@mcptoolshop/research-os 0.3.0 → 0.3.2

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 = "0.3.2";
   }
 });
 
@@ -12173,12 +12311,55 @@ 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({
@@ -12210,6 +12391,7 @@ 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");
 }
@@ -12220,11 +12402,15 @@ 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();
@@ -12238,7 +12424,7 @@ 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")));
@@ -12266,15 +12452,43 @@ 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`);
@@ -12284,6 +12498,11 @@ 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")
     );
@@ -12592,7 +12811,7 @@ 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") : "";