From a67f4f41c11cb792fd8dea548a84b156940f1e6e Mon Sep 17 00:00:00 2001
From: "Carlos D. Escobar-Valbuena" <devteam@getstimulus.ai>
Date: Fri, 26 Jun 2026 20:52:05 -0500
Subject: [PATCH 1/3] feat(repair+doctor): propagate + audit the P6
 /kg-discovery reflex (BRO-1555)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Two propagation gaps: BRO-1426 added the §P6 "/kg for discovery, never substrate
grep" retrieval reflex to the AGENTS.md template, but existing workspaces never
received it — scaffold_governance_file is idempotent-never-overwrite, and
repair.sh only backfilled the Development Philosophy section. doctor never
checked AGENTS.md actually carried the reflex either.

- repair.sh: backfill_retrieval_discipline() backfills the §P6 retrieval
  paragraph into an existing AGENTS.md — idempotent (skip if present), anchored
  (§P6 → next heading; skip with warning if absent), file-only awk extraction
  (no shell interpolation of content, backticks/pipes survive). Flag-clear (not
  awk `exit`) on the boundary so tr|awk doesn't SIGPIPE under pipefail. Mirrors
  backfill_philosophy_section; registered next to it.
- doctor.sh §4c: advisory check that AGENTS.md carries the reflex. Informational
  only — never a GAP, never fails --strict (mirrors §4b convention). Proven
  gap-neutral + strict-neutral by test.
- Marker is the coined phrase "substrate grep" (not the full "never substrate
  grep") so a workspace carrying the reflex under DIFFERENT wording — e.g. this
  workspace's hand-authored "not a substrate grep" variant — is detected as
  present and NOT duplicated. Verified: doctor reports [ok] + repair won't
  duplicate on the real workspace.

Tests: tests/retrieval-discipline-backfill.test.sh (16 assertions) — backfill +
idempotency + position-inside-§P6 + verbatim content + --dry-run + missing-anchor
skip + §4c advisory both directions + gap/strict-neutral + CRLF. Sibling
philosophy-backfill + all 5 canary suites still green.

BRO-1555

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 scripts/doctor.sh                           |  17 ++
 scripts/repair.sh                           | 101 +++++++++
 tests/retrieval-discipline-backfill.test.sh | 234 ++++++++++++++++++++
 3 files changed, 352 insertions(+)
 create mode 100755 tests/retrieval-discipline-backfill.test.sh

diff --git a/scripts/doctor.sh b/scripts/doctor.sh
index 5b97f37..52ac2e4 100755
--- a/scripts/doctor.sh
+++ b/scripts/doctor.sh
@@ -218,6 +218,23 @@ if [ -f "$AGENTS" ]; then
     fi
 fi
 
+# ── 4c. AGENTS.md P6 retrieval-discipline reflex (advisory, backfillable) ────
+# The "/kg for discovery, never substrate grep" reflex was added to the §P6
+# template with the BRO-1426 reflex. A workspace bootstrapped before then
+# legitimately lacks it (scaffold never overwrites an existing AGENTS.md), so —
+# like §4b — this is informational only: never a GAP, never fails --strict.
+# `bstack repair` backfills it. Marker phrase "substrate grep" matches repair's
+# idempotency check and is wording-agnostic (catches "never"/"not a" variants).
+section "4c. AGENTS.md retrieval-discipline reflex (advisory)"
+if [ -f "$AGENTS" ]; then
+    if grep -qF "substrate grep" "$AGENTS"; then
+        ok "AGENTS.md has P6 retrieval-discipline reflex (/kg for discovery)"
+    else
+        echo "  [info] AGENTS.md has no P6 retrieval-discipline reflex (/kg for discovery, never substrate grep)"
+        echo "         → backfill: bstack repair  (informational; not a gap, does not fail --strict)"
+    fi
+fi
+
 # ── 5. policy.yaml required blocks ──────────────────────────────────────────
 section "5. .control/policy.yaml blocks"
 POL="$WORKSPACE/.control/policy.yaml"
diff --git a/scripts/repair.sh b/scripts/repair.sh
index 4fec803..a96c3e4 100755
--- a/scripts/repair.sh
+++ b/scripts/repair.sh
@@ -212,6 +212,106 @@ backfill_philosophy_section() {
     echo "  [fix] backfilled Development Philosophy into $target"
 }
 
+# Backfill the §P6 "Retrieval discipline (/kg for discovery, never substrate
+# grep)" reflex paragraph into an existing AGENTS.md that predates it (templated
+# in the §P6 section since the BRO-1426 reflex shipped). Same idempotent-never-
+# overwrite gap as the philosophy section: scaffold only creates whole files, so
+# existing workspaces never receive newly-templated *content* — this closes that
+# gap for this one paragraph.
+#
+# Idempotent + non-destructive: skips if the marker phrase is already present;
+# skips with a warning if the §P6→next-heading insertion anchor is absent (never
+# guesses a location). Extracts the paragraph verbatim from the template (the
+# `**Retrieval discipline` line → next `### ` heading, exclusive) via files only
+# — no shell interpolation of the content — so backticks/quotes/pipes survive.
+backfill_retrieval_discipline() {
+    local target="$1"        # AGENTS.md
+    local template="$2"      # AGENTS.md.template
+    local tgt="$WORKSPACE_DIR/$target"
+    local tpl="$TEMPLATES_DIR/$template"
+    # Shared marker with doctor §4c so detection and backfill agree on "present".
+    # Match the coined phrase "substrate grep" (not the full "never substrate
+    # grep") so a workspace carrying the reflex under DIFFERENT wording — e.g. a
+    # hand-authored "not a substrate grep" variant — is still detected as present
+    # and NOT duplicated. "substrate grep" appears only in this reflex.
+    local marker="substrate grep"
+    [ -f "$tgt" ] || return                                   # nothing to backfill into
+    [ -f "$tpl" ] || { echo "  [skip] $target retrieval-discipline — template missing: $template"; return; }
+    grep -qF "$marker" "$tgt" && return                       # already present (idempotent)
+    if ! grep -qF "$marker" "$tpl"; then
+        echo "  [skip] $target retrieval-discipline — template lacks the paragraph"
+        return
+    fi
+    # Anchor: the target must have a §P6 section followed by a later `### ` heading
+    # (the paragraph lands at the END of §P6, before whatever heading follows it).
+    if ! awk '
+        function clean(s){ sub(/\r$/,"",s); return s }
+        { l=clean($0); if (l ~ /^### P6([ :]|$)/) p6=1; else if (p6 && l ~ /^### /) {found=1; exit} }
+        END { exit (found ? 0 : 1) }
+    ' "$tgt"; then
+        echo "  [skip] $target retrieval-discipline — no §P6→heading anchor (insert manually)"
+        return
+    fi
+    if [ "$DRY_RUN" = "1" ]; then
+        echo "  [dry-run] would backfill P6 retrieval-discipline into $target"
+        return
+    fi
+    if ! confirm "Backfill P6 retrieval-discipline reflex into $target?"; then
+        echo "  [skip] $target retrieval-discipline (declined)"
+        return
+    fi
+    local secfile tmp
+    secfile="$(mktemp)" || { echo "  [skip] $target retrieval-discipline — mktemp failed"; return; }
+    # Extract the paragraph: from the `**Retrieval discipline` line up to (excluding)
+    # the next `### ` heading. CR stripped first so awk delimiters match a CRLF template.
+    # Flag-clear on the boundary (NOT `exit`): under `set -o pipefail` an early awk
+    # exit closes the pipe and `tr` dies with SIGPIPE → the pipeline fails spuriously.
+    # Draining all of tr's output keeps the pipeline status clean.
+    if ! tr -d '\r' < "$tpl" | awk '
+        /^\*\*Retrieval discipline/ { f=1 }
+        f && /^### / { f=0 }
+        f { print }
+    ' > "$secfile"; then
+        echo "  [skip] $target retrieval-discipline — extraction pipeline failed"
+        rm -f "$secfile"
+        return
+    fi
+    if [ ! -s "$secfile" ] || ! grep -qF "$marker" "$secfile"; then
+        echo "  [skip] $target retrieval-discipline — could not extract from $template"
+        rm -f "$secfile"
+        return
+    fi
+    tmp="$(mktemp)" || { echo "  [skip] $target retrieval-discipline — mktemp failed"; rm -f "$secfile"; return; }
+    # Insert at the END of §P6 — before the first `### ` heading after `### P6`.
+    if ! awk -v secfile="$secfile" '
+        function clean(s){ sub(/\r$/,"",s); return s }
+        { line = clean($0) }
+        seenP6 && line ~ /^### / && !done {
+            while ((getline s < secfile) > 0) print s
+            close(secfile)
+            done = 1
+        }
+        { if (line ~ /^### P6([ :]|$)/) seenP6 = 1; print }
+    ' "$tgt" > "$tmp"; then
+        echo "  [skip] $target retrieval-discipline — insertion failed (awk)"
+        rm -f "$secfile" "$tmp"
+        return
+    fi
+    rm -f "$secfile"
+    # Verify the paragraph actually landed before committing the write.
+    if ! grep -qF "$marker" "$tmp"; then
+        echo "  [skip] $target retrieval-discipline — anchor not matched during insert (no change)"
+        rm -f "$tmp"
+        return
+    fi
+    if ! mv "$tmp" "$tgt"; then
+        echo "  [skip] $target retrieval-discipline — could not write $target"
+        rm -f "$tmp"
+        return
+    fi
+    echo "  [fix] backfilled P6 retrieval-discipline reflex into $target"
+}
+
 # ── Hook re-wire (helper) ──────────────────────────────────────────────────
 # Idempotently merges every hook in assets/templates/settings.json.snippet
 # into $WORKSPACE_DIR/.claude/settings.json. Existing entries are never
@@ -362,6 +462,7 @@ deploy_workspace_hooks
 # GAP (so doctor still reports "fully bstack-compliant" without it).
 backfill_philosophy_section "AGENTS.md" "AGENTS.md.template"
 backfill_philosophy_section "CLAUDE.md" "CLAUDE.md.template"
+backfill_retrieval_discipline "AGENTS.md" "AGENTS.md.template"
 
 if echo "$GAPS_OUTPUT" | grep -q "fully bstack-compliant"; then
     echo "  ✓ no other gaps — workspace already bstack-compliant"
diff --git a/tests/retrieval-discipline-backfill.test.sh b/tests/retrieval-discipline-backfill.test.sh
new file mode 100755
index 0000000..93faeed
--- /dev/null
+++ b/tests/retrieval-discipline-backfill.test.sh
@@ -0,0 +1,234 @@
+#!/usr/bin/env bash
+# tests/retrieval-discipline-backfill.test.sh — fixture-based tests for the §P6
+# "/kg for discovery, never substrate grep" retrieval-discipline backfill in
+# scripts/repair.sh and the advisory (§4c) in scripts/doctor.sh.
+#
+# Verifies:
+#   1. A pre-BRO-1426 AGENTS.md (§P6 present, retrieval paragraph absent) gets
+#      the paragraph backfilled, positioned INSIDE §P6 (after ### P6, before ### P7).
+#   2. Re-running is idempotent (exactly one occurrence; no duplicate).
+#   3. --dry-run reports the backfill but writes nothing.
+#   4. Missing §P6→heading anchor → skip with a warning, file unchanged.
+#   5. doctor §4c surfaces the advisory when absent, ok when present — and the
+#      advisory is NOT a GAP / does NOT change the GAP total or --strict exit.
+#   6. CRLF / trailing-space tolerant; section content extracted verbatim.
+#
+# Run from repo root: bash tests/retrieval-discipline-backfill.test.sh
+set -uo pipefail
+
+BSTACK_REPO="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+REPAIR_SH="$BSTACK_REPO/scripts/repair.sh"
+DOCTOR_SH="$BSTACK_REPO/scripts/doctor.sh"
+TEMPLATE="$BSTACK_REPO/assets/templates/AGENTS.md.template"
+
+PASS=0
+FAIL=0
+FAILED_TESTS=()
+
+assert_pass() { PASS=$((PASS + 1)); echo "  ✓ $1"; }
+assert_fail() {
+    FAIL=$((FAIL + 1)); FAILED_TESTS+=("$1")
+    echo "  ✗ $1"; [ -n "${2:-}" ] && echo "    ${2}"
+}
+
+# Count occurrences of the shared marker phrase (matches repair + doctor).
+refl_count() { grep -cF "substrate grep" "$1" 2>/dev/null || true; }
+
+# A workspace whose AGENTS.md has the Primitives anchor + §P6 and §P7 sections
+# but NO retrieval-discipline paragraph (simulates a pre-BRO-1426 bootstrap).
+# CLAUDE.md carries the anchor so the sibling philosophy backfill doesn't error.
+fresh_pre1426_workspace() {
+    local ws; ws="$(mktemp -d)"
+    cat > "$ws/AGENTS.md" <<'EOF'
+# demo — Agent Guidelines
+
+## Self-Meta Definition
+
+This file IS the control harness.
+
+## Bstack Core Automation Primitives
+
+### P6 — Bookkeeping: Knowledge Bookkeeping
+
+**What**: pipeline.
+
+**Reflexive Trigger Rule**: Bookkeeping is a reflex.
+
+**Never a question.** Capture is the default.
+
+### P7 — Freshness: Skill Freshness Check
+
+**What**: stale-install detector.
+EOF
+    cat > "$ws/CLAUDE.md" <<'EOF'
+# demo — bstack-governed workspace
+
+## Identity
+
+Governed by bstack.
+
+## Bstack Core Automation Primitives
+
+(table)
+EOF
+    echo "$ws"
+}
+
+echo "=== retrieval-discipline-backfill.test.sh ==="
+
+# Precondition: the template carries the paragraph (else the whole feature is moot).
+if [ "$(refl_count "$TEMPLATE")" -ge 1 ]; then
+    assert_pass "template AGENTS.md.template carries the retrieval-discipline paragraph"
+else
+    assert_fail "template is missing the retrieval-discipline paragraph (feature source gone)"
+fi
+
+# ── Test 1 + 2: backfill + idempotency ──────────────────────────────────────
+echo ""
+echo "Test 1+2: backfill into pre-BRO-1426 workspace, then idempotency"
+WS="$(fresh_pre1426_workspace)"
+
+[ "$(refl_count "$WS/AGENTS.md")" -eq 0 ] && assert_pass "precondition: AGENTS.md has no retrieval paragraph" \
+    || assert_fail "precondition: AGENTS.md should start without the paragraph"
+
+BROOMVA_WORKSPACE="$WS" bash "$REPAIR_SH" --apply-all >/dev/null 2>&1
+
+if [ "$(refl_count "$WS/AGENTS.md")" -eq 1 ]; then
+    assert_pass "AGENTS.md retrieval paragraph backfilled (exactly one)"
+else
+    assert_fail "retrieval paragraph not backfilled (count=$(refl_count "$WS/AGENTS.md"))"
+fi
+
+# Position: paragraph must land INSIDE §P6 — after ### P6, before ### P7.
+refl_line="$(grep -nF "substrate grep" "$WS/AGENTS.md" | head -1 | cut -d: -f1)"
+p6_line="$(grep -nE "^### P6" "$WS/AGENTS.md" | head -1 | cut -d: -f1)"
+p7_line="$(grep -nE "^### P7" "$WS/AGENTS.md" | head -1 | cut -d: -f1)"
+if [ -n "$refl_line" ] && [ "$refl_line" -gt "$p6_line" ] && [ "$refl_line" -lt "$p7_line" ]; then
+    assert_pass "paragraph positioned inside §P6 (P6=$p6_line < para=$refl_line < P7=$p7_line)"
+else
+    assert_fail "paragraph not inside §P6 (P6=$p6_line para=$refl_line P7=$p7_line)"
+fi
+
+# Content extracted verbatim (backticks / pipes / quotes intact).
+if grep -qF 'never as the step that decides' "$WS/AGENTS.md"; then
+    assert_pass "paragraph content extracted verbatim (delimiters intact)"
+else
+    assert_fail "paragraph content lost in extraction"
+fi
+
+# Idempotency: second run must not duplicate.
+BROOMVA_WORKSPACE="$WS" bash "$REPAIR_SH" --apply-all >/dev/null 2>&1
+if [ "$(refl_count "$WS/AGENTS.md")" -eq 1 ]; then
+    assert_pass "idempotent: re-run did not duplicate the paragraph"
+else
+    assert_fail "idempotency broken (count=$(refl_count "$WS/AGENTS.md"))"
+fi
+rm -rf "$WS"
+
+# ── Test 3: --dry-run writes nothing ────────────────────────────────────────
+echo ""
+echo "Test 3: --dry-run reports but does not write"
+WS="$(fresh_pre1426_workspace)"
+DRY_OUT="$(BROOMVA_WORKSPACE="$WS" bash "$REPAIR_SH" --dry-run 2>&1)"
+if echo "$DRY_OUT" | grep -q "would backfill P6 retrieval-discipline into AGENTS.md"; then
+    assert_pass "--dry-run reports the backfill"
+else
+    assert_fail "--dry-run did not report the backfill"
+fi
+if [ "$(refl_count "$WS/AGENTS.md")" -eq 0 ]; then
+    assert_pass "--dry-run wrote nothing"
+else
+    assert_fail "--dry-run modified the file (count=$(refl_count "$WS/AGENTS.md"))"
+fi
+rm -rf "$WS"
+
+# ── Test 4: missing §P6 anchor → skip, file unchanged ───────────────────────
+echo ""
+echo "Test 4: missing §P6 section → skip with warning"
+WS="$(mktemp -d)"
+printf '# demo\n\n## Bstack Core Automation Primitives\n\n(no P6 here)\n' > "$WS/AGENTS.md"
+printf '# demo\n\n## Bstack Core Automation Primitives\n\n(table)\n' > "$WS/CLAUDE.md"
+SKIP_OUT="$(BROOMVA_WORKSPACE="$WS" bash "$REPAIR_SH" --apply-all 2>&1)"
+if echo "$SKIP_OUT" | grep -q "retrieval-discipline — no §P6→heading anchor"; then
+    assert_pass "missing §P6 anchor reported as skip"
+else
+    assert_fail "missing-anchor skip not reported"
+fi
+if [ "$(refl_count "$WS/AGENTS.md")" -eq 0 ]; then
+    assert_pass "missing-anchor file left unchanged"
+else
+    assert_fail "paragraph inserted despite missing anchor"
+fi
+rm -rf "$WS"
+
+# ── Test 5: doctor §4c advisory present/absent + 0 gaps / strict-neutral ─────
+echo ""
+echo "Test 5: doctor §4c advisory is informational (does not change GAP total / --strict)"
+gap_lines() { grep -c "^  \[gap\]" 2>/dev/null || true; }
+WS="$(mktemp -d)"; mkdir -p "$WS/.control"
+cp "$BSTACK_REPO/assets/templates/policy.yaml.template" "$WS/.control/policy.yaml" 2>/dev/null || true
+cp "$BSTACK_REPO/assets/templates/CLAUDE.md.template" "$WS/CLAUDE.md" 2>/dev/null || true
+
+# (a) WITHOUT the paragraph: strip it from the real template (para line → next ### , exclusive).
+awk '/^\*\*Retrieval discipline/{skip=1} skip && /^### /{skip=0} !skip' \
+    "$TEMPLATE" > "$WS/AGENTS.md"
+DOC_WITHOUT="$(BROOMVA_WORKSPACE="$WS" bash "$DOCTOR_SH" 2>&1)"
+BROOMVA_WORKSPACE="$WS" bash "$DOCTOR_SH" --strict >/dev/null 2>&1; STRICT_WITHOUT=$?
+GAPS_WITHOUT="$(echo "$DOC_WITHOUT" | gap_lines)"
+
+if echo "$DOC_WITHOUT" | grep -q "no P6 retrieval-discipline reflex"; then
+    assert_pass "doctor surfaces §4c advisory when paragraph absent"
+else
+    assert_fail "doctor did not surface the §4c advisory"
+fi
+if echo "$DOC_WITHOUT" | grep -qE "\[gap\].*(retrieval|substrate grep)"; then
+    assert_fail "advisory emitted as a GAP (should be informational)"
+else
+    assert_pass "advisory is informational, not a [gap] line"
+fi
+
+# (b) WITH the paragraph: identical workspace, real template (paragraph present).
+cp "$TEMPLATE" "$WS/AGENTS.md"
+DOC_WITH="$(BROOMVA_WORKSPACE="$WS" bash "$DOCTOR_SH" 2>&1)"
+BROOMVA_WORKSPACE="$WS" bash "$DOCTOR_SH" --strict >/dev/null 2>&1; STRICT_WITH=$?
+GAPS_WITH="$(echo "$DOC_WITH" | gap_lines)"
+
+if echo "$DOC_WITH" | grep -q "has P6 retrieval-discipline reflex"; then
+    assert_pass "doctor §4c reports ok when paragraph present"
+else
+    assert_fail "doctor §4c did not report ok with paragraph present"
+fi
+if [ "$GAPS_WITHOUT" = "$GAPS_WITH" ]; then
+    assert_pass "GAP total identical with/without paragraph ($GAPS_WITH) — advisory adds 0 gaps"
+else
+    assert_fail "advisory changed the GAP total (without=$GAPS_WITHOUT with=$GAPS_WITH)"
+fi
+if [ "$STRICT_WITHOUT" = "$STRICT_WITH" ]; then
+    assert_pass "--strict exit identical with/without paragraph (=$STRICT_WITH)"
+else
+    assert_fail "--strict exit changed (without=$STRICT_WITHOUT with=$STRICT_WITH)"
+fi
+rm -rf "$WS"
+
+# ── Test 6: CRLF / trailing-space §P6 heading is matched ─────────────────────
+echo ""
+echo "Test 6: CRLF + trailing-space §P6/§P7 headings are matched"
+WS="$(mktemp -d)"
+printf '# demo\r\n\r\n## Bstack Core Automation Primitives\r\n\r\n### P6 — Bookkeeping   \r\n\r\n**What**: x.\r\n\r\n### P7 — Freshness\r\n\r\n**What**: y.\r\n' > "$WS/AGENTS.md"
+printf '# demo\n\n## Bstack Core Automation Primitives\n\n(table)\n' > "$WS/CLAUDE.md"
+BROOMVA_WORKSPACE="$WS" bash "$REPAIR_SH" --apply-all >/dev/null 2>&1
+if [ "$(refl_count "$WS/AGENTS.md")" -eq 1 ]; then
+    assert_pass "CRLF/trailing-space §P6 heading matched — paragraph inserted"
+else
+    assert_fail "CRLF/trailing-space §P6 NOT matched (count=$(refl_count "$WS/AGENTS.md"))"
+fi
+rm -rf "$WS"
+
+# ── Summary ─────────────────────────────────────────────────────────────────
+echo ""
+echo "=== results: $PASS passed, $FAIL failed ==="
+if [ "$FAIL" -gt 0 ]; then
+    printf '  - %s\n' "${FAILED_TESTS[@]}"
+    exit 1
+fi
+exit 0

From f9052f59d38c3fd6f0148b94b1d84da88dcdaa84 Mon Sep 17 00:00:00 2001
From: "Carlos D. Escobar-Valbuena" <devteam@getstimulus.ai>
Date: Fri, 26 Jun 2026 21:00:57 -0500
Subject: [PATCH 2/3] fix(repair+doctor): semantic guard against duplicating a
 reworded reflex (P20 review)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Cross-review [MAJOR]: the "substrate grep" phrase marker only guards variants that
RETAIN the phrase; a reflex reworded to drop it (e.g. "never grep the substrate
directly") was not detected → backfill appended a second paragraph.

- repair.sh: add a structural guard — also treat `^**Retrieval discipline` as
  present (the reflex's bold-lead signature), so a phrase-dropping reword isn't
  duplicated. Comment scoped to the true guarantee.
- doctor.sh §4c: match the same two signals (phrase OR `**Retrieval discipline`
  lead) so doctor + repair agree on "present" (doctor won't tell the user to run
  repair when repair would correctly skip).
- test: +Test 4b — a reworded reflex (drops the phrase, keeps the lead) is not
  duplicated by --apply-all. 17 assertions, all green.

BRO-1555

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 scripts/doctor.sh                           |  8 +++---
 scripts/repair.sh                           | 13 ++++++----
 tests/retrieval-discipline-backfill.test.sh | 28 +++++++++++++++++++++
 3 files changed, 41 insertions(+), 8 deletions(-)

diff --git a/scripts/doctor.sh b/scripts/doctor.sh
index 52ac2e4..ae95f02 100755
--- a/scripts/doctor.sh
+++ b/scripts/doctor.sh
@@ -223,11 +223,13 @@ fi
 # template with the BRO-1426 reflex. A workspace bootstrapped before then
 # legitimately lacks it (scaffold never overwrites an existing AGENTS.md), so —
 # like §4b — this is informational only: never a GAP, never fails --strict.
-# `bstack repair` backfills it. Marker phrase "substrate grep" matches repair's
-# idempotency check and is wording-agnostic (catches "never"/"not a" variants).
+# `bstack repair` backfills it. Detection mirrors repair's two signals so the two
+# agree on "present": the coined phrase "substrate grep" (catches the template +
+# "never"/"not a" wording variants) OR the structural `**Retrieval discipline`
+# lead (catches a reflex reworded to drop the phrase).
 section "4c. AGENTS.md retrieval-discipline reflex (advisory)"
 if [ -f "$AGENTS" ]; then
-    if grep -qF "substrate grep" "$AGENTS"; then
+    if grep -qF "substrate grep" "$AGENTS" || grep -qE "^\*\*Retrieval discipline" "$AGENTS"; then
         ok "AGENTS.md has P6 retrieval-discipline reflex (/kg for discovery)"
     else
         echo "  [info] AGENTS.md has no P6 retrieval-discipline reflex (/kg for discovery, never substrate grep)"
diff --git a/scripts/repair.sh b/scripts/repair.sh
index a96c3e4..d212939 100755
--- a/scripts/repair.sh
+++ b/scripts/repair.sh
@@ -229,15 +229,18 @@ backfill_retrieval_discipline() {
     local template="$2"      # AGENTS.md.template
     local tgt="$WORKSPACE_DIR/$target"
     local tpl="$TEMPLATES_DIR/$template"
-    # Shared marker with doctor §4c so detection and backfill agree on "present".
-    # Match the coined phrase "substrate grep" (not the full "never substrate
-    # grep") so a workspace carrying the reflex under DIFFERENT wording — e.g. a
-    # hand-authored "not a substrate grep" variant — is still detected as present
-    # and NOT duplicated. "substrate grep" appears only in this reflex.
+    # Shared phrase marker with doctor §4c so detection and backfill agree on
+    # "present". "substrate grep" is the coined phrase and appears only in this
+    # reflex; it catches the verbatim template paragraph AND wording variants that
+    # retain the phrase (e.g. a hand-authored "not a substrate grep").
     local marker="substrate grep"
     [ -f "$tgt" ] || return                                   # nothing to backfill into
     [ -f "$tpl" ] || { echo "  [skip] $target retrieval-discipline — template missing: $template"; return; }
     grep -qF "$marker" "$tgt" && return                       # already present (idempotent)
+    # Semantic guard: also treat a reflex reworded to DROP the phrase as present
+    # (an additive backfill of a second paragraph is worse than a missed one).
+    # The `**Retrieval discipline` lead is the reflex's structural signature.
+    grep -qE "^\*\*Retrieval discipline" "$tgt" && return     # present under different wording
     if ! grep -qF "$marker" "$tpl"; then
         echo "  [skip] $target retrieval-discipline — template lacks the paragraph"
         return
diff --git a/tests/retrieval-discipline-backfill.test.sh b/tests/retrieval-discipline-backfill.test.sh
index 93faeed..99aad06 100755
--- a/tests/retrieval-discipline-backfill.test.sh
+++ b/tests/retrieval-discipline-backfill.test.sh
@@ -161,6 +161,34 @@ else
 fi
 rm -rf "$WS"
 
+# ── Test 4b: reflex present under DIFFERENT wording → no duplication ─────────
+echo ""
+echo "Test 4b: a reworded reflex (drops the phrase, keeps the **Retrieval discipline lead) is not duplicated"
+WS="$(fresh_pre1426_workspace)"
+# Inject a reworded reflex into §P6 that OMITS the phrase "substrate grep" but
+# carries the structural **Retrieval discipline lead.
+awk '
+    { print }
+    /^### P6 / && !done {
+        print ""
+        print "**Retrieval discipline.** Use `/kg` for discovery; never grep `research/entities/` directly."
+        done = 1
+    }
+' "$WS/AGENTS.md" > "$WS/AGENTS.md.tmp" && mv "$WS/AGENTS.md.tmp" "$WS/AGENTS.md"
+lead_before="$(grep -cE '^\*\*Retrieval discipline' "$WS/AGENTS.md")"
+BROOMVA_WORKSPACE="$WS" bash "$REPAIR_SH" --apply-all >/dev/null 2>&1
+lead_after="$(grep -cE '^\*\*Retrieval discipline' "$WS/AGENTS.md")"
+if [ "$lead_before" -eq 1 ] && [ "$lead_after" -eq 1 ]; then
+    assert_pass "reworded reflex not duplicated (lead count stayed 1)"
+else
+    assert_fail "reworded reflex duplicated (before=$lead_before after=$lead_after)"
+fi
+# doctor must report ok on the reworded variant (consistency with repair).
+if BROOMVA_WORKSPACE="$WS" bash "$DOCTOR_SH" 2>&1 | grep -q "has P6 retrieval-discipline reflex"; then
+    : # need .control for doctor to run sections; skip strict check here
+fi
+rm -rf "$WS"
+
 # ── Test 5: doctor §4c advisory present/absent + 0 gaps / strict-neutral ─────
 echo ""
 echo "Test 5: doctor §4c advisory is informational (does not change GAP total / --strict)"

From 8d3ccece09620a7fda109c19f31c69be2754f2a6 Mon Sep 17 00:00:00 2001
From: "Carlos D. Escobar-Valbuena" <devteam@getstimulus.ai>
Date: Fri, 26 Jun 2026 21:13:21 -0500
Subject: [PATCH 3/3] test(retrieval-backfill): real doctor assertion in Test
 4b (CodeRabbit) + pipefail fix
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

CodeRabbit: Test 4b's doctor-consistency check was a silent no-op (`: # skip`).
Turned it into a real assertion that doctor §4c recognizes the reworded
(phrase-less) reflex. Surfaced a test-harness bug: `doctor | grep -q` under
`set -o pipefail` returns doctor's exit (non-zero on a gappy fixture), not grep's
— capture the output to a var first, then grep (the pattern Test 5 uses).

Verified non-vacuous by mutation: removing doctor's structural OR-clause makes
Test 4b fail; restoring passes. 18/18 green.

BRO-1555

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 tests/retrieval-discipline-backfill.test.sh | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/tests/retrieval-discipline-backfill.test.sh b/tests/retrieval-discipline-backfill.test.sh
index 99aad06..cd7c4b2 100755
--- a/tests/retrieval-discipline-backfill.test.sh
+++ b/tests/retrieval-discipline-backfill.test.sh
@@ -183,9 +183,19 @@ if [ "$lead_before" -eq 1 ] && [ "$lead_after" -eq 1 ]; then
 else
     assert_fail "reworded reflex duplicated (before=$lead_before after=$lead_after)"
 fi
-# doctor must report ok on the reworded variant (consistency with repair).
-if BROOMVA_WORKSPACE="$WS" bash "$DOCTOR_SH" 2>&1 | grep -q "has P6 retrieval-discipline reflex"; then
-    : # need .control for doctor to run sections; skip strict check here
+# doctor §4c must ALSO report ok on the reworded variant (drops the phrase,
+# keeps the **Retrieval discipline lead) — proving doctor's structural signal
+# agrees with repair's. Needs .control so doctor runs its sections. Capture the
+# output to a var first: the bare fixture has real gaps so doctor exits non-zero,
+# and `doctor | grep -q` under `set -o pipefail` would return doctor's exit, not
+# grep's — a false failure. Grepping the captured string avoids that.
+mkdir -p "$WS/.control"
+cp "$BSTACK_REPO/assets/templates/policy.yaml.template" "$WS/.control/policy.yaml" 2>/dev/null || true
+DOC_REWORDED="$(BROOMVA_WORKSPACE="$WS" bash "$DOCTOR_SH" 2>&1)"
+if echo "$DOC_REWORDED" | grep -q "has P6 retrieval-discipline reflex"; then
+    assert_pass "doctor §4c treats the reworded (phrase-less) reflex as present"
+else
+    assert_fail "doctor §4c did not recognize the reworded reflex (structural signal broken)"
 fi
 rm -rf "$WS"