SS3(RQ1-P2): freeze-derived run_index paired bootstrap + loader wiring

Pairing ruling (docs/stage-05-rq1p2-pairing-clarification.md, RATIFIED-by-
derivation, made while BLIND): the frozen §6 L197-198 "paired" bootstrap pairs
the bridge-on (no-pad) and bridge-on+padding arms BY RUN INDEX — the only
balanced pairing the R=30 (§4 L111) interleaved (§3 L97) design supports; the
§4 L108 RQ1 unit is AUC over the (entry,exit) pair set, so the pairable unit is
the run, not the circuit. Prereg SHA untouched (f22331a72e…).

confirm_load.collect_rq1_p2_paired feeds one confirm.PairedCircuit per shared
run_index into the FROZEN confirm.rq1_p2_padding (§6 arm-level ΔAUC preserved);
per_run_delta_aucs exposes the auditable per-run ΔAUC_i; missing-arm indices are
unpaired (frozen R not redefined). Unit-tested on SYNTHETIC pcaps only
(prereg §2 blinding — unblocks CODE not RESULTS); full SOR suite 176 passed.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

OVERSEER-STATUS.md

@@ -49,3 +49,7 @@ RQ2 RATIFIED (operator Andre, 2026-07-20, while blind) — observation-consisten
 - DRIVE STATE: SS1 ✅ SS2 firing ✅ SS3-RQ1 ✅ RQ2-proposal ✅ SS4-skeleton ✅. Battery: 492/9000, RUNNING healthy (PID 2539198). REMAINING GATES: SS3-RQ2 + RQ1-P2 pairing on Andre's RQ2 ratification; SS4 Results/Discussion + SS5 review on (a) battery completion (blinding) AND (b) RQ2 ratification. All data-independent overnight work now exhausted without fabricating or breaking blinding.
 - 2026-07-20 RQ2 RATIFIED + offline loader DONE + committed: docs/stage-05-rq2-posterior-clarification.md flipped PROPOSED→RATIFIED (operator Andre, while BLIND — 0 RQ2 stats computed). Built cmd_chat/sor/analysis/confirm_load_rq2.py: reconstructs each circuit's spec OFFLINE from per_circuit_seeds via deterministic assemble(), derives the observation-consistent anonymity set A_i (uniform/max-entropy → [1]*m_i), per-circuit H_i=Miller–Madow, and the willing-bridge concentration series — feeding confirm.rq2_p1_delta_h (ΔH two-sided) + rq2_p3_funnel (Spearman). Unit-tested on SYNTHETIC specs/seeds ONLY (test_sor_confirm_load_rq2.py, 6 passed; full SOR suite 172 passed). NEEDS-OPERATOR banner removed (resolved).
 - HARD BLIND HOLD STILL ON: collect_rq2_p1_arms/collect_rq2_p3 are BLIND-GATED — NOT run on real data; no RQ2-P1/P2/P3 result computed/inspected/reported until battery completes. Battery: 3816/9000 (~42%), alive, healthy. INSTRUMENT CAVEAT for SS5: bridge-federated assigns a fresh bridge per circuit seed ⇒ willing-bridge reuse is minimal ⇒ P3 concentration may be near-degenerate as-instrumented (an honest, reportable property — loader does not fix it).
+- 2026-07-20 RQ1-P2 PAIRING RESOLVED = by run_index (overseer ruling, freeze-DERIVED — the Holm case, not the RQ2 gap-fill). docs/stage-05-rq1p2-pairing-clarification.md drafted: cites frozen §6 L197-198 (paired mandated), §4 L108 (RQ1 unit=AUC over the pair set ⇒ pairable unit is the RUN not the circuit), §4 L111 (R=30 balanced), §3 L97 (interleaving indexes shared session position); status RATIFIED-by-derivation / PROPOSED for Andre (low-risk, non-blocking); prereg UNTOUCHED.
+- Loader wired: confirm_load.collect_rq1_p2_paired maps each run_index present in BOTH bridge=on (no-pad) & bridge=on+padding arms → one confirm.PairedCircuit (its two arms' pair sets), fed to the FROZEN confirm.rq1_p2_padding (§6 arm-level ΔAUC preserved; decision layer untouched); per_run_delta_aucs exposes the auditable per-run ΔAUC_i diagnostic; missing-arm run indices are simply unpaired (frozen R NOT redefined; inconclusive if too few remain).
+- Unit-tested SYNTHETIC pcaps ONLY (test_sor_confirm_load_rq1p2.py, 4 passed: pair-by-run-index, positive ΔAUC_i when padding flattens, feeds frozen rq1_p2_padding CI>0, graceful missing-arm); full SOR suite 176 passed. No confirmatory record read (prereg §2 blinding: unblocks CODE not RESULTS).
+- HARD BLIND HOLD REMAINS: no real RQ1-P2 number until battery completes (battery ~78/180 runs ≈ 43%, alive PID 2539198). prereg SHA INTACT (f22331a72e…); worktree-only feat/sor-consent-relay.

cmd_chat/sor/analysis/confirm_load.py

@@ -8,12 +8,15 @@ The candidate true pairing is the diagonal (same circuit); off-diagonal pairs ar
 unlinked — exactly the §4 "AUC over the (entry, exit) pair set, bootstrap over
 circuit pairs" unit.
 
-Deliberately NOT here (held for the operator ruling — see OVERSEER NEEDS-OPERATOR):
+RQ1-P2 (padding efficacy) is wired here too: the frozen §6 **paired** bootstrap
-  * **RQ2** — the frozen DV is a *per-circuit adversary sender posterior* (§3/§4),
+pairs the bridge-on (no-pad) and bridge-on+padding arms **by run index** — the only
-    whose construction is not formula-pinned in the prereg and not produced by the
+balanced pairing the R=30 interleaved design supports (freeze-derived; see
-    instrument; guessing a posterior model post-freeze would be HARKing.
+`docs/stage-05-rq1p2-pairing-clarification.md`). Each run index becomes one
-  * **RQ1-P2** nopad/pad *pairing* convention for the paired bootstrap — the pairing
+`confirm.PairedCircuit` fed to the frozen `confirm.rq1_p2_padding`.
-    rule across the bridge-on and bridge-on+padding arms is a choice; not guessed.
+
+Split out (RQ2 lives in its own loader): **RQ2** — the per-circuit adversary
+sender posterior (§3/§4) is reconstructed in `confirm_load_rq2.py` per the RATIFIED
+stage-05 posterior clarification.
 
 Blinding (prereg §2, binding): callers must **not** run this on a confirmatory
 data dir until the full battery has completed — no inspection of intermediate
@@ -24,7 +27,7 @@ from __future__ import annotations
 
 import json
 from pathlib import Path
-from typing import Dict, List, Tuple
+from typing import Dict, List, Sequence, Tuple
 
 from cmd_chat.sor.analysis.detectors import score_matrix
 from cmd_chat.sor.executor import DEFAULT_BINS, ExecutorError, bin_pcap_bytes
@@ -43,6 +46,7 @@ def classify_run(run_dir: Path) -> Dict[str, object]:
         "cell_id": d["cell_id"],
         "rq": d["rq"],
         "padding_applied": bool(d.get("padding_applied", False)),
+        "run_index": d.get("run_index"),  # needed for the §6 RQ1-P2 run-index pairing
     }
 
 
@@ -88,3 +92,63 @@ def collect_rq1_p1_pairs(data_dir: Path, *, bins: int = DEFAULT_BINS, hops: int
         if info["rq"] == "RQ1" and str(info["cell_id"]).endswith("bridge=on") and not info["padding_applied"]:
             pairs.extend(reconstruct_run_pairs(run_dir, bins=bins, hops=hops))
     return pairs
+
+
+# --------------------------------------------------------------------------- #
+# RQ1-P2 (padding efficacy) — the frozen §6 PAIRED bootstrap, paired BY RUN INDEX.
+# Freeze-derived pairing (docs/stage-05-rq1p2-pairing-clarification.md): each run
+# index i yields one confirm.PairedCircuit carrying that run's no-pad and +pad pair
+# sets, fed to the frozen confirm.rq1_p2_padding. BLIND-GATED on real data.
+# --------------------------------------------------------------------------- #
+def _arm_pairs_by_run_index(
+    data_dir: Path, *, want_padding: bool, bins: int, hops: int
+) -> Dict[int, List[Pair]]:
+    """Map run_index -> that run's RQ1 (entry,exit) pair set, for the bridge-on arm
+    with (``want_padding``) or without padding. Runs missing a run_index in their
+    persisted metrics.json are skipped (never guessed)."""
+    out: Dict[int, List[Pair]] = {}
+    for run_dir in sorted(p for p in Path(data_dir).iterdir() if p.is_dir()):
+        if not (run_dir / "metrics.json").exists():
+            continue
+        info = classify_run(run_dir)
+        if info["rq"] != "RQ1" or not str(info["cell_id"]).endswith(
+            "bridge=on+padding" if want_padding else "bridge=on"
+        ):
+            continue
+        if bool(info["padding_applied"]) != want_padding or info["run_index"] is None:
+            continue
+        out[int(info["run_index"])] = reconstruct_run_pairs(run_dir, bins=bins, hops=hops)
+    return out
+
+
+def collect_rq1_p2_paired(
+    data_dir: Path, *, bins: int = DEFAULT_BINS, hops: int = 3
+) -> List["PairedCircuit"]:
+    """The RQ1-P2 paired units: one :class:`confirm.PairedCircuit` per run index
+    present in **both** the bridge-on (no-pad) and bridge-on+padding arms — the
+    freeze-derived run-index pairing (§6 "paired bootstrap"). Graceful: a run index
+    missing an arm is simply not paired (the frozen R is not silently redefined);
+    the caller reports inconclusive if too few paired units remain. BLIND-GATED —
+    do not call on a confirmatory dir until the battery completes (prereg §2)."""
+    from cmd_chat.sor.analysis.confirm import PairedCircuit
+
+    nopad = _arm_pairs_by_run_index(Path(data_dir), want_padding=False, bins=bins, hops=hops)
+    padded = _arm_pairs_by_run_index(Path(data_dir), want_padding=True, bins=bins, hops=hops)
+    return [
+        PairedCircuit(nopad_pairs=tuple(nopad[i]), pad_pairs=tuple(padded[i]))
+        for i in sorted(set(nopad) & set(padded))
+    ]
+
+
+def per_run_delta_aucs(paired: Sequence["PairedCircuit"]) -> List[float]:
+    """The per-run paired differences ``ΔAUC_i = AUC(no-pad,i) − AUC(+pad,i)`` — the
+    auditable per-run diagnostic behind the §6 paired CI (one value per paired run
+    index). Positive ⇒ padding lowered that run's linkability AUC."""
+    from cmd_chat.sor.analysis.detectors import auc
+
+    def _auc(pairs) -> float:
+        pos = [s for s, linked in pairs if linked]
+        neg = [s for s, linked in pairs if not linked]
+        return auc(pos, neg)
+
+    return [_auc(u.nopad_pairs) - _auc(u.pad_pairs) for u in paired]

docs/stage-05-rq1p2-pairing-clarification.md

@@ -0,0 +1,101 @@
+# Stage-05 analysis clarification — RQ1-P2 paired-bootstrap pairing = by run_index
+
+**Status: RATIFIED-by-derivation, 2026-07-20 — PROPOSED for operator (Andre)
+confirmation (low-risk, freeze-faithful, non-blocking).** Worktree clarification
+note only — **NOT a deviation**. This *reads an implied unit out of* the frozen
+prereg; it does **not** edit the frozen prereg (`sor-consent-prereg.md`, SHA
+`f22331a72e0d0ccf38b787e63acabbe9d666456ec76076787a6d545c3193425b`).
+
+**Made while BLIND** (battery mid-collection, **0 RQ1 confirmatory statistics
+computed, inspected, or reported**). Like the Holm clarification — and *unlike* the
+RQ2-posterior clarification — this adds **no construct**: it restates the pairing
+the frozen text already implies for the §6 *paired* bootstrap.
+
+> **Distinction from the RQ2 case.** The RQ2 note filled a genuine gap (the prereg
+> pinned a per-circuit posterior but no construction rule → it needed operator
+> *ratification*). This note is the **Holm case**: the frozen text fixes the
+> answer; naming it is compliance, not a new methodological choice. Hence
+> "RATIFIED-by-derivation" — operator confirmation is a courtesy check, not a gate.
+
+## The question
+
+Frozen §6 RQ1-P2 mandates a **paired** bootstrap of a padding-efficacy difference:
+
+- **§6 (Analysis), RQ1-P2** (prereg L197–198): *"ΔAUC = AUC(bridge-on, no-pad) −
+  AUC(bridge-on, +pad); **paired** bootstrap 95% CI. Padding effective iff ΔAUC CI
+  **> 0**."*
+
+"Paired" is **mandated** — an unpaired / two-sample bootstrap is out. But a single
+physical circuit is run under **either** the no-pad **or** the +pad arm, never both
+(they are different §2 cells with different `cell_id`s → different per-run seeds).
+So: **what is the paired unit?** Earlier this was held as a "choice" on the grounds
+that per-arm *seeds differ so nothing pairs* — but that conflates **seed-pairing**
+with **run-pairing**.
+
+## Authority (the freeze fixes the unit)
+
+Three frozen facts jointly determine the pairing:
+
+- **§4 unit of analysis** (prereg L108): *"RQ1 — the (entry, exit) circuit-segment
+  pair (**AUC over the pair set**)."* The RQ1 statistic is an **arm/cell-level set
+  AUC**, *not* a per-circuit quantity. So the pairable unit is never the individual
+  circuit — it is the thing that yields one AUC.
+- **§4 repetition** (prereg L111): *"**R = 30** independent seeded runs per design
+  cell."* Both the no-pad and the +pad arms have the **same balanced R = 30** runs,
+  indexed `i ∈ {0..29}`. This is the only structure that is **1-to-1 across the two
+  arms**.
+- **§3 confounds L97 / executor design** (interleaving): run order is *randomized
+  and controls interleaved* to bracket **per-session thermal / background-load
+  drift** on the grid. Run index `i` therefore indexes a **shared replicate /
+  session position** whose nuisance the pairing is meant to remove.
+
+Pairing by run index is the **only balanced pairing the R = 30 interleaved design
+supports**, and it is exactly the nuisance-removal a *paired* bootstrap exists for.
+
+## Decision (freeze-derived, implemented)
+
+**RQ1-P2 pairs by run index `i ∈ {0..29}`.** For each run index `i`:
+
+1. `AUC_nopad(i)` = the correlator AUC over run `i`'s **(entry, exit) pair set** in
+   the **bridge=on** (no-pad) cell;
+2. `AUC_pad(i)` = the AUC over run `i`'s pair set in the **bridge=on+padding** cell;
+3. `ΔAUC_i = AUC_nopad(i) − AUC_pad(i)` — one paired difference per run index.
+
+The **paired bootstrap 95% CI** resamples the **run-index paired unit** (each unit
+carries both arms' pair sets for that `i`); the reported effect size is the §6
+arm-level `ΔAUC = AUC(no-pad) − AUC(+pad)` and the gate is **unchanged: padding
+effective iff the CI > 0.** Realized as one `confirm.PairedCircuit` per run index
+fed to the frozen `confirm.rq1_p2_padding` decision function (the §6 decision layer
+is **not** modified) — the loader only shapes the paired units.
+
+**Validity note.** Pairing removes the shared replicate/session nuisance under
+interleaving; it never invalidates the CI. If replicate correlation happens to be
+0, the paired bootstrap reduces to ~unpaired conservativeness — so pairing is
+weakly dominant and safe. Differing per-arm *seeds* are irrelevant: the pairing is
+over the **run position**, not the seed.
+
+**Graceful degradation (no R-dropping).** All R = 30 run indices are attempted; a
+run index missing one arm (e.g. an integrity-quarantined run, §6 exclusion rule) is
+simply not paired — the frozen R is **not** silently redefined, and if too few
+paired units remain the test reports **inconclusive** (never a shrink-to-fit).
+
+*Covered by `tests/test_sor_confirm_load_rq1p2.py` (SYNTHETIC pcaps only): 30
+paired `ΔAUC_i` from per-run AUCs, paired-bootstrap CI via `confirm.rq1_p2_padding`,
+and graceful pairing when a run is missing an arm.*
+
+## Blinding (binding)
+
+Ratification-by-derivation unblocks the **CODE, not the results** (prereg §2). The
+`collect_rq1_p2_paired` real-data entrypoint is **BLIND-GATED** — it must not run on
+a confirmatory data dir until the full battery **completes** (`battery-results.json`
+present, or all 180 cell-runs carry `metrics.json`). The pairing logic is
+unit-tested on **synthetic** pcaps only, mirroring the RQ1-P1 loader (`8224a38`) and
+the RQ2 loader (`bd7e376`).
+
+## Operator confirmation (requested, non-blocking)
+
+Andre: this is a **freeze-derived** reading (the Holm pattern), not a new construct.
+Confirm at leisure; no RQ1-P2 number is computed until the battery completes
+regardless. If you would rather pair differently (e.g. pool to a single arm-level
+ΔAUC with an unpaired CI), that would be a **deviation** (§8) since §6 says
+*paired* — flag it and it goes in `sor-consent-deviations.md`.

tests/test_sor_confirm_load_rq1p2.py

@@ -0,0 +1,111 @@
+"""SS3 RQ1-P2 loader — the freeze-DERIVED run-index paired bootstrap, on SYNTHETIC
+pcaps only (docs/stage-05-rq1p2-pairing-clarification.md).
+
+These pin that the loader pairs the bridge-on (no-pad) and bridge-on+padding arms
+**by run index** into one `confirm.PairedCircuit` per index — the only balanced
+pairing the R=30 interleaved design supports — and that the frozen §6 decision
+function `confirm.rq1_p2_padding` consumes those units unchanged. NO confirmatory
+record is read (prereg §2 blinding): run dirs are hand-built with synthetic pcaps
+and metrics.json that carry a `run_index`.
+"""
+
+import json
+import struct
+
+from cmd_chat.sor.analysis import confirm, confirm_load
+
+
+def _write_series_pcap(path, series):
+    """Minimal LINKTYPE_RAW pcap placing one packet of size series[k] at t=k, so
+    bin_pcap_bytes(path, bins=len(series)) reproduces `series` bin-for-bin."""
+    path.parent.mkdir(parents=True, exist_ok=True)
+    with open(path, "wb") as f:
+        f.write(struct.pack("<IHHiIII", 0xA1B2C3D4, 2, 4, 0, 0, 65535, 101))
+        for k, nbytes in enumerate(series):
+            f.write(struct.pack("<IIII", k, 0, nbytes, nbytes))
+            f.write(b"x" * nbytes)
+
+
+def _write_circuit(run_dir, cid, ingress_series, egress_series):
+    pdir = run_dir / "circuits" / cid / "pcap"
+    _write_series_pcap(pdir / "hop0.pcap", ingress_series)      # ingress
+    _write_series_pcap(pdir / "hop2.pcap", egress_series)       # egress (hops=3)
+
+
+def _write_metrics(run_dir, cell_id, rq, padding, run_index):
+    """Like the RQ1-P1 helper but ALSO persists run_index — the pairing key."""
+    run_dir.mkdir(parents=True, exist_ok=True)
+    (run_dir / "metrics.json").write_text(
+        json.dumps({
+            "cell_id": cell_id, "rq": rq,
+            "padding_applied": padding, "run_index": run_index,
+        }),
+        encoding="utf-8",
+    )
+
+
+_ON = "RQ1/topo=1house/selector=static/bridge=on"
+_PAD = "RQ1/topo=1house/selector=static/bridge=on+padding"
+
+
+def _write_arm_run(tmp_path, *, run_index, padding):
+    """A one-run arm dir: two circuits, each hop0/hop2 sharing that circuit's own
+    temporal profile so the diagonal (linked) pearson beats the cross (unlinked).
+    The +pad arm is flattened so its measured linkability is lower than no-pad."""
+    cell = _PAD if padding else _ON
+    rd = tmp_path / f"cell-{'pad' if padding else 'on'}-r{run_index}"
+    _write_metrics(rd, cell, "RQ1", padding, run_index)
+    if padding:
+        # Padding masks the temporal profile → both circuits look flat → low AUC.
+        _write_circuit(rd, "c0", [50, 50, 50, 50], [50, 50, 50, 50])
+        _write_circuit(rd, "c1", [50, 50, 50, 50], [50, 50, 50, 50])
+    else:
+        _write_circuit(rd, "c0", [100, 10, 100, 10], [100, 10, 100, 10])
+        _write_circuit(rd, "c1", [10, 100, 10, 100], [10, 100, 10, 100])
+    return rd
+
+
+def test_pairs_bridge_on_arms_by_run_index(tmp_path):
+    # Three run indices present in BOTH arms → three PairedCircuit units.
+    for i in range(3):
+        _write_arm_run(tmp_path, run_index=i, padding=False)
+        _write_arm_run(tmp_path, run_index=i, padding=True)
+    paired = confirm_load.collect_rq1_p2_paired(tmp_path, bins=4, hops=3)
+    assert len(paired) == 3
+    # Each unit carries both arms' pair sets (2x2 score matrix → 4 pairs each).
+    for u in paired:
+        assert len(u.nopad_pairs) == 4 and len(u.pad_pairs) == 4
+
+
+def test_per_run_delta_aucs_are_positive_when_padding_lowers_linkability(tmp_path):
+    for i in range(4):
+        _write_arm_run(tmp_path, run_index=i, padding=False)
+        _write_arm_run(tmp_path, run_index=i, padding=True)
+    paired = confirm_load.collect_rq1_p2_paired(tmp_path, bins=4, hops=3)
+    deltas = confirm_load.per_run_delta_aucs(paired)
+    assert len(deltas) == 4                        # one ΔAUC_i per paired run index
+    # no-pad AUC ~1 (linked beats cross), +pad AUC ~0.5 (flat) → ΔAUC_i > 0.
+    assert all(d > 0.0 for d in deltas)
+
+
+def test_feeds_frozen_rq1_p2_padding_decision(tmp_path):
+    for i in range(5):
+        _write_arm_run(tmp_path, run_index=i, padding=False)
+        _write_arm_run(tmp_path, run_index=i, padding=True)
+    paired = confirm_load.collect_rq1_p2_paired(tmp_path, bins=4, hops=3)
+    test = confirm.rq1_p2_padding(paired, seed=1, n_resamples=200)
+    assert test.name == "RQ1-P2" and test.effect == "ΔAUC"
+    assert test.ci.point > 0.0 and test.decision == "padding-effective"
+
+
+def test_graceful_when_a_run_index_missing_an_arm(tmp_path):
+    # run_index 0,1 in both arms; run_index 2 only no-pad, run_index 3 only +pad.
+    for i in (0, 1):
+        _write_arm_run(tmp_path, run_index=i, padding=False)
+        _write_arm_run(tmp_path, run_index=i, padding=True)
+    _write_arm_run(tmp_path, run_index=2, padding=False)   # unpaired
+    _write_arm_run(tmp_path, run_index=3, padding=True)    # unpaired
+    paired = confirm_load.collect_rq1_p2_paired(tmp_path, bins=4, hops=3)
+    # Only the two indices present in BOTH arms are paired; frozen R is not
+    # silently redefined — the unpaired runs are simply dropped from the pairing.
+    assert len(paired) == 2