v0.4.2: README — document updating properly

The Updating section told you to run update.sh, but never said how to GET it. It
ships inside the patch, so any clone older than v0.4.0 does not have it -- the docs
described a script the reader did not possess. There is now an explicit bootstrap
step, including the fix for the "insufficient permission for adding an object to
repository database" failure that past `sudo git pull`s leave behind.

Rewrote "After a TrueNAS update". It never explained that apply.sh re-applies the
patch at every boot (so you never reinstall), and it soft-pedalled what a failure
costs: "fail-safe" means the BOX stays up, not that your backups keep running. A
[FAIL] providers is a broken backup, and the docs now say that plainly instead of
implying everything degrades gracefully.

Added a repo map -- patch/mw_patch.py and tools/release_notes.py were documented
nowhere -- and fixed `ruff check patch tests`, which skips tools/.

Every command and file path in the README was then verified to exist and run:
all five update.sh flags, the ruff/pytest commands, every file in the repo map,
and the truecloud_nested.py cleanup CLI.

132 tests, ruff and shellcheck -S style clean.

CHANGELOG.md

@@ -1,5 +1,61 @@
 # Changelog
 
+## v0.4.2 — 2026-07-13
+
+### Docs
+
+- **The Updating section never said how to *get* `update.sh`.** It ships inside the
+  patch, so a clone older than v0.4.0 doesn't have it — the docs told you to run a
+  script you didn't have. There is now an explicit bootstrap step (`git pull &&
+  bash install.sh`, once), including the fix for the *"insufficient permission for
+  adding an object to repository database"* failure that past `sudo git pull`s
+  cause.
+
+- **`After a TrueNAS update` rewritten.** It didn't explain that the patch
+  re-applies itself at every boot (so you never reinstall), and it didn't say what
+  each failure actually costs you. "Fail-safe" means *the box stays up* — not that
+  your backups keep running. A `[FAIL] providers` is a **broken backup**, and the
+  docs now say so rather than implying everything degrades gracefully.
+
+- Added a repo map. `patch/mw_patch.py` and `tools/release_notes.py` were
+  documented nowhere.
+
+- `Development` told you to run `ruff check patch tests`, which misses `tools/`.
+
+- Every command and file path in the README is now verified to exist and run.
+
+## v0.4.1 — 2026-07-13
+
+### Fixed
+
+- **`update.sh` would have picked a release candidate as "the newest release".**
+  Git's version sort ranks `v0.5.0-rc1` *above* `v0.5.0` (verified), and the
+  release workflow deliberately supports rc/beta tags — so an RC would have been
+  installed as though it were the latest stable. Tag selection is now filtered to
+  plain `vX.Y.Z`.
+
+- **`update.sh` would have died mid-update on an untracked file.** The dirty-tree
+  guard uses `--untracked-files=no`, so an untracked file that the *target* tracks
+  slipped past it — and `git checkout` then aborts. Under `set -e` the script died
+  with a raw git error, *after* recording the rollback point. This is exactly what
+  blocked a pull on a real box (a hand-copied `patch/wait_restart.sh`). It now
+  detects the collision up front and names the files. Gitignored files are
+  correctly *not* treated as blockers — git overwrites those silently.
+
+  Special case: if `update.sh` *itself* is the blocker, you hand-copied it in to
+  bootstrap — and "delete `update.sh`, then re-run `update.sh`" is impossible. It
+  now says so and prints the git commands that bootstrap it properly.
+
+- **`--rollback` skipped that check entirely**, so it would have hit the identical
+  failure. The check is now a shared function used by both paths, and rollback also
+  validates that the recorded revision still exists (history can be rewritten).
+
+- `install.sh`'s `chmod` aborted under `set -e` if any listed file was missing. The
+  file set changes between versions, so `update.sh --rollback` to an older revision
+  must not be killed by a filename this version happens to know about.
+
+- `--to` with no value was silently ignored and fell back to the default target.
+
 ## v0.4.0 — 2026-07-13
 
 ### Added

README.md

@@ -46,6 +46,22 @@ The patch is two independent modules — **providers** (B2/S3) and **nested**
 (snapshots on nested datasets) — and each retires on its own once TrueNAS ships
 that capability natively. See [Native support](#if-truenas-adds-native-support).
 
+## What's in the repo
+
+| Path | What it is |
+|---|---|
+| `install.sh` | Registers the PREINIT boot hook, applies the patch, restarts middlewared. Also `--enable/--disable-nested-snapshots`. |
+| `update.sh` | Fetch a newer **release** and apply it. `--check`, `--rollback`, `--to`, `--main`. |
+| `uninstall.sh` | Remove everything: boot hook, patched files, UI bundle, staging mounts. |
+| `recover.sh` | Emergency: set the kill switch and restart middlewared against stock files. |
+| `patch/apply.sh` | The PREINIT script. Runs at **every boot**; re-applies the patch into a fresh overlay. |
+| `patch/mw_patch.py` | The one implementation of apply/revert for the `TRUECLOUD_PATCH` blocks. Used by `apply.sh` *and* `uninstall.sh`. |
+| `patch/truecloud_nested.py` | Nested-dataset staging: plan, mount, verify, tear down, sweep snapshots. Also `… cleanup` as a CLI. |
+| `patch/patch_ui.py` | Widens the Angular credential dropdown. Refuses to write a bundle whose parens it unbalanced. |
+| `patch/create_task.py` | Create TrueCloud tasks with S3/B2 credentials; `verify` the patch state. |
+| `patch/wait_restart.sh` | Waits for boot to actually settle before restarting middlewared. |
+| `tools/release_notes.py` | Extracts a version's CHANGELOG section; enforces version consistency. Used by CI. |
+
 ## Development
 
 Parts of this project were written with AI assistance (Claude). All of it is
@@ -54,14 +70,24 @@ make that review meaningful. Bugs are mine.
 
 ```bash
 pip install pytest ruff
-ruff check patch tests
+ruff check patch tests tools
 pytest tests
 ```
 
-CI runs shellcheck, `bash -n`, ruff, and pytest on Python 3.11–3.13. The tests
+CI runs shellcheck, `bash -n`, ruff, and pytest on Python 3.11–3.13. Two checks
-include a pass that `compile()`s the `*_BLOCK` strings in `patch/apply.sh` —
+are worth calling out, because nothing else would catch what they catch:
-those are Python source appended into live `middlewared` modules, so a syntax
+
-error there would break the box at boot.
+- The tests **`compile()` the `*_BLOCK` strings** in `patch/apply.sh`. Those are
+  Python source appended into live `middlewared` modules — a syntax error there
+  breaks the box at boot, and they're string literals, so nothing else type-checks
+  them.
+- CI asserts **every script declares the same version**, and that it matches the
+  newest CHANGELOG entry. `VERSION=` had silently drifted to three different
+  values across the scripts before anything checked.
+
+Releases are automated: push a `vX.Y.Z` tag and the workflow runs the full suite,
+verifies the version matches, and cuts a GitHub release whose body **is** the
+matching `CHANGELOG.md` section — one source of truth for release notes.
 
 ---
 
@@ -342,28 +368,71 @@ Refresh your browser. S3 and B2 credentials now appear in the
 ## Updating
 
 ```bash
+cd /mnt/tank/truenas-truecloud-patch
 bash update.sh              # to the newest release, with a confirmation
-bash update.sh --check      # show what would happen; change nothing
-bash update.sh --rollback   # undo the last update
 ```
 
-It preserves your nested-snapshot opt-in setting, shows you the commits and
+| | |
-release notes you don't have yet, and asks before changing anything. It records
+|---|---|
-the previous revision *before* moving, so `--rollback` works even if `install.sh`
+| `bash update.sh` | Update to the newest release tag. Shows what's coming, asks first. |
-dies halfway.
+| `bash update.sh --check` | Show what *would* happen. Changes nothing. |
+| `bash update.sh --rollback` | Undo the last update. |
+| `bash update.sh --to v0.3.5` | Go to a specific tag or commit. |
+| `bash update.sh --main` | Track **unreleased** `main`. You're on your own. |
+| `bash update.sh --yes` | Skip the confirmation (for a scripted, *attended* run). |
 
-**Run it by hand. Never from cron or a systemd timer.** This patch injects Python
+Run it as **root** — it calls `install.sh`, which needs to reload middlewared.
-into `middlewared` and re-applies itself at every boot, so an unattended pull would
+
-let any bad upstream commit reach your box with no human in the loop and take
+### First time: bootstrapping `update.sh`
-effect on the next reboot. v0.0.4 shipped exactly such a bug and took every app on
+
-the box down. The manual step *is* the safety gate — if you want convenience, watch
+`update.sh` ships *inside* the patch, so a clone older than v0.4.0 doesn't have it
-the [releases](https://github.com/sudolulo/truenas-truecloud-patch/releases) feed,
+yet. Bootstrap it once with git:
+
+```bash
+cd /mnt/tank/truenas-truecloud-patch
+git pull                 # or: git checkout v0.4.1
+bash install.sh
+```
+
+Every update after that is just `bash update.sh`.
+
+> If a plain `git pull` fails with *"insufficient permission for adding an object
+> to repository database"*, past `sudo git pull`s left root-owned objects in
+> `.git`. Fix it once as root: `chown -R <you>:<you> .git`. (`update.sh` repairs
+> this automatically from then on.)
+
+### What it does for you
+
+- **Preserves your nested-snapshot opt-in setting** — updating never flips it.
+- **Shows the commits and release notes you don't have**, then asks before moving.
+- **Records the previous revision *before* checking out**, so `--rollback` works
+  even if `install.sh` dies halfway through.
+- **Refuses to run over a dirty working tree**, rather than merging across
+  hand-edited or scp'd files and losing them.
+- **Detects untracked files that would be clobbered** by the checkout and names
+  them, instead of dying on a raw git error mid-update.
+- **Repairs `.git` ownership** left root-owned by past `sudo git pull`s.
+
+It updates to the newest **release tag**, not `main`. `main` can be mid-refactor;
+a tag is the tested artifact, and CI gates every release. Pre-release tags
+(`-rc`, `-beta`) are skipped — `--to` them explicitly if you want one.
+
+After updating, the checkout is pinned to a release tag (detached HEAD). That is
+what you want for a deployment: plain `git pull` no longer applies, and
+`update.sh` is the supported path.
+
+### Why there is no auto-update
+
+**Never put this in cron or a systemd timer.** This patch injects Python into
+`middlewared` and re-applies itself at *every boot*, so an unattended pull would
+let any bad upstream commit reach your box with no human in the loop — and
+detonate on the next reboot. That is not hypothetical: **v0.0.4 shipped exactly
+such a bug and took all 54 apps on a box down.**
+
+The manual step *is* the safety gate. If you want convenience, watch the
+[releases feed](https://github.com/sudolulo/truenas-truecloud-patch/releases);
 don't automate the pull.
 
-It updates to the newest **release tag**, not `main` — `main` can be mid-refactor,
-and a tag is the tested artifact. `--main` exists if you want unreleased code, and
-says so loudly.
-
 ## Creating a task via CLI
 
 If the UI still shows only Storj after refreshing (e.g. the JS bundle pattern
@@ -460,12 +529,34 @@ tail -20 /mnt/tank/truenas-truecloud-patch/apply.log
 
 ## After a TrueNAS update
 
-1. Check the log: `cat /mnt/tank/truenas-truecloud-patch/apply.log | tail -30`
+A TrueNAS update replaces `/usr/` wholesale, wiping the patch. You do **not** need
-2. If you see "WARNING: … pattern not found", the UI patch needs updating.
+to reinstall: `patch/apply.sh` runs at every boot and re-applies itself from your
-   [Open an issue](https://github.com/sudolulo/truenas-truecloud-patch/issues)
+clone. But it targets internal APIs with no stability contract, so an update *can*
-   with your TrueNAS version number.
+break it — and the failure is quiet by design (middlewared starts fine; the patch
-3. The backend patch (B2 support + URL fix) is more stable — check that a
+just doesn't).
-   B2 backup job still completes successfully after any update.
+
+**Check the log after any TrueNAS update:**
+
+```bash
+tail -30 /mnt/tank/truenas-truecloud-patch/apply.log
+python3 /mnt/tank/truenas-truecloud-patch/patch/create_task.py verify
+```
+
+| What you see | What it means |
+|---|---|
+| `[OK] providers`, `[OK]`/`[SKIP] nested_snapshots` | Fine. Nothing to do. |
+| `WARNING: … pattern not found` (UI) | The Angular bundle changed. The UI dropdown reverts to Storj-only, but **backups keep working** — create tasks with `create_task.py` meanwhile, and [open an issue](https://github.com/sudolulo/truenas-truecloud-patch/issues) with your TrueNAS version. |
+| `[FAIL] providers` | **Your B2/S3 backups will not run.** middlewared is fine, but the credential/URL handling is gone. Open an issue with your version. |
+| `[FAIL] nested_snapshots` | The stock guard is back, so tasks with `snapshot = true` on a nested dataset will fail validation. Turn the option off on those tasks until it's fixed. |
+
+"Fail-safe" means *the box stays up* — not that your backups keep running. A
+`[FAIL] providers` is a broken backup, so check the log rather than assume.
+
+Then update the patch itself if a newer release fixes it:
+
+```bash
+bash /mnt/tank/truenas-truecloud-patch/update.sh
+```
 
 ---
 

install.sh

@@ -18,7 +18,7 @@
 
 set -euo pipefail
 
-VERSION="0.4.0"
+VERSION="0.4.2"
 
 # The directory containing install.sh is the permanent install location.
 PATCH_DIR="$(cd "$(dirname "$0")" && pwd)"
@@ -95,8 +95,14 @@ fi
 # ── Set permissions ───────────────────────────────────────────────────────────
 
 echo "Setting permissions ..."
-chmod +x "$PATCH_DIR/patch/apply.sh" "$PATCH_DIR/patch/create_task.py" \
+# Guard each path: under `set -e` a chmod on a missing file aborts the install.
-          "$PATCH_DIR/recover.sh" "$PATCH_DIR/uninstall.sh" "$PATCH_DIR/update.sh"
+# The file set changes between versions, so `update.sh --rollback` to an older
+# revision must not be killed by a name this version happens to know about.
+for _exe in patch/apply.sh patch/create_task.py recover.sh uninstall.sh update.sh; do
+    if [ -f "$PATCH_DIR/$_exe" ]; then
+        chmod +x "$PATCH_DIR/$_exe"
+    fi
+done
 echo "Done."
 echo ""
 

patch/apply.sh

@@ -32,7 +32,7 @@
 # Derive PATCH_DIR from this script's location (parent of the patch/ directory).
 PATCH_DIR="$(cd "$(dirname "$0")/.." && pwd)"
 LOG="$PATCH_DIR/apply.log"
-VERSION="0.4.0"
+VERSION="0.4.2"
 
 # Rotate log at 512 KB to avoid unbounded growth on a system volume.
 # Keep two prior generations (.1 and .2) so the last three boots are always available.

patch/create_task.py

@@ -52,7 +52,7 @@ import subprocess
 import sys
 import time
 
-__version__ = "0.4.0"
+__version__ = "0.4.2"
 
 _PATCH_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 _STATUS_FILE = os.path.join(_PATCH_DIR, "hook_status.json")

recover.sh

@@ -17,7 +17,7 @@
 #   bash /mnt/tank/truenas-truecloud-patch/patch/apply.sh
 #   systemctl restart middlewared
 
-VERSION="0.4.0"
+VERSION="0.4.2"
 
 PATCH_DIR="$(cd "$(dirname "$0")" && pwd)"
 

uninstall.sh

@@ -3,7 +3,7 @@
 
 set -euo pipefail
 
-VERSION="0.4.0"
+VERSION="0.4.2"
 
 PATCH_DIR="$(cd "$(dirname "$0")" && pwd)"
 _HOOK_COMMENT='TrueCloud provider patch (S3/B2)'

update.sh

@@ -19,7 +19,7 @@
 
 set -euo pipefail
 
-VERSION="0.4.0"
+VERSION="0.4.2"
 
 PATCH_DIR="$(cd "$(dirname "$0")" && pwd)"
 _PREV_FILE="$PATCH_DIR/.update_previous"
@@ -46,9 +46,59 @@ Updating preserves your nested-snapshot opt-in setting either way.
 USAGE
 }
 
+# An UNTRACKED file that the target tracks makes `git checkout` abort. The dirty-
+# tree check deliberately ignores untracked files, so this slips past it and the
+# checkout then dies mid-operation. Not hypothetical: a hand-copied
+# patch/wait_restart.sh blocked a pull on a real box exactly this way.
+#
+# Used by BOTH the update and the rollback path -- rolling back moves the tree too,
+# and would hit the identical failure.
+_abort_if_untracked_blockers() {
+    local ref="$1" blocking
+
+    # Set intersection of {untracked, not ignored} and {tracked by the target}. Two
+    # git calls, not one `ls-files --error-unmatch` per file in the target tree.
+    # --exclude-standard is deliberate: git silently overwrites *ignored* files on
+    # checkout, so those are not blockers — only untracked-and-not-ignored ones are.
+    blocking="$(comm -12 \
+        <(git ls-files --others --exclude-standard | sort) \
+        <(git ls-tree -r --name-only "$ref" | sort) \
+        | sed 's/^/    /')"
+
+    [ -n "$blocking" ] || return 0
+
+    echo "ERROR: these untracked files would be overwritten:" >&2
+    printf '%s\n\n' "$blocking" >&2
+    echo "  They exist here but git does not track them — most likely hand-copied" >&2
+    echo "  or scp'd in. Move or delete them, then re-run." >&2
+
+    # "Delete update.sh, then re-run update.sh" is impossible. If the script itself
+    # is a blocker, it was hand-copied in to bootstrap; the honest answer is to
+    # bootstrap with git instead, which installs it properly.
+    case "$blocking" in
+        *update.sh*)
+            echo "" >&2
+            echo "  update.sh itself is untracked here — you copied it in to bootstrap." >&2
+            echo "  Do that with git instead, once; it installs update.sh properly:" >&2
+            echo "" >&2
+            echo "    rm -f $PATCH_DIR/update.sh" >&2
+            echo "    git -C $PATCH_DIR checkout $ref" >&2
+            echo "    bash $PATCH_DIR/install.sh" >&2
+            echo "" >&2
+            echo "  Every later update is then just: bash update.sh" >&2
+            ;;
+    esac
+    exit 1
+}
+
 while [ $# -gt 0 ]; do
     case "$1" in
-        --to)       _target="${2:-}"; shift ;;
+        --to)
+            if [ -z "${2:-}" ]; then
+                echo "ERROR: --to needs a tag, branch, or commit." >&2
+                exit 1
+            fi
+            _target="$2"; shift ;;
         --main)     _use_main=1 ;;
         --check)    _check_only=1 ;;
         --rollback) _rollback=1 ;;
@@ -103,8 +153,15 @@ if [ "$_rollback" -eq 1 ]; then
         exit 1
     fi
     _prev="$(cat "$_PREV_FILE")"
+    if ! git rev-parse --verify --quiet "${_prev}^{commit}" >/dev/null; then
+        echo "ERROR: recorded revision '$_prev' is not a valid commit." >&2
+        echo "  The history may have been rewritten. Pick a target explicitly:" >&2
+        echo "    bash update.sh --to <tag>" >&2
+        exit 1
+    fi
+    _abort_if_untracked_blockers "$_prev"
     echo "Rolling back to $_prev ..."
-    git checkout -q "$_prev"
+    git checkout -q --detach "$_prev"
     echo "Reverted. Re-applying ..."
     echo ""
     bash "$PATCH_DIR/install.sh"
@@ -128,7 +185,13 @@ else
     # correct while tags are created in ascending version order; it breaks the
     # moment a hotfix is tagged out of band (a v0.3.6 released after v0.4.0 would
     # sort as "newest" by date and silently downgrade the box).
-    _target="$(git tag -l 'v*' --sort=-version:refname | head -1)"
+    #
+    # Filter to PLAIN vX.Y.Z: git's version sort ranks `v0.5.0-rc1` ABOVE `v0.5.0`
+    # (verified), so without this a release candidate would be installed as though
+    # it were the newest release. The release workflow deliberately supports
+    # rc/beta/alpha tags, so they will exist.
+    _target="$(git tag -l 'v*' --sort=-version:refname \
+                 | grep -E '^v[0-9]+\.[0-9]+\.[0-9]+$' | head -1)"
     if [ -z "$_target" ]; then
         echo "ERROR: no release tags found; use --main to track unreleased code." >&2
         exit 1
@@ -149,6 +212,8 @@ if [ "$_current" = "$_target_sha" ]; then
     exit 0
 fi
 
+_abort_if_untracked_blockers "$_target_sha"
+
 # ── Show what is coming ───────────────────────────────────────────────────────
 
 echo "Commits you do not have yet:"
@@ -217,6 +282,12 @@ echo ""
 echo "=== Update complete ==="
 echo "  $_current_desc  ->  $(git describe --tags --always)"
 echo ""
+if ! git symbolic-ref -q HEAD >/dev/null; then
+    echo "NOTE: the checkout is now pinned to a release tag (detached HEAD), which is"
+    echo "      what you want for a deployment. Plain \`git pull\` will not work here —"
+    echo "      use \`bash update.sh\` from now on."
+    echo ""
+fi
 echo "If anything looks wrong:"
 echo "  bash $PATCH_DIR/update.sh --rollback    # back to $_current_desc"
 echo "  bash $PATCH_DIR/recover.sh              # kill switch + restart"