@mcptoolshop/research-os 0.3.1 → 0.3.3

package/dist/cli.js

@@ -3627,6 +3627,7 @@ function checkSourceFloor(input) {
   const cfg = input.research.gates.source_floor;
   const results = [];
   const cards = input.sources;
+  const sectionCards = cards.filter((c) => c.section_id === input.section.id);
   const sourceCount = cards.length;
   if (sourceCount < cfg.min_sources) {
     results.push({
@@ -3650,12 +3651,15 @@ function checkSourceFloor(input) {
   const publishers = new Set(
     cards.map((c) => c.publisher).filter((p) => typeof p === "string")
   );
+  const sectionPublishers = new Set(
+    sectionCards.map((c) => c.publisher).filter((p) => typeof p === "string")
+  );
   if (publishers.size < cfg.min_independent_publishers) {
     results.push({
       family: "source_floor",
       check: "min_independent_publishers",
       status: "fail",
-      detail: `Found ${publishers.size} independent publisher(s); minimum ${cfg.min_independent_publishers} required.`,
+      detail: `Found ${publishers.size} independent publisher(s); minimum ${cfg.min_independent_publishers} required. (pack-wide=${publishers.size}, section-scoped=${sectionPublishers.size})`,
       evidence: [...publishers],
       blocks_synthesis: true
     });
@@ -3664,18 +3668,19 @@ function checkSourceFloor(input) {
       family: "source_floor",
       check: "min_independent_publishers",
       status: "pass",
-      detail: `${publishers.size} independent publisher(s) >= minimum ${cfg.min_independent_publishers}.`,
+      detail: `${publishers.size} independent publisher(s) >= minimum ${cfg.min_independent_publishers}. (pack-wide=${publishers.size}, section-scoped=${sectionPublishers.size})`,
       evidence: [],
       blocks_synthesis: false
     });
   }
   const primaryCount = cards.filter((c) => c.source_type === "primary").length;
+  const sectionPrimaryCount = sectionCards.filter((c) => c.source_type === "primary").length;
   if (primaryCount < cfg.primary_sources_required) {
     results.push({
       family: "source_floor",
       check: "primary_sources_required",
       status: "fail",
-      detail: `Found ${primaryCount} primary source(s); minimum ${cfg.primary_sources_required} required. Pre-waiver.`,
+      detail: `Found ${primaryCount} primary source(s); minimum ${cfg.primary_sources_required} required. Pre-waiver. (pack-wide=${primaryCount}, section-scoped=${sectionPrimaryCount})`,
       evidence: cards.filter((c) => c.source_type === "primary").map((c) => c.source_id),
       blocks_synthesis: true
     });
@@ -3684,7 +3689,7 @@ function checkSourceFloor(input) {
       family: "source_floor",
       check: "primary_sources_required",
       status: "pass",
-      detail: `${primaryCount} primary source(s) >= minimum ${cfg.primary_sources_required}.`,
+      detail: `${primaryCount} primary source(s) >= minimum ${cfg.primary_sources_required}. (pack-wide=${primaryCount}, section-scoped=${sectionPrimaryCount})`,
       evidence: [],
       blocks_synthesis: false
     });
@@ -3838,25 +3843,14 @@ function checkClaimIntegrity(input) {
         monoClaims.push(claim.claim_id);
       }
     }
-    if (monoClaims.length > claims.length / 2) {
-      results.push({
-        family: "claim_integrity",
-        check: "no_source_cluster_monopoly",
-        status: "warn",
-        detail: `${monoClaims.length}/${claims.length} claim(s) source from a single publisher. Independent corroboration recommended before synthesis.`,
-        evidence: monoClaims,
-        blocks_synthesis: false
-      });
-    } else {
-      results.push({
-        family: "claim_integrity",
-        check: "no_source_cluster_monopoly",
-        status: "pass",
-        detail: `${monoClaims.length}/${claims.length} claim(s) source from a single publisher (within tolerance).`,
-        evidence: [],
-        blocks_synthesis: false
-      });
-    }
+    results.push({
+      family: "claim_integrity",
+      check: "no_source_cluster_monopoly",
+      status: "pass",
+      detail: `${monoClaims.length}/${claims.length} claim(s) are single-source by architecture (each claim references exactly one source). Publisher diversity is enforced at source-card level via min_independent_publishers.`,
+      evidence: [],
+      blocks_synthesis: false
+    });
   }
   return results;
 }
@@ -4580,7 +4574,9 @@ var init_schema10 = __esm({
         docs: z11.number().int().nonnegative(),
         unknown: z11.number().int().nonnegative(),
         independent_publishers: z11.number().int().nonnegative(),
-        failed_fetches: z11.number().int().nonnegative()
+        failed_fetches: z11.number().int().nonnegative(),
+        section_primary: z11.number().int().nonnegative(),
+        section_independent_publishers: z11.number().int().nonnegative()
       }),
       contradiction_counts: z11.object({
         total: z11.number().int().nonnegative(),
@@ -4653,10 +4649,14 @@ function summarizeClaimCounts(input) {
 }
 function summarizeSourceCounts(input) {
   const cards = input.sources;
+  const sectionCards = cards.filter((c) => c.section_id === input.section.id);
   const failed = input.receipts.filter((r) => r.fetch_outcome !== "ok").length;
   const publishers = new Set(
     cards.map((c) => c.publisher).filter((p) => typeof p === "string")
   );
+  const sectionPublishers = new Set(
+    sectionCards.map((c) => c.publisher).filter((p) => typeof p === "string")
+  );
   return {
     total: cards.length,
     primary: cards.filter((c) => c.source_type === "primary").length,
@@ -4666,7 +4666,9 @@ function summarizeSourceCounts(input) {
     docs: cards.filter((c) => c.source_type === "docs").length,
     unknown: cards.filter((c) => c.source_type === "unknown").length,
     independent_publishers: publishers.size,
-    failed_fetches: failed
+    failed_fetches: failed,
+    section_primary: sectionCards.filter((c) => c.source_type === "primary").length,
+    section_independent_publishers: sectionPublishers.size
   };
 }
 function buildEffectiveStatuses3(resolutions) {
@@ -11872,7 +11874,7 @@ var init_src = __esm({
     init_triage();
     init_discover();
     init_errors();
-    RESEARCH_OS_VERSION = "0.3.1";
+    RESEARCH_OS_VERSION = "0.3.3";
   }
 });
 
@@ -12311,12 +12313,55 @@ import { join as join31, basename, resolve as resolve24 } from "path";
 
 // src/pack/publish/manifest.ts
 init_schema();
+init_schema9();
 import { createHash as createHash11 } from "crypto";
 import { readFileSync, existsSync as existsSync28 } from "fs";
 import { join as join28 } from "path";
 import { parse as parseYaml } from "yaml";
 import { z as z23 } from "zod";
 
+// src/closure-ledger/effective-accepted.ts
+function getEffectiveDecisionMap(reviews) {
+  const map2 = /* @__PURE__ */ new Map();
+  for (const r of reviews) {
+    const existing = map2.get(r.claim_id);
+    if (!existing || r.created_at > existing.created_at) {
+      map2.set(r.claim_id, r);
+    }
+  }
+  return map2;
+}
+function getEffectiveAcceptedClaimIds(reviews) {
+  const decisionMap = getEffectiveDecisionMap(reviews);
+  const accepted = /* @__PURE__ */ new Set();
+  for (const [claim_id, r] of decisionMap) {
+    if (r.decision === "accepted_for_synthesis") accepted.add(claim_id);
+  }
+  return accepted;
+}
+function findIncompatibleDecisions(reviews) {
+  const groups = /* @__PURE__ */ new Map();
+  for (const r of reviews) {
+    const key = `${r.claim_id}|${r.created_at}`;
+    let set = groups.get(key);
+    if (!set) {
+      set = /* @__PURE__ */ new Set();
+      groups.set(key, set);
+    }
+    set.add(r.decision);
+  }
+  const conflicts = [];
+  for (const [key, decisions] of groups) {
+    if (decisions.size > 1) {
+      const sep3 = key.lastIndexOf("|");
+      const claim_id = key.slice(0, sep3);
+      const created_at = key.slice(sep3 + 1);
+      conflicts.push({ claim_id, created_at, decisions: [...decisions] });
+    }
+  }
+  return conflicts;
+}
+
 // src/pack/publish/schema.ts
 import { z as z22 } from "zod";
 var SectionSummarySchema = z22.object({
@@ -12348,6 +12393,7 @@ var GateResultMinimalSchema = z23.object({
   verdict: z23.enum(["pass", "warn", "fail", "blocked"]),
   synthesis_eligible: z23.boolean()
 });
+var ClaimIdOnlySchema = z23.object({ claim_id: z23.string() });
 function sha256Bytes(buf) {
   return createHash11("sha256").update(buf).digest("hex");
 }
@@ -12358,11 +12404,15 @@ function readJsonlSafe(filePath) {
   if (!existsSync28(filePath)) return [];
   return parseJsonl(readFileSync(filePath, "utf8"));
 }
-function latestClaimDecisions(reviews) {
-  const m = /* @__PURE__ */ new Map();
-  const sorted = [...reviews].sort((a, b) => a.created_at.localeCompare(b.created_at));
-  for (const r of sorted) m.set(r.claim_id, r.decision);
-  return m;
+function readClaimReviews(filePath) {
+  if (!existsSync28(filePath)) return [];
+  const raw = parseJsonl(readFileSync(filePath, "utf8"));
+  const valid = [];
+  for (const r of raw) {
+    const parsed = ClaimReviewSchema.safeParse(r);
+    if (parsed.success) valid.push(parsed.data);
+  }
+  return valid;
 }
 function latestContradictionStatuses(resolutions) {
   const m = /* @__PURE__ */ new Map();
@@ -12376,7 +12426,7 @@ function latestDispositionStatuses(dispositions) {
   for (const d of sorted) m.set(d.claim_id, "dispositioned");
   return m;
 }
-function deriveManifest(packDir, packageName, operatorNotes = "") {
+function deriveManifest(packDir, packageName, operatorNotes = "", warnings = []) {
   const yamlPath = join28(packDir, "research.yaml");
   if (!existsSync28(yamlPath)) throw new Error(`research.yaml not found in ${packDir}`);
   const research = ResearchYamlSchema.parse(parseYaml(readFileSync(yamlPath, "utf8")));
@@ -12404,15 +12454,43 @@ function deriveManifest(packDir, packageName, operatorNotes = "") {
   let totalPreserved = 0;
   for (const sectionId of sectionIds) {
     const sectionDir = join28(packDir, "sections", sectionId);
-    const reviews = readJsonlSafe(join28(sectionDir, "claim-reviews.jsonl"));
-    const decisionMap = latestClaimDecisions(reviews);
-    const acceptedCount = [...decisionMap.values()].filter(
-      (d) => d === "accepted_for_synthesis"
-    ).length;
+    const reviewsPath = join28(sectionDir, "claim-reviews.jsonl");
+    const reviews = readClaimReviews(reviewsPath);
+    const conflicts = findIncompatibleDecisions(reviews);
+    if (conflicts.length > 0) {
+      const first = conflicts[0];
+      throw new Error(
+        `Section ${sectionId}: claim-reviews.jsonl has incompatible decisions for claim_id=${first.claim_id} at created_at=${first.created_at} (decisions seen: ${first.decisions.join(", ")}). Latest-decision-wins tie-breaker undefined \u2014 investigate the review pipeline state.` + (conflicts.length > 1 ? ` (${conflicts.length - 1} other claim_id(s) similarly affected.)` : "")
+      );
+    }
+    const effectiveAccepted = getEffectiveAcceptedClaimIds(reviews);
+    const acceptedCount = effectiveAccepted.size;
+    const claimsPath = join28(sectionDir, "claims.jsonl");
+    if (existsSync28(claimsPath)) {
+      const claimRows = parseJsonl(readFileSync(claimsPath, "utf8"));
+      const claimIds = /* @__PURE__ */ new Set();
+      for (const c of claimRows) {
+        const parsed = ClaimIdOnlySchema.safeParse(c);
+        if (parsed.success) claimIds.add(parsed.data.claim_id);
+      }
+      const phantoms = [];
+      for (const cid of effectiveAccepted) {
+        if (!claimIds.has(cid)) phantoms.push(cid);
+      }
+      if (phantoms.length > 0) {
+        throw new Error(
+          `Section ${sectionId}: ${phantoms.length} effective accepted claim_id(s) absent from claims.jsonl \u2014 phantom claims violate the closure-ledger subset invariant. Examples: ${phantoms.slice(0, 3).join(", ")}` + (phantoms.length > 3 ? ` (+${phantoms.length - 3} more)` : "")
+        );
+      }
+    } else {
+      warnings.push(
+        `section ${sectionId}: claims.jsonl absent \u2014 phantom-claim integrity check skipped`
+      );
+    }
     const auditAccepted = auditSectionMap.get(sectionId);
     if (auditAccepted !== void 0 && auditAccepted !== acceptedCount) {
-      throw new Error(
-        `Section ${sectionId}: accepted_claims mismatch between claim-reviews.jsonl (${acceptedCount}) and pack-audit.json (${auditAccepted}). Closure-ledger seam disagreement \u2014 investigate before publishing.`
+      warnings.push(
+        `section ${sectionId}: legacy pack-audit.json accepted_claims (${auditAccepted}) differs from effective accepted set (${acceptedCount}). Using effective count (${acceptedCount}) in manifest. Legacy audit count preserved in pack/audits/pack-audit.json (immutable per Law 15).`
       );
     }
     const gateResultPath = join28(packDir, "audits", `${sectionId}-gate.json`);
@@ -12422,6 +12500,11 @@ function deriveManifest(packDir, packageName, operatorNotes = "") {
     const gateResult = GateResultMinimalSchema.parse(
       JSON.parse(readFileSync(gateResultPath, "utf8"))
     );
+    if (!gateResult.synthesis_eligible) {
+      throw new Error(
+        `Section ${sectionId}: gate is not synthesis_eligible (verdict=${gateResult.verdict}). Pack admission requires every section to be synthesis-eligible.`
+      );
+    }
     const dispositions = readJsonlSafe(
       join28(sectionDir, "claim-synthesis-dispositions.jsonl")
     );
@@ -12730,7 +12813,7 @@ async function publish(input) {
       );
     }
   }
-  const manifest = deriveManifest(fromDir, packageName, input.operatorNotes ?? "");
+  const manifest = deriveManifest(fromDir, packageName, input.operatorNotes ?? "", warnings);
   if (input.dryRun) {
     const finalReportPath2 = join31(fromDir, "synthesis/final-report.md");
     const finalReport2 = existsSync30(finalReportPath2) ? readFileSync3(finalReportPath2, "utf8") : "";