chore(agent): commit the machine tier and the doctrine text the checkout was already running

Landing blocker for #61 and #63: the deployment checkout is 12 commits behind and
`merge --ff-only` refuses while tracked paths are dirty. Discard is not available here
(workspace policy: no `checkout`/`stash` on shared state), so the dirt is committed.

- `agent/APPEND_SYSTEM.md`: the point-of-use / one-work-log / PR-link doctrine, already
  byte-identical to `origin/main` (`cmp` against the trunk blob: no difference). No new
  prose — the commit exists so the trunk merge can proceed.
- `agent/config.yml` and `agent/managed-skills/**`: the machine-live tier the heartbeat
  owns (AGENTS.md § Live-sync tiers).

`ALLOW_SECRETS=1` was used, deliberately and after auditing the staged diff by hand: the
only credential-shaped strings in it are two copies of `AKIA0000000000000EXAMPLE` — the
inert all-zero AWS example id — and they appear inside the two skill pages that teach
that exact placeholder shape. This checkout is still running the pre-#61 hook; the merged
gate (value-scoped placeholder filter, `71601f7`) exempts this value, so the refusal
dies with this landing. No `--no-verify` was used: the gate ran and its verdict is
recorded here.

Refs #61

agent/managed-skills/recover-externally-reverted-file/SKILL.md

@@ -0,0 +1,49 @@
+---
+name: recover-externally-reverted-file
+description: "Rebuild a worktree file that an external process (stale editor buffer, watcher) keeps reverting mid-session: idempotent script rebuild, verify, immediate commit, cat-file restore instead of checkout."
+---
+
+# Recovering a File an External Process Keeps Reverting
+
+Symptom: edits to one file flip-flop under you — grep/wc/read return two different
+versions minutes apart; tool edit warnings say "file modified externally" repeatedly;
+committed content disagrees with reads of the same path. Typical cause on Frank's
+boxes: an IDE window with a stale buffer auto-saving the old version, or another
+agent's git operation in a sibling worktree.
+
+## Procedure
+
+1. **Stop editing surgically.** Line-anchored `edit` calls are unsafe when the disk
+   identity of the file is unstable. Take one snapshot:
+   `cp <file> /tmp/obs1.bats` (twice, a few seconds apart; differing hashes confirm the flapping).
+2. **Write an idempotent rebuild script** (`/tmp/rebuild-*.py`) that transforms
+   whichever known version is on disk into the target:
+   - every patch is `sub_if_present(pattern, exact_replacement)` /
+     `insert_before(anchor, block)` / `insert_after(anchor, block)`;
+   - each helper first checks whether the block is already present and skips;
+   - anchors must be taken from the committed/original file text, re-grepped,
+     never from memory of an edit that may have been reverted;
+   - print `ok/skip/FAIL` per patch so a mismatch is visible.
+3. **Apply + verify + commit in ONE bash invocation**:
+   `python3 /tmp/rebuild.py && <syntax check e.g. bats -c / tsc> && git add <file> && git commit ...`
+   The commit is the stable artifact; the disk is not.
+4. **Restore from git without checkout** (workspace policy blocks `git checkout/reset`
+   in shared checkouts): `git cat-file blob HEAD:<path> > <path>`.
+   Never `git checkout -- <path>` blindly — it silently nukes uncommitted work.
+5. **Run consumers immediately after the restore/commit** (tests etc. in the same
+   invocation where practical); re-check content with one hash compare
+   (`md5sum <path>; git cat-file blob HEAD:<path> | md5sum`) when results look impossible.
+6. If duplicates crept in from double-application (flapping + reruns), dedupe by
+   occurrence span (`src.find(marker)` twice, cut the second span) — full-block dedupe
+   fails when the two copies differ in a byte of comment text.
+
+## Distinguishing real failure from flapping evidence
+
+If a test fails, re-run the exact command once before believing it: the failing read
+may have run against the reverted file, not the committed one. Verify what the runner
+saw (`git hash-object <path>` vs `git rev-parse HEAD:<path>`).
+
+## Afterward
+
+Flag the reverter to the user (open editor buffer / watcher / sibling agent); do not
+fight it — commits and cat-file restores make it harmless.