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/omp-worktree-path-gotchas/SKILL.md

@@ -1,49 +1,22 @@
 ---
 name: omp-worktree-path-gotchas
-description: "Use in ~/.omp (or any multi-worktree repo) when an edit lands in the wrong checkout, git checkout is policy-refused, or an omp session id is needed — relative-path tool resolution, shared-worktree branch law, session-id lookup, edit auto-prefix trap."
+description: "Multi-worktree edits/tests land in the wrong checkout: bash persistent-cwd drift, phantom file reverts, which tree a tool really touched"
 ---
 
-# Multi-worktree gotchas in ~/.omp-style repos
+## Purpose
+Answer "why did my file/tests revert or behave differently than what I just wrote?" in repos with several worktrees (e.g. `~/.omp`, `~/Projects/wt-*`, `~/.omp/wt/*`).
 
-Measured 2026-10-18 building PR #12/#14 in `dank/command-center` worktrees.
+## Failure modes and fixes
 
-## 1. Relative paths resolve to the SESSION worktree — always edit by absolute path
-`edit`/`read`/`write` with a relative `path` resolve against the session CWD
-(the harness worktree you were spawned in), NEVER the worktree you `cd`'d into
-via bash. Identical file content in sibling worktrees yields identical
-`[path#tag]` hashes, so an edit can "succeed" against the WRONG checkout with
-no warning; only a rejected stale-hash edit reveals it.
+1. **Bash tool persistent-cwd drift** (the expensive one): the persistent shell keeps its cwd across calls; a call *without* an explicit `cwd` runs in whatever the *previous* call left, which after interleaved work may be a DIFFERENT worktree. Result: reads/greps/appends hit tree A while `git`/`bats` hit tree B — symptoms are "file keeps reverting to HEAD", duplicate test names at shifting line numbers, scenario `CALLS 0` for scenarios that exist, mismatched `grep -n` vs tool-reported line numbers.
+   - **Diagnose:** `pwd` in the same call as the failing command; `wc -l <file>` in BOTH candidate worktrees; compare md5s. The file is not flapping — two files exist and commands alternate between them.
+   - **Fix/prevent:** pass an explicit `cwd` on EVERY bash call once two or more checkouts are in play; never trust a read taken without one as evidence about "the" file.
 
-- When working in a second worktree, ALL file-tool paths: absolute.
-- Symptom seen: edit rejected "hash #X is not from this session" while the
-  bash-side `git status` showed the file clean — two different files, two
-  worktrees. Recovery: revert the stray edit (CUT the inserted lines) in the
-  wrong tree, re-read the right tree, redo with absolute header.
+2. **Symlinked or stale `git` state**: `git status` in a worktree shows a clean tree while the disk file differs from what you intended — the corruption is already committed. Audit committed blobs (`git log --oneline -- <file>`; per-commit `git show <c>:<path> | grep -c <sentinel>`) instead of re-reading the disk copy repeatedly.
 
-## 2. Branching: shared worktrees refuse git checkout
-Workspace policy blocks `git checkout` (branch switches AND `--` discards) in
-harness-managed worktrees — concurrent agents depend on them. To start a
-branch off fresh trunk:
+3. **Same-name files across worktrees** (`tests/behavior.bats` exists in each): a `find`/`grep` rooted above the worktrees mixes copies; anchor the search path to one worktree root.
 
-```bash
-git -C ~/.omp worktree add -q -b <type>/<issue#>-<slug> ~/.omp/wt/<name> origin/main
-```
-
-Never force past the refusal; the new-worktree route is strictly safer.
-Custom worktrees not matching `wt/wt-*` are invisible to the live-sync reaper —
-prune them by hand after merge (`git worktree remove`, `git branch -d`).
-
-## 3. omp session id for attribution footers
-Fleet law requires `session:` in issue/PR bodies. Authoritative source:
-`~/.omp/agent/sessions/<cwd-slug>/<timestamp>_<UUID>.jsonl` — the `<UUID>` is
-the session id. Pick the newest file whose first `{"type":"title"}` line names
-this conversation to prove the id is yours. The `wt/<ts>-<hash>` dir suffix is
-NOT the session id (it persists across sessions per cwd).
-
-## 4. edit-tool auto-prefix trap (recurring)
-A body row written bare (intending it as the "original line" anchor or as
-context) is AUTO-PREFIXED with `+` and INSERTED — leaving the old line plus a
-duplicate. `PUT n.=n:` therefore behaves like insert, not replace, whenever
-the anchor row lacks an explicit marker. After any `PUT` where the response
-warns "Auto-prefixed bare body row(s)", immediately `CUT` the stale line number
-shown in the response (descending order for multiple CUTs).
+## Repair recipe for a corrupted-but-committed test file
+- Inventory both versions: `grep -o '@test "[^"]*"' | sort` and `grep -o 'case "[a-z]*":' | sort -u`; `comm` the sets to find lost scenarios and duplicate tests.
+- Rebuild from the committed copy (`git show HEAD:<path> > <path>`, no checkout), then re-apply only the true deltas: restore missing scenario blocks from the last clean base, dedupe imports, rename scratch-dir mkdtemp prefixes that collide with a test's own orphan-census glob (e.g. `dankvoice-stage-` matching `dankvoice-*`).
+- Re-run the targeted tests, then the full suite single-process.