feat: intake reconcile mode — flag shipped-but-stale backlog prompts

agents/conductors/intake/AGENTS.md

@@ -75,6 +75,7 @@ schema — light structure over free-form prose.
 | **census** | `intake census` | inventory every filed prompt (work-type/target/difficulty/status + hygiene flags); always read-only |
 | **dashboard** | `intake dashboard` | render the census as the Mind **backlog** page; `--apply` writes `PyAutoMind/dashboard.md` |
 | **formalise** | `intake formalise [prefix]` | retroactively header the prompts census flags — derive the missing fields, insert in place, prose untouched; `--apply` writes |
+| **reconcile** | `intake reconcile [prefix]` | rank backlog prompts that look already-shipped (vs `complete.md` / `issued/`); always read-only — retiring stays human |
 
 Census/dashboard are the Mind *backlog* view — deliberately distinct from
 Heart's `/health status` health view (see "must never do"). The prompt-taxonomy
@@ -87,6 +88,14 @@ Type/Target from the folder, keeps every existing field value and every line of
 prose, and turns work-type disagreements into **re-home suggestions** — it never
 moves or deletes a file.
 
+Reconcile exists because a prompt's `Status:` header is **not** a completeness
+signal — formalise preserves an existing Status verbatim, so shipped work can
+still read `Status: planned`. It cross-references each backlog prompt against
+`complete.md` (path references + `## header` topic overlap), `issued/`
+basenames, and hand-set Status values, then ranks suspects (high/medium/low)
+with the evidence shown. The final verification — the target repo's git log /
+merged PRs — and the retirement itself stay human.
+
 ## Machine sources (one staging surface)
 
 Conception input increasingly arrives from the organism itself — research
@@ -120,6 +129,7 @@ bin/pyauto-brain intake dashboard                                  # backlog pag
 bin/pyauto-brain intake --apply dashboard                          # write PyAutoMind/dashboard.md
 bin/pyauto-brain intake formalise                                  # propose retroactive headers (dry-run)
 bin/pyauto-brain intake --apply formalise bug/                     # write them, only under bug/
+bin/pyauto-brain intake reconcile                                  # rank shipped-but-stale suspects (read-only)
 ```
 
 **Writes only under `--apply`; dry-run is the default.** Exit codes: `0` produced

agents/conductors/intake/INTAKE_TAXONOMY.md

@@ -121,6 +121,17 @@ confidence it emits a *re-home suggestion*; it never moves or deletes a file.
 Optional path-prefix argument scopes the run (`intake formalise bug/`); writes
 only under `--apply` and re-runs are no-ops (nothing left missing).
 
+**reconcile** audits the opposite failure: prompts whose work shipped but whose
+status went stale (a header `Status:` is display metadata — formalise preserves
+an existing value verbatim, so `Status: planned` can outlive the work by
+months). Per backlog prompt it collects four Mind-local signals — a
+`complete.md` line referencing its path (follow-up/restore/parked wording
+downgrades it to likely-open), a duplicate basename in `issued/`, token overlap
+with a completed task's `## header`, and a hand-set Status — then ranks
+suspects high/medium/low with the evidence shown. Always read-only: the final
+verification (target repo git log / merged PRs) and the retirement to
+`issued/` stay human.
+
 ## 7. What intake does NOT own
 
 - The difficulty heuristic, prompt parsing, repo sets → the **sizing faculty**.

agents/conductors/intake/_intake.py

@@ -587,6 +587,124 @@ def emit_formalise(res: dict):
         print("\n(dry-run — re-run `intake --apply formalise` to write the headers)")
 
 
+# --- reconcile (shipped-but-stale audit) ----------------------------------------
+# A prompt's Status: header is NOT a completeness signal — formalise preserves an
+# existing Status verbatim, so shipped work can still read "Status: planned" (the
+# PyAutoHeart M0-M5 cluster sat exactly like that). Reconcile cross-references
+# the backlog against the Mind's shipped-state records and RANKS suspects for a
+# human to retire. Read-only, always: retiring a prompt (moving it to issued/)
+# stays a human act, and the final verification — the target repo's git log /
+# merged PRs — stays out of scope by design.
+_STOPWORDS = frozenset(
+    "the a an of to in for and or is are be with on by via from into as at it "
+    "this that use using make add new fix update support get set can we i you "
+    "our my need should will when once each all its".split())
+# Wording in a complete.md reference line that marks the prompt as a deferred
+# follow-up (still open) rather than the shipped task itself.
+_FOLLOWUP_WORDS = ("follow", "restore", "parked", "remain", "blocked", "later",
+                   "next step", "next-step", "deferred")
+
+
+def _tokens(s: str) -> set:
+    return {w for w in re.findall(r"[a-z0-9]+", s.lower())
+            if len(w) > 2 and w not in _STOPWORDS}
+
+
+def reconcile(mind: Path, prefix: str = "") -> dict:
+    """Rank backlog prompts that look already-shipped, for a human to retire.
+
+    Four Mind-local signals per prompt: a complete.md line referencing its path
+    (follow-up wording downgrades it), a duplicate basename in issued/, token
+    overlap with a completed task's `## header`, and a hand-set Status the
+    formalise pass deliberately preserved. Never writes anything.
+    """
+    c = census(mind)
+    comp = mind / "complete.md"
+    comp_lines = (comp.read_text(encoding="utf-8", errors="replace").splitlines()
+                  if comp.is_file() else [])
+    headers = [(ln[3:].strip(), _tokens(ln[3:].replace("-", " ")))
+               for ln in comp_lines if ln.startswith("## ")]
+    issued = mind / "issued"
+    issued_names = ({p.name for p in issued.glob("*.md")}
+                    if issued.is_dir() else set())
+
+    suspects = []
+    for r in c["records"]:
+        if prefix and not r["path"].startswith(prefix):
+            continue
+        path = r["path"]
+        base = path.rsplit("/", 1)[-1]
+        sans_wt = path.split("/", 1)[1] if "/" in path else path
+        findings = []
+        score = 0.0
+
+        for ln in comp_lines:
+            if base in ln or sans_wt in ln:
+                kind = ("referenced-followup"
+                        if any(w in ln.lower() for w in _FOLLOWUP_WORDS)
+                        else "referenced")
+                findings.append((kind, ln.strip()))
+
+        if base in issued_names:
+            findings.append(("issued-duplicate", f"issued/{base} already exists"))
+
+        sig = _tokens(base.replace("_", " ")) | _tokens(r["title"])
+        best = (0.0, "", set())
+        for h, ht in headers:
+            if not sig or not ht:
+                continue
+            shared = sig & ht
+            j = len(shared) / len(sig | ht)
+            if (j, len(shared)) > (best[0], len(best[2])):
+                best = (j, h, shared)
+        if best[0] >= 0.40 or len(best[2]) >= 3:
+            score = best[0]
+            findings.append(("topic-overlap",
+                             f"complete.md '## {best[1]}' "
+                             f"(shared: {', '.join(sorted(best[2]))})"))
+
+        if r["status"] not in ("-", "formalised"):
+            findings.append(("stale-status",
+                             f"Status: {r['status']} — hand-set; verify against "
+                             "shipped state"))
+
+        if findings:
+            kinds = {k for k, _ in findings}
+            if "issued-duplicate" in kinds or "referenced" in kinds:
+                conf = "high"
+            elif "topic-overlap" in kinds:
+                conf = "medium"
+            else:
+                conf = "low"       # follow-up reference / stale status only
+            suspects.append({
+                "path": path, "title": r["title"], "confidence": conf,
+                "overlap_score": round(score, 2),
+                "findings": [{"kind": k, "evidence": e} for k, e in findings],
+            })
+
+    order = {"high": 0, "medium": 1, "low": 2}
+    suspects.sort(key=lambda s: (order[s["confidence"]],
+                                 -s["overlap_score"], s["path"]))
+    return {"generated": _dt.date.today().isoformat(), "scanned": c["total"],
+            "suspects": suspects}
+
+
+def emit_reconcile(res: dict):
+    print(f"== Intake reconcile: {len(res['suspects'])} suspect(s) of "
+          f"{res['scanned']} scanned ==")
+    if not res["suspects"]:
+        print("  backlog reconciles clean against complete.md / issued/.")
+    for s in res["suspects"]:
+        print(f"[{s['confidence']:>6}] {s['path']}")
+        for f in s["findings"]:
+            ev = f["evidence"]
+            if len(ev) > 160:
+                ev = ev[:157] + "…"
+            print(f"         {f['kind']}: {ev}")
+    print("\nRetiring a prompt stays human: verify against the target repo's "
+          "git log / merged\nPRs, then move it to issued/ by hand.")
+
+
 # --- ideas.md scanning --------------------------------------------------------
 def scan_ideas(mind: Path):
     """Yield (bullet_text, context_header) for substantive ideas.md lines."""
@@ -679,6 +797,11 @@ def main(argv=None):
                     help="only formalise prompts under this path prefix "
                          "(e.g. bug/)")
 
+    rc = sub.add_parser("reconcile", help="rank backlog prompts that look "
+                                          "already-shipped (always read-only)")
+    rc.add_argument("prefix", nargs="?", default="",
+                    help="only reconcile prompts under this path prefix")
+
     a = ap.parse_args(argv)
     mind = Path(a.mind)
 
@@ -687,6 +810,14 @@ def main(argv=None):
         print(json.dumps(res, indent=2)) if a.as_json else emit_formalise(res)
         return 0
 
+    if a.cmd == "reconcile":
+        if a.apply:
+            print("intake reconcile is read-only — retiring prompts stays "
+                  "human (--apply ignored).", file=sys.stderr)
+        res = reconcile(mind, prefix=a.prefix)
+        print(json.dumps(res, indent=2)) if a.as_json else emit_reconcile(res)
+        return 0
+
     if a.cmd == "census":
         c = census(mind)
         print(json.dumps(c, indent=2)) if a.as_json else emit_census(c)

agents/conductors/intake/intake.sh

@@ -24,6 +24,9 @@
 #   intake formalise [prefix]    retroactively header the backlog prompts the
 #                                census flags (word-vomit is intent, not defect);
 #                                --apply writes the headers in place
+#   intake reconcile [prefix]    rank backlog prompts that look already-shipped
+#                                (vs complete.md / issued/); always read-only —
+#                                retiring a prompt stays human
 #
 # Flags (place before the subcommand; both default OFF):
 #   --apply    write the formal prompt file(s) / dashboard.md; else dry-run only
@@ -45,7 +48,7 @@ apply=0
 forward=()
 while [[ $# -gt 0 ]]; do
   case "$1" in
-    -h|--help) sed -n '2,36p' "${BASH_SOURCE[0]}" | sed 's/^# \{0,1\}//'; exit 0 ;;
+    -h|--help) sed -n '2,39p' "${BASH_SOURCE[0]}" | sed 's/^# \{0,1\}//'; exit 0 ;;
     --json) as_json=1; shift ;;
     --apply) apply=1; shift ;;
     *) forward+=("$1"); shift ;;
@@ -61,7 +64,7 @@ fi
 # A bare first token that is not a known subcommand -> classify mode on the rest,
 # so `intake "raw idea"` and `intake --file p.md` both work as the front door.
 case "${forward[0]}" in
-  classify|ideas|census|dashboard|formalise) ;;
+  classify|ideas|census|dashboard|formalise|reconcile) ;;
   *) forward=(classify "${forward[@]}") ;;
 esac
 

skills/intake/intake.md

@@ -38,6 +38,11 @@ dev workflow (issue, branch, plan). Do not bypass the Brain.
   fields, inserts them in place with all prose verbatim, reports re-home
   suggestions instead of ever moving files. Dry-run proposes; `--apply` writes
   (then regenerate the dashboard).
+- `bin/pyauto-brain intake reconcile [prefix]` — ranks backlog prompts that
+  look already-shipped (cross-referenced against `complete.md` and `issued/`;
+  a stale hand-set `Status:` is a signal, never proof). Always read-only:
+  verify each suspect against the target repo's git log / merged PRs, then
+  retire it to `issued/` by hand.
 
 ## Boundary