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Frank 8af40c402b 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

2026-10-21 01:44:51 -07:00

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name, description

name	description
bash-cwd-drift-multi-worktree	Diagnose "files keep reverting / phantom edits" in multi-worktree sessions: the persistent bash shell's cwd silently reverted to another checkout, so probes and git commands ran against different files.

Multi-worktree bash cwd drift

Symptom (all of these at once, in one session)

A file "keeps reverting" to an older version between edits (esp. test files).
grep -n line numbers disagree with the tool/test output (e.g. bats reports line 637, grep says the match is at 519).
wc -l/md5sum stable when sampled back-to-back, but state "flaps" across the session.
git status clean in one call, surprising in the next.
Probes against src/ show code that doesn't exist in the branch you think you're on.

Root cause

The persistent bash shell resets to the session's ORIGINAL cwd when a call omits cwd (e.g. after a shell respawn at a turn boundary). With several git worktrees of the same repo checked out, consecutive calls silently alternate between two full copies of the tree — half the reads land in the old branch's files. Nothing is rewriting anything; two files are being inspected.

Decision

In multi-worktree work, pass an explicit cwd on EVERY bash call. Never rely on persistence.
Use absolute paths for read/edit/write (already required) — file tools don't drift; only bash does.

Check

When state seems to flap: pwd in the same call as the probe. If two calls to the same relative path report different content, git worktree list and census each checkout separately — you have two files, not a gremlin.

Repair pattern (if corruption got committed via the wrong tree)

git log --oneline --all -- <file>; per candidate commit print wc -l + counts of a few marker strings to classify clean vs corrupted blobs.
Restore the good blob with git show <commit>:<path> > <path> (no checkout — safe under worktree policies).
Re-apply the intended additions as surgical edits; verify with targeted tests before the full suite.

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