash
# Hardware-specific pacman repository extensions that must survive the final
# pacman.conf restore.
if lspci -nn | grep "106b:180[12]" >/dev/null; then
  if ! grep -q '^\[arch-mact2\]' /etc/pacman.conf; then
    cat >> /etc/pacman.conf <<'EOF'

[arch-mact2]
Server = https://github.com/NoaHimesaka1873/arch-mact2-mirror/releases/download/release
SigLevel = Never
EOF
  fi
fi
```

So the repo is added deliberately for this hardware and is meant to survive a template restore — but the refresh path is missing the `source "$OMARCHY_INSTALL/hardware/pacman.sh"` line. No migration re-adds it either (`grep -rn arch-mact2 migrations/` returns nothing).

Note the ordering hazard: `pacman -Syyuu --noconfirm` runs immediately afterwards, so the full upgrade proceeds with the repo already missing.

## Reproduction

1. Apple T2 Mac (`lspci -nn` shows `106b:1801` / `106b:1802`) installed via the T2 path, with `[arch-mact2]` in `/etc/pacman.conf`
2. Upgrade to 4.x (or run `omarchy refresh pacman`)
3. `grep arch-mact2 /etc/pacman.conf` → gone
4. `pacman -Si linux-t2` → no repository

## Evidence from the affected machine

`/etc/pacman.conf` before the upgrade (`/etc/pacman.conf.bak`, 15:53) ended with:

```
[omarchy]
SigLevel = Optional TrustAll
Server = https://pkgs.omarchy.org/stable/$arch

[arch-mact2]
Server = https://github.com/NoaHimesaka1873/arch-mact2-mirror/releases/download/release
SigLevel = Never
```

The upgrade's own backup (`/etc/pacman.conf.omarchy-upgrade-to-quattro.20260902155457.bak`, 15:54) already ends at `[omarchy]` — `[arch-mact2]` is gone.

Resulting state:

```
$ pacman -Q linux-t2
linux-t2 7.1.8.arch1-3

$ pacman -Si linux-t2
error: package 'linux-t2' was not found
```

`arch-mact2-mirrorlist` was also removed.

## Suggested fix

Re-apply hardware repository additions in `omarchy-refresh-pacman` after the template copy and before `pacman -Syyuu`, mirroring what `install/post-install/pacman.sh` already does:

```bash
sudo cp -f "$OMARCHY_PATH/default/pacman/pacman-$channel.conf" /etc/pacman.conf
sudo cp -f "$OMARCHY_PATH/default/pacman/mirrorlist-$channel" /etc/pacman.d/mirrorlist

source "$OMARCHY_INSTALL/hardware/pacman.sh"   # <-- add

omarchy-hook pre-refresh-pacman

sudo env OMARCHY_UPDATE_PACMAN=1 pacman -Syyuu --noconfirm
```

`install/hardware/pacman.sh` is already idempotent (it guards on `grep -q '^\[arch-mact2\]'`), so this is safe to run unconditionally on every refresh.

A migration to repair already-upgraded machines would also help, since affected users have no symptom to prompt them to look.

## Workaround

Re-append the stanza to `/etc/pacman.conf` manually, or add a
`~/.config/omarchy/hooks/pre-refresh-pacman.d/` hook that re-adds it on each refresh.

## Note on scope

The removal of `tiny-dfr` by migration `1785944594.sh` is **not** part of this report — that is clearly deliberate and well-reasoned ("the optional daemon holds stale device descriptors across suspend with t2bce"), and matches this machine's experience. Only the loss of the repository appears unintended.

---

*This issue was researched and written by Claude (Claude Code) running on the affected machine, and filed by the repository account owner. All command output above was collected from that machine.*