@mcptoolshop/research-os 0.3.0 → 0.3.1

package/CHANGELOG.md

@@ -2,6 +2,122 @@
 
 All notable changes to `research-os` are documented here.
 
+## [0.3.1] — 2026-05-09
+
+Tight release. One real, tested, dogfooded improvement: section-scoped
+source-floor waivers + reviewer-side acknowledgement. Earned by Experiment 3
+XRPL pack Session 2 — canonical-protocol sections (XRPL XLS standards,
+single-foundation chain documentation, walled-garden API specs) inverted
+the assumption that publisher diversity is a proxy for truth quality. No
+other v0.3.x candidates shipped — F-01 (init version-stamp), F-02
+(packs-dir docs), F-05 (discover --query example), F-08 (Windows process
+recovery), F-16 (unused SectionSchema fields), F-17 (sections/<id>/gates.yaml
+runtime wiring) are deferred to their own scoped releases.
+
+### Added
+
+- **`primary_source_waiver.section_waivers[]`** — section-scoped source-floor
+  waivers. Each entry carries `section_id`, `scope` (`min_independent_publishers`
+  or `primary_sources_required`), `reason` (non-empty), and
+  `compensating_controls[]` (at least one entry). Schema enforcement: empty
+  `reason` or empty `compensating_controls[]` fail validation. Pack policy
+  `gates.source_floor.primary_source_waiver_allowed: false` blocks both
+  pack-level and section-scoped waivers — operators cannot smuggle a waiver
+  past pack policy by rerouting it to section scope.
+
+  Multiple entries can target different sections, or the same section with
+  different scopes. Pack-level `primary_source_waiver` semantics unchanged;
+  the new `section_waivers[]` is additive and defaults to `[]` for backward
+  compatibility. Existing packs unaffected. Full reference:
+  [`docs/section-scoped-waivers.md`](docs/section-scoped-waivers.md).
+
+- **Reviewer-side acknowledgement** — when a section has a matching
+  `min_independent_publishers` waiver in effect, the calibrated reviewer's
+  section-wide `source_cluster_monopoly` finding remains visible in the
+  findings ledger but does NOT, by itself, route claims to
+  `needs_source_repair`. The finding is annotated as
+  `(severity, waived)` in the claim-review's reason string so operators
+  reading the ledger can see the finding is present but neutralised. Other
+  source-quality findings (per-claim `source_quality_problem`,
+  `scope_widening`, `overgeneralized_claim`, etc.) continue to drive their
+  own routing normally.
+
+- **Audit-side disclosure** — `weak-sources.{json,md}` and
+  `source-diversity-gaps.{json,md}` rollups annotate waived rows with
+  `waived: true` and `waiver_reason: <verbatim>` when a matching section
+  waiver is active. Rows are NOT removed (Law 16: waivers do not hide
+  evidence). The publisher-monopoly fact is still surfaced in the rollup;
+  it's disclosed as deliberately accepted rather than as an open blocker.
+
+- **13 new tests** in `test/section-scoped-waivers.test.ts` covering
+  schema validation (valid shape, missing reason, empty compensating
+  controls, invalid scope enum, bad section_id regex), gate-side
+  conversion (section_id match, section_id mismatch, primary_sources_required
+  scope, pack-level regression, pack-policy refusal, multiple sections,
+  multiple scopes for same section, disclosure in WaiverApplication),
+  reviewer-side acknowledgement (waived monopoly → accepted, per-claim
+  quality still routes, regression without waiver), and audit-side
+  annotation.
+
+- **`docs/section-scoped-waivers.md`** — full operator reference: schema,
+  behavior contract, valid-cases / invalid-cases enumeration, required
+  operator discipline (synthesis-time disclosure beyond the schema), and
+  the release thesis. Opens with the canonical phrasing:
+  *"Use section-scoped source waivers when publisher diversity is
+  structurally incompatible with the section's truth source, not when a
+  section merely failed to find enough sources."*
+
+- **Handbook page** at `/handbook/section-scoped-waivers` — condensed
+  reference matching the docs page.
+
+### Changed
+
+- **Pack-level `min_independent_publishers: 0` workaround DEPRECATED**
+  in the canonical `research-packs/docs/operator-playbook.md` and the
+  research-os handbook mirror. The pack-level pattern remains valid for
+  already-frozen packs (e.g., `packages/comfyui-workflow-durability/`)
+  whose freeze receipts are unchanged; new packs should prefer the
+  section-scoped pattern. Forward notes added to
+  [`docs/experiment-1-proof.md`](docs/experiment-1-proof.md) at the
+  references to the deprecated workaround — historical content
+  preserved, not rewritten.
+
+### Documentation
+
+- README status block updated to v0.3.1; version badge updated.
+- `docs/roadmap.md` Experiment 3 progress: section-scoped source waivers
+  shipped in v0.3.1; pack #2 of 3 (XRPL) earned both v0.3.0 and v0.3.1
+  fixes. Two more external-domain packs required for closure.
+- **Cross-repo:** `research-packs/docs/operator-playbook.md` updated in
+  the same release window. Adds the section-scoped waiver pattern as the
+  canonical guidance with the same anti-misuse framing as the research-os
+  docs page (public guidance is consistent across the surface by design).
+  Deprecates the `min_independent_publishers: 0` pack-level workaround.
+
+### Tests
+
+- **540 total** (527 at v0.3.0 → 540 at v0.3.1, +13 from
+  `test/section-scoped-waivers.test.ts`).
+
+### Migration notes
+
+No code-level migration required. Existing packs continue to work
+unchanged — `section_waivers` defaults to `[]`. Frozen packs' freeze
+receipts remain valid (the schema addition is additive).
+
+For new canonical-protocol packs: prefer section-scoped waivers over the
+deprecated pack-level `min_independent_publishers: 0` workaround. The
+section-scoped pattern preserves the publisher-diversity floor on every
+section that doesn't waive it explicitly.
+
+For operators with packs already using the deprecated pack-level
+workaround: the pattern remains valid; no migration is required. If you
+want to tighten the global default and waive specific sections instead,
+that's a clean per-section migration — set
+`min_independent_publishers` back to its non-zero pack default and add
+section_waivers entries for the sections that need them, with
+`reason` and `compensating_controls[]` documented.
+
 ## [0.3.0] — 2026-05-09
 
 Tight release. One real, tested, dogfooded improvement: `--detector` flag on

package/README.md

@@ -7,7 +7,7 @@
 </p>
 
 <p align="center">
-  <a href="https://github.com/mcp-tool-shop-org/research-os/releases/tag/v0.3.0"><img src="https://img.shields.io/badge/version-0.3.0-blue" alt="version 0.3.0"></a>
+  <a href="https://github.com/mcp-tool-shop-org/research-os/releases/tag/v0.3.1"><img src="https://img.shields.io/badge/version-0.3.1-blue" alt="version 0.3.1"></a>
   <a href="https://github.com/mcp-tool-shop-org/research-os/actions/workflows/ci.yml"><img src="https://github.com/mcp-tool-shop-org/research-os/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
   <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-green" alt="MIT License"></a>
   <img src="https://img.shields.io/badge/node-%E2%89%A520-brightgreen" alt="Node ≥20">
@@ -151,9 +151,11 @@ This is the structural alternative to *search → summarize → pretty report*.
 
 ## Status
 
-**v0.3.0** — published to npm as `@mcptoolshop/research-os@0.3.0`, 2026-05-09. Ships the `--detector <auto|heuristic|ollama-intern>` flag on `contradict map` (F-09 chain-blocker fix from Experiment 3 Session 1, XRPL pack). 527/527 vitest passing. See [CHANGELOG.md](CHANGELOG.md) and [`docs/contradict-map.md`](docs/contradict-map.md).
+**v0.3.1** — published to npm as `@mcptoolshop/research-os@0.3.1`, 2026-05-09. Ships section-scoped source-floor waivers (`primary_source_waiver.section_waivers[]`) plus reviewer-side acknowledgement so a waived section-wide `source_cluster_monopoly` finding becomes a visible caveat rather than auto-routing all claims to `needs_source_repair`. Earned by Experiment 3 XRPL pack Session 2 — canonical-protocol sections (single-foundation chains, walled-garden API specs, standards-body docs) inverted the assumption that publisher diversity is a proxy for truth quality. 540/540 vitest passing. See [CHANGELOG.md](CHANGELOG.md) and [`docs/section-scoped-waivers.md`](docs/section-scoped-waivers.md).
 
-**`contradict map --detector`** — Detector selection is now an explicit operator choice instead of a state-dependent env-var dance. `auto` (default) preserves prior behavior; `heuristic` always works without LLM and completes quickly on narrow-topic documentation sections; `ollama-intern` requires the configured model and exits visibly if unavailable. Mode is announced visibly on every run. The earlier "clear `OLLAMA_INTERN_MODEL` to force heuristic" workaround is superseded by `--detector heuristic` as the canonical operator surface; see the [research-packs operator playbook](https://github.com/mcp-tool-shop-org/research-packs/blob/main/docs/operator-playbook.md) and the [handbook contradict-map page](https://mcp-tool-shop-org.github.io/research-os/handbook/contradict-map/).
+**Section-scoped source waivers** — Use them when publisher diversity is structurally incompatible with the section's truth source, not when a section merely failed to find enough sources. Schema-enforced `reason` + non-empty `compensating_controls[]`. Pack policy `primary_source_waiver_allowed: false` blocks both pack-level and section-scoped waivers. The pre-v0.3.1 pack-level `min_independent_publishers: 0` workaround is now deprecated; existing frozen packs remain valid under their existing receipts. See [`docs/section-scoped-waivers.md`](docs/section-scoped-waivers.md) and the [research-packs operator playbook](https://github.com/mcp-tool-shop-org/research-packs/blob/main/docs/operator-playbook.md).
+
+**v0.3.0** — published 2026-05-09. Shipped the `--detector <auto|heuristic|ollama-intern>` flag on `contradict map` (F-09 chain-blocker fix from Experiment 3 Session 1, XRPL pack). 527/527 vitest then. Detector selection is now an explicit operator choice instead of a state-dependent env-var dance; mode is announced visibly on every run. See [`docs/contradict-map.md`](docs/contradict-map.md).
 
 **v0.2.0** — published 2026-05-09. Shipped `research-os pack publish` (Experiment 2) and the Pattern 2 readiness predicate fix. 515/515 vitest passing then. See [CHANGELOG.md](CHANGELOG.md). Frozen packs export to the canonical `research-packs` archive with a single command; admission contract is enforced by code, not checklist. See [`docs/pack-publish.md`](docs/pack-publish.md).
 
@@ -165,7 +167,7 @@ This is the structural alternative to *search → summarize → pretty report*.
 
 ### What v0.3 is not
 
-- Not battle-tested by external users. Two dogfood arcs have closed — one self-referential, one external-domain — and Experiment 3 (API stability under external pressure) is in progress: pack #1 of 3 (XRPL creator-token durability) earned the v0.3.0 `--detector` flag. Two more external-domain packs required for Experiment 3 closure.
+- Not battle-tested by external users. Two dogfood arcs have closed — one self-referential, one external-domain — and Experiment 3 (API stability under external pressure) is in progress: pack #1 of 3 (XRPL creator-token durability) earned both the v0.3.0 `--detector` flag and the v0.3.1 section-scoped source waivers. Two more external-domain packs required for Experiment 3 closure.
 - Not a synthesis writer. The `synth workspace` command generates the structured workspace; humans (or Cowork) write the prose against accepted claim IDs.
 - Not API-stable under semver. v1.0.0 is an earned state, not a calendar date — see [`docs/roadmap.md`](docs/roadmap.md) for the six experiments that close the gap.
 

package/dist/cli.js

@@ -106,11 +106,12 @@ __export(schema_exports, {
   ReviewProfilePresetSchema: () => ReviewProfilePresetSchema,
   SectionBudgetGateSchema: () => SectionBudgetGateSchema,
   SectionSchema: () => SectionSchema,
+  SectionScopedWaiverSchema: () => SectionScopedWaiverSchema,
   SectionStatusSchema: () => SectionStatusSchema,
   SourceFloorGateSchema: () => SourceFloorGateSchema
 });
 import { z } from "zod";
-var SectionStatusSchema, SectionSchema, SourceFloorGateSchema, ClaimIntegrityGateSchema, FreshnessGateSchema, ContradictionGateSchema, SectionBudgetGateSchema, GateConfigSchema, PrimarySourceWaiverSchema, FreshnessRequirementsSchema, ReviewProfilePresetSchema, DEFAULT_REVIEW_PROFILES, ResearchYamlSchema;
+var SectionStatusSchema, SectionSchema, SourceFloorGateSchema, ClaimIntegrityGateSchema, FreshnessGateSchema, ContradictionGateSchema, SectionBudgetGateSchema, GateConfigSchema, SectionScopedWaiverSchema, PrimarySourceWaiverSchema, FreshnessRequirementsSchema, ReviewProfilePresetSchema, DEFAULT_REVIEW_PROFILES, ResearchYamlSchema;
 var init_schema = __esm({
   "src/intake/schema.ts"() {
     "use strict";
@@ -160,10 +161,20 @@ var init_schema = __esm({
       contradiction: ContradictionGateSchema.default({}),
       section_budget: SectionBudgetGateSchema.default({})
     });
+    SectionScopedWaiverSchema = z.object({
+      section_id: z.string().regex(/^[0-9]{2}-[a-z0-9-]+$/, 'Section id must look like "01-landscape"'),
+      scope: z.enum(["min_independent_publishers", "primary_sources_required"]),
+      reason: z.string().min(1),
+      compensating_controls: z.array(z.string()).min(1)
+    });
     PrimarySourceWaiverSchema = z.object({
       status: z.enum(["none", "requested", "granted"]).default("none"),
       reason: z.string().optional(),
-      compensating_controls: z.array(z.string()).default([])
+      compensating_controls: z.array(z.string()).default([]),
+      // Section-scoped waivers; each entry is its own waiver record. Independent
+      // of the pack-level status/reason/compensating_controls fields above.
+      // Defaults to [] for backward compatibility — existing packs unaffected.
+      section_waivers: z.array(SectionScopedWaiverSchema).default([])
     });
     FreshnessRequirementsSchema = z.object({
       required: z.boolean().default(true),
@@ -4207,9 +4218,28 @@ function applyWaivers(input, results) {
   const updated = results.map((r) => ({ ...r }));
   const applied = [];
   const validationFailures = [];
-  if (waiver.status !== "granted") {
-    return { updatedResults: updated, waivers_applied: applied, waiver_validation_failures: validationFailures };
+  applyPackLevelWaiver({
+    waiver,
+    cfg,
+    updated,
+    applied,
+    validationFailures
+  });
+  for (const sw of waiver.section_waivers ?? []) {
+    if (sw.section_id !== input.section.id) continue;
+    applySectionScopedWaiver({
+      waiver: sw,
+      cfg,
+      updated,
+      applied,
+      validationFailures
+    });
   }
+  return { updatedResults: updated, waivers_applied: applied, waiver_validation_failures: validationFailures };
+}
+function applyPackLevelWaiver(args) {
+  const { waiver, cfg, updated, applied, validationFailures } = args;
+  if (waiver.status !== "granted") return;
   if (!waiver.reason || waiver.reason.trim().length === 0) {
     validationFailures.push({
       family: "waivers",
@@ -4219,7 +4249,7 @@ function applyWaivers(input, results) {
       evidence: [],
       blocks_synthesis: true
     });
-    return { updatedResults: updated, waivers_applied: applied, waiver_validation_failures: validationFailures };
+    return;
   }
   if (waiver.compensating_controls.length === 0) {
     validationFailures.push({
@@ -4230,7 +4260,7 @@ function applyWaivers(input, results) {
       evidence: [],
       blocks_synthesis: true
     });
-    return { updatedResults: updated, waivers_applied: applied, waiver_validation_failures: validationFailures };
+    return;
   }
   if (!cfg.primary_source_waiver_allowed) {
     validationFailures.push({
@@ -4241,7 +4271,7 @@ function applyWaivers(input, results) {
       evidence: [],
       blocks_synthesis: true
     });
-    return { updatedResults: updated, waivers_applied: applied, waiver_validation_failures: validationFailures };
+    return;
   }
   for (let i = 0; i < updated.length; i += 1) {
     const r = updated[i];
@@ -4263,7 +4293,62 @@ function applyWaivers(input, results) {
       });
     }
   }
-  return { updatedResults: updated, waivers_applied: applied, waiver_validation_failures: validationFailures };
+}
+function applySectionScopedWaiver(args) {
+  const { waiver, cfg, updated, applied, validationFailures } = args;
+  if (!waiver.reason || waiver.reason.trim().length === 0) {
+    validationFailures.push({
+      family: "waivers",
+      check: "section_scoped_waiver_reason_required",
+      status: "fail",
+      detail: `Section-scoped waiver for ${waiver.section_id}/${waiver.scope} is missing a reason. Waiver is invalid; original failure stands.`,
+      evidence: [waiver.section_id],
+      blocks_synthesis: true
+    });
+    return;
+  }
+  if (waiver.compensating_controls.length === 0) {
+    validationFailures.push({
+      family: "waivers",
+      check: "section_scoped_waiver_compensating_controls_required",
+      status: "fail",
+      detail: `Section-scoped waiver for ${waiver.section_id}/${waiver.scope} has empty compensating_controls. Waiver is invalid; original failure stands.`,
+      evidence: [waiver.section_id],
+      blocks_synthesis: true
+    });
+    return;
+  }
+  if (!cfg.primary_source_waiver_allowed) {
+    validationFailures.push({
+      family: "waivers",
+      check: "section_scoped_waiver_allowed_by_pack",
+      status: "fail",
+      detail: `Pack policy gates.source_floor.primary_source_waiver_allowed=false; section-scoped waiver for ${waiver.section_id}/${waiver.scope} cannot be applied.`,
+      evidence: [waiver.section_id],
+      blocks_synthesis: true
+    });
+    return;
+  }
+  for (let i = 0; i < updated.length; i += 1) {
+    const r = updated[i];
+    if (r.family === "source_floor" && r.check === waiver.scope && r.status === "fail") {
+      const original = r.status;
+      updated[i] = {
+        ...r,
+        status: "pass_with_waiver",
+        detail: `${r.detail} Section-scoped waiver granted for ${waiver.section_id} with ${waiver.compensating_controls.length} compensating control(s); converted from fail to pass_with_waiver.`,
+        blocks_synthesis: false
+      };
+      applied.push({
+        family: "source_floor",
+        check: waiver.scope,
+        reason: waiver.reason,
+        compensating_controls: waiver.compensating_controls,
+        original_status: original,
+        new_status: "pass_with_waiver"
+      });
+    }
+  }
 }
 var init_waivers = __esm({
   "src/gates/checks/waivers.ts"() {
@@ -5520,9 +5605,11 @@ function pickHighestPriority(decisions) {
   return "accepted_for_synthesis";
 }
 function deriveClaimReviews(args) {
-  const { claims, findings, reviewer, reviewMethod } = args;
+  const { claims, findings, reviewer, reviewMethod, activeSectionWaivers } = args;
   const reviews = [];
   const now = (/* @__PURE__ */ new Date()).toISOString();
+  const monopolyWaived = Array.isArray(activeSectionWaivers) && activeSectionWaivers.some((w) => w.scope === "min_independent_publishers");
+  const isWaivedFinding = (f) => monopolyWaived && f.category === "source_cluster_monopoly";
   for (const claim of claims) {
     const claimFindings = findings.filter((f) => f.claim_ids.includes(claim.claim_id));
     if (claimFindings.length === 0) {
@@ -5539,6 +5626,7 @@ function deriveClaimReviews(args) {
     }
     let decisions = [];
     for (const f of claimFindings) {
+      if (isWaivedFinding(f)) continue;
       if (f.severity === "block") {
         decisions.push(BLOCK_TO_DECISION[f.category] ?? "rejected");
       } else if (f.severity === "warn") {
@@ -5555,7 +5643,9 @@ function deriveClaimReviews(args) {
       );
     }
     const decision = pickHighestPriority(decisions);
-    const reasonParts = claimFindings.filter((f) => f.severity !== "info").map((f) => `${f.category} (${f.severity})`);
+    const reasonParts = claimFindings.filter((f) => f.severity !== "info").map(
+      (f) => isWaivedFinding(f) ? `${f.category} (${f.severity}, waived)` : `${f.category} (${f.severity})`
+    );
     const reason = reasonParts.length > 0 ? `Findings: ${reasonParts.join("; ")}.` : "Only info-level findings; accepted.";
     reviews.push({
       claim_id: claim.claim_id,
@@ -5936,7 +6026,8 @@ async function review(options) {
     candidateClaims,
     drafts: acceptedDrafts,
     llmFindingsRejected,
-    profile: options.profile ?? DEFAULT_PROFILE
+    profile: options.profile ?? DEFAULT_PROFILE,
+    research
   });
 }
 async function runMultiPassReview(args) {
@@ -5998,7 +6089,8 @@ async function runMultiPassReview(args) {
     candidateClaims: args.candidateClaims,
     drafts: merged,
     llmFindingsRejected,
-    profile: args.options.profile ?? DEFAULT_PROFILE
+    profile: args.options.profile ?? DEFAULT_PROFILE,
+    research: args.research
   });
 }
 async function reviewWithSpecificReviewer(args) {
@@ -6026,7 +6118,8 @@ async function reviewWithSpecificReviewer(args) {
     candidateClaims: args.candidateClaims,
     drafts: result.drafts,
     llmFindingsRejected: 0,
-    profile: args.options.profile ?? DEFAULT_PROFILE
+    profile: args.options.profile ?? DEFAULT_PROFILE,
+    research: args.research
   });
 }
 async function finalizeReview(args) {
@@ -6049,11 +6142,15 @@ async function finalizeReview(args) {
     seen.add(f.finding_id);
     dedupedFindings.push(f);
   }
+  const activeSectionWaivers = args.research.primary_source_waiver.section_waivers.filter(
+    (w) => w.section_id === args.sectionId
+  );
   const claimReviews = deriveClaimReviews({
     claims: args.candidateClaims,
     findings: dedupedFindings,
     reviewer: args.reviewer,
-    reviewMethod: args.reviewMethod
+    reviewMethod: args.reviewMethod,
+    activeSectionWaivers
   });
   const decisionCounts = {
     accepted_for_synthesis: 0,
@@ -8780,6 +8877,19 @@ function buildStaleSources(input) {
   }
   return out;
 }
+function findSectionWaiver(research, sectionId, scope) {
+  return (research.primary_source_waiver.section_waivers ?? []).find(
+    (w) => w.section_id === sectionId && w.scope === scope
+  );
+}
+function annotateWeakSource(row, waiver) {
+  if (!waiver) return row;
+  return { ...row, waived: true, waiver_reason: waiver.reason };
+}
+function annotateDiversityGap(row, waiver) {
+  if (!waiver) return row;
+  return { ...row, waived: true, waiver_reason: waiver.reason };
+}
 function buildWeakSources(input) {
   const out = [];
   const cfg = input.research.gates.source_floor;
@@ -8789,33 +8899,50 @@ function buildWeakSources(input) {
     const publishers = new Set(
       sectionSources.map((c) => c.publisher).filter((p) => typeof p === "string")
     );
+    const monopolyWaiver = findSectionWaiver(input.research, sid, "min_independent_publishers");
+    const primaryWaiver = findSectionWaiver(input.research, sid, "primary_sources_required");
     if (publishers.size === 1 && sectionSources.length >= 2) {
-      out.push({
-        reason: "source_cluster_monopoly",
-        section_id: sid,
-        details: `Every source in this section traces to a single publisher (${[...publishers][0]}).`,
-        evidence_ids: sectionSources.map((s) => s.source_id),
-        artifact_path: `sections/${sid}/sources.jsonl`
-      });
+      out.push(
+        annotateWeakSource(
+          {
+            reason: "source_cluster_monopoly",
+            section_id: sid,
+            details: `Every source in this section traces to a single publisher (${[...publishers][0]}).`,
+            evidence_ids: sectionSources.map((s) => s.source_id),
+            artifact_path: `sections/${sid}/sources.jsonl`
+          },
+          monopolyWaiver
+        )
+      );
     }
     if (publishers.size < cfg.min_independent_publishers) {
-      out.push({
-        reason: "low_independent_publishers",
-        section_id: sid,
-        details: `${publishers.size} independent publisher(s) \u2014 pack policy requires at least ${cfg.min_independent_publishers}.`,
-        evidence_ids: [...publishers],
-        artifact_path: `sections/${sid}/sources.jsonl`
-      });
+      out.push(
+        annotateWeakSource(
+          {
+            reason: "low_independent_publishers",
+            section_id: sid,
+            details: `${publishers.size} independent publisher(s) \u2014 pack policy requires at least ${cfg.min_independent_publishers}.`,
+            evidence_ids: [...publishers],
+            artifact_path: `sections/${sid}/sources.jsonl`
+          },
+          monopolyWaiver
+        )
+      );
     }
     const primary = sectionSources.filter((c) => c.source_type === "primary").length;
     if (primary < cfg.primary_sources_required) {
-      out.push({
-        reason: "missing_primary_source",
-        section_id: sid,
-        details: `${primary} primary source(s) \u2014 pack policy requires at least ${cfg.primary_sources_required}.`,
-        evidence_ids: sectionSources.filter((c) => c.source_type === "primary").map((c) => c.source_id),
-        artifact_path: `sections/${sid}/sources.jsonl`
-      });
+      out.push(
+        annotateWeakSource(
+          {
+            reason: "missing_primary_source",
+            section_id: sid,
+            details: `${primary} primary source(s) \u2014 pack policy requires at least ${cfg.primary_sources_required}.`,
+            evidence_ids: sectionSources.filter((c) => c.source_type === "primary").map((c) => c.source_id),
+            artifact_path: `sections/${sid}/sources.jsonl`
+          },
+          primaryWaiver
+        )
+      );
     }
     const types = /* @__PURE__ */ new Map();
     for (const c of sectionSources) types.set(c.source_type, (types.get(c.source_type) ?? 0) + 1);
@@ -8930,20 +9057,31 @@ function buildSourceDiversityGaps(input) {
       });
       continue;
     }
+    const monopolyWaiver = findSectionWaiver(input.research, sid, "min_independent_publishers");
     if (publishers.size === 1 && sectionSources.length >= 2) {
-      out.push({
-        reason: "section_publisher_monopoly",
-        section_id: sid,
-        details: `Section sources monopolized by ${[...publishers][0]}.`,
-        evidence_ids: sectionSources.map((s) => s.source_id)
-      });
+      out.push(
+        annotateDiversityGap(
+          {
+            reason: "section_publisher_monopoly",
+            section_id: sid,
+            details: `Section sources monopolized by ${[...publishers][0]}.`,
+            evidence_ids: sectionSources.map((s) => s.source_id)
+          },
+          monopolyWaiver
+        )
+      );
     } else if (publishers.size < cfg.min_independent_publishers) {
-      out.push({
-        reason: "low_section_publisher_count",
-        section_id: sid,
-        details: `${publishers.size} publisher(s); pack policy requires ${cfg.min_independent_publishers}.`,
-        evidence_ids: [...publishers]
-      });
+      out.push(
+        annotateDiversityGap(
+          {
+            reason: "low_section_publisher_count",
+            section_id: sid,
+            details: `${publishers.size} publisher(s); pack policy requires ${cfg.min_independent_publishers}.`,
+            evidence_ids: [...publishers]
+          },
+          monopolyWaiver
+        )
+      );
     }
   }
   const pubSectionCount = /* @__PURE__ */ new Map();
@@ -11734,7 +11872,7 @@ var init_src = __esm({
     init_triage();
     init_discover();
     init_errors();
-    RESEARCH_OS_VERSION = "0.3.0";
+    RESEARCH_OS_VERSION = "0.3.1";
   }
 });