Re-apply and verify the patch before the deferred restart

Patching at PREINIT and restarting minutes later is only sound while the
patched files are still on the live path when middlewared re-imports them,
and PREINIT cannot guarantee that. The overlay sits inside /usr, so anything
that remounts that hierarchy detaches it — a systemd-sysext merge/refresh
from another PREINIT hook, or middlewared's own docker.configure_nvidia at
runtime. Init scripts run sequentially in id order, so a hook registered
after this one always wins, and reordering them would not help because
docker.configure_nvidia fires long after PREINIT is done.

Observed on 25.10.6: the overlay was mounted at 16:41:56, a sysext refresh
unmerged and remerged /usr four seconds later, and the deferred restart at
16:47:24 loaded stock modules. Every B2 cloud_backup task then failed with
NotImplementedError for nineteen hours across four scheduled runs while
apply.log and hook_status.json both reported the patch active.

wait_restart.sh now re-applies immediately before restarting — after boot has
settled, which is also after every sysext merge and docker nvidia
configuration — verifies the marker is on the live path, restarts, and
verifies again, retrying once. It is no longer exec'd, so something can run
after the restart to find out what it loaded. apply.sh records the resolved
middlewared directory in .mw_dir for that check, and honours TRUECLOUD_REAPPLY
so the re-apply pass does not schedule a second restart.

_ensure_writable treated "one of our overlays is listed here" as "already
done", but it only reaches that check when the directory is not writable, and
a live overlay of ours always is — a shadowed overlay was indistinguishable
from a healthy one. It is now detached and re-mounted, reusing the upperdir so
files patched earlier in the boot survive, with a fresh workdir and a retry on
a private one, since overlayfs refuses a workdir a detached mount still holds.

Add a CRITICAL hourly alert for the case none of this can prevent: the patch
being on disk but not in the running process. apply.log can only report the
first. The alert asks the second question from inside middlewared, where the
patch's own stamps make it exact, and checks both halves since either can go
missing alone. It stays quiet when the kill switch is set or the providers
module has been retired as native, and is not muted by update_alerts_disabled.

wait_restart.sh also logs to apply.log now: journald retention on a busy box
is easily shorter than the interval between reboots, and the boot that caused
this had already rotated away by the time it was investigated.

CHANGELOG.md

@@ -39,6 +39,62 @@ worse than no alert, because one day it carries a security fix.
 
 ### Fixed
 
+- **The patch survived being applied and then silently stopped existing, because
+  something else remounted `/usr` four seconds later.** On a box running
+  TrueNAS 25.10.6 the boot of 2026-08-19 went: 16:41:56 `apply.sh` mounts its
+  overlay on `/usr/lib/python3/dist-packages`, patches `b2.py`/`restic.py`, logs
+  every step `OK`; **16:42:00** a second PREINIT hook runs `systemd-sysext
+  refresh` over `/usr` — `Unmerged '/usr'.` / `Merged extensions into '/usr'.` —
+  and our overlay, which lives *inside* that hierarchy, is torn off with it;
+  16:47:24 our own deferred restart fires exactly as designed and middlewared
+  imports the **stock** modules. Every B2 TrueCloud Backup task then failed with
+  `NotImplementedError` from stock `rclone/base.py` for nineteen hours, across
+  four scheduled runs, while `apply.log` and `hook_status.json` both said the
+  patch was active.
+
+  Nothing in the patch was wrong, which is the point: applying at PREINIT and
+  restarting later is only sound if the patched files are still on the live path
+  when middlewared re-imports them, and **that is not something PREINIT can
+  guarantee**. Init scripts run sequentially in id order, so any hook registered
+  after ours always wins. Worse, hook ordering cannot fix it either —
+  middlewared's own `docker.configure_nvidia` merges a sysext over `/usr` at
+  *runtime*, long after every PREINIT hook is finished.
+
+  So the deferred restart no longer trusts the PREINIT pass. `wait_restart.sh`
+  now re-applies immediately before it restarts middlewared — after boot has
+  settled, which is also after every sysext merge and docker nvidia
+  configuration — verifies the marker is genuinely on the live path, restarts,
+  and verifies again, retrying once if the patch was torn off in between. It is
+  no longer `exec systemctl try-restart middlewared`, because something has to
+  run afterwards to find out what that restart actually loaded.
+
+  Two supporting fixes fell out of the same failure. `_ensure_writable` treated
+  "one of our overlays is listed on this directory" as "already done" — but it
+  only ever reaches that check when the directory is **not** writable, and a live
+  overlay of ours always is. A shadowed overlay was therefore indistinguishable
+  from a healthy one; it is now detached and re-mounted, reusing the same
+  upperdir so everything patched earlier in the boot reappears intact, with a
+  fresh workdir because overlayfs refuses one left behind by a detached mount.
+
+- **middlewared now says so when it is running stock.** The gap that let this
+  cost nineteen hours was not the remount, it was that nothing could tell the
+  difference between "patched on disk" and "patched in the running process".
+  `apply.log` can only ever report the first. A new CRITICAL alert asks the
+  second question from inside middlewared, hourly, where it is exact: the patch
+  stamps the objects it replaces, so a missing stamp means this interpreter
+  imported stock code. It checks both halves — `restic.py`'s `_truecloud_patched`
+  marker and whether `B2RcloneRemote.get_restic_config` is still the base class's
+  — since either can go missing alone. It stays quiet when the kill switch is
+  set or the providers module has been retired as native, and it is deliberately
+  **not** silenced by `update_alerts_disabled`: that mutes release notifications,
+  not a broken backup path.
+
+  Boot-time diagnosis also no longer depends on the journal. `wait_restart.sh`
+  logged only to the journal, and journald retention on a busy box is easily
+  shorter than the interval between reboots — the 2026-08-19 boot had already
+  rotated away by the time it was investigated. It now writes to `apply.log`
+  alongside everything else.
+
 - **The next maintenance release was never checked, and it is the one that reaches
   users.** Shipped versions were discovered from `TS-*` tags and unreleased ones from
   `release/*` branches carrying `-BETA`/`-RC`. A branched-but-untagged *maintenance*