fix(signals): recognize the qualified owner/repo#N closing-issue syntax

src/db/repositories.ts

@@ -5406,7 +5406,7 @@ function toPullRequestRecord(repoFullName: string, pr: GitHubPullRequestPayload)
     // subsequent DB round-trip) sees the same value instead of `undefined`.
     createdAt: pr.created_at,
     labels: (pr.labels ?? []).flatMap((label) => (label.name ? [label.name] : [])),
-    linkedIssues: extractLinkedIssueNumbers(pr.body ?? ""),
+    linkedIssues: extractLinkedIssueNumbers(pr.body ?? "", repoFullName),
   };
   /* v8 ignore stop */
 }
@@ -7001,13 +7001,19 @@ export type LinkedIssueExtractionResult = {
   overflow: boolean;
 };
 
-export function extractLinkedIssueNumbersWithOverflow(text: string, limit = MAX_LINKED_ISSUE_NUMBERS): LinkedIssueExtractionResult {
+export function extractLinkedIssueNumbersWithOverflow(text: string, repoFullName: string, limit = MAX_LINKED_ISSUE_NUMBERS): LinkedIssueExtractionResult {
   const normalizedLimit = Math.max(0, Math.floor(limit));
+  const target = repoFullName.toLowerCase();
 
   const linkedIssues: number[] = [];
   const seen = new Set<number>();
-  for (const match of text.matchAll(/\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+#(\d+)\b/gi)) {
-    const value = Number(match[1]);
+  // Matches both GitHub's bare `KEYWORD #N` and fully-qualified `KEYWORD owner/repo#N` closing syntax (#3862) --
+  // the qualified form only counts when owner/repo case-insensitively matches THIS repo; a reference to a
+  // different repo closes an issue there, not here, and must not spoof a same-repo linked-issue match.
+  for (const match of text.matchAll(/\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+(?:([\w.-]+\/[\w.-]+)#|#)(\d+)\b/gi)) {
+    const owner = match[1];
+    if (owner && owner.toLowerCase() !== target) continue;
+    const value = Number(match[2]);
     if (!Number.isInteger(value) || value <= 0 || seen.has(value)) continue;
     seen.add(value);
     if (linkedIssues.length >= normalizedLimit) return { numbers: linkedIssues, overflow: true };
@@ -7016,8 +7022,8 @@ export function extractLinkedIssueNumbersWithOverflow(text: string, limit = MAX_
   return { numbers: linkedIssues, overflow: false };
 }
 
-export function extractLinkedIssueNumbers(text: string, limit = MAX_LINKED_ISSUE_NUMBERS): number[] {
-  return extractLinkedIssueNumbersWithOverflow(text, limit).numbers;
+export function extractLinkedIssueNumbers(text: string, repoFullName: string, limit = MAX_LINKED_ISSUE_NUMBERS): number[] {
+  return extractLinkedIssueNumbersWithOverflow(text, repoFullName, limit).numbers;
 }
 
 function extractLinkedPrNumbers(text: string): number[] {

src/github/backfill.ts

@@ -803,7 +803,7 @@ export async function refreshContributorActivity(
         openPullRequests: openPullRequestCount,
         issues: issueCount,
         stalePullRequests: openNodes.filter((node) => node.updatedAt && daysSince(node.updatedAt) >= 14).length,
-        unlinkedPullRequests: openNodes.filter((node) => extractLinkedIssueNumbers(node.body ?? "").length === 0).length,
+        unlinkedPullRequests: openNodes.filter((node) => extractLinkedIssueNumbers(node.body ?? "", repo.fullName).length === 0).length,
         dominantLabels: topItems(labelNames, 8),
         lastActivityAt: latestDate([
           ...compactNodes(allPullRequests).map((node) => node.updatedAt ?? node.mergedAt),
@@ -3915,7 +3915,7 @@ function toRecentMergedPullRequest(repoFullName: string, pr: GitHubPullRequestPa
     htmlUrl: pr.html_url,
     mergedAt: pr.merged_at,
     labels: (pr.labels ?? []).flatMap((label) => (label.name ? [label.name] : [])),
-    linkedIssues: extractLinkedIssueNumbers(pr.body ?? ""),
+    linkedIssues: extractLinkedIssueNumbers(pr.body ?? "", repoFullName),
     changedFiles: files.map((file) => file.filename),
     payload: pr as unknown as Record<string, JsonValue>,
   };

src/queue/processors.ts

@@ -7013,6 +7013,7 @@ export async function runAiReviewForAdvisory(
               resolveEnrichmentLinkedIssueNumbers(
                 args.pr.linkedIssues,
                 args.pr.body,
+                args.repoFullName,
               ),
             ),
             githubToken: isReesGithubTokenForwardingEnabled(env)

src/review/enrichment-wire.ts

@@ -260,10 +260,11 @@ export function resolveEnrichmentAnalyzerSelection(
 export function resolveEnrichmentLinkedIssueNumbers(
   linkedIssues: number[] | undefined,
   body: string | null | undefined,
+  repoFullName: string,
 ): number[] {
   const explicit = (linkedIssues ?? []).filter((candidate) => Number.isInteger(candidate) && candidate > 0);
   if (explicit.length > 0) return explicit;
-  return extractLinkedIssueNumbers(body ?? "");
+  return extractLinkedIssueNumbers(body ?? "", repoFullName);
 }
 
 /** Resolve the PR's primary linked issue into the compact REES envelope (#1478). */

src/review/linked-issue-hard-rules.ts

@@ -158,7 +158,7 @@ export async function resolveLinkedIssueHardRule(args: {
     args.config.missingPointLabelClose === "block" ||
     args.config.maintainerOnlyLabelClose === "block";
   if (!anyRuleOn) return undefined;
-  if (extractLinkedIssueNumbersWithOverflow(args.body ?? "").overflow) {
+  if (extractLinkedIssueNumbersWithOverflow(args.body ?? "", args.repoFullName).overflow) {
     return {
       violated: true,
       reason: "PR body links more issues than Gittensory can safely verify automatically; please reduce linked closing references or request maintainer review.",

src/signals/engine.ts

@@ -24,6 +24,7 @@ import { gittensoryFooter, gittensorRepoEarnUrl } from "../github/footer";
 import type { FocusManifestReviewConfig, ReviewFieldKey } from "./focus-manifest";
 import type { GittensorContributorSnapshot } from "../gittensor/api";
 import { nowIso } from "../utils/json";
+import { extractLinkedIssueNumbers } from "../db/repositories";
 import { sanitizePublicComment } from "../queue-intelligence";
 import { labelMatchesPattern, projectLinkedIssueMultiplierForPlannedSolve, type LinkedIssueMultiplierStatus } from "../scoring/preview";
 import { hasLocalTestEvidence, hasValidationNote, isTestPath } from "./test-evidence";
@@ -5312,18 +5313,6 @@ export function tokenize(value: string): string[] {
     .filter((term) => term.length > 2 && !STOPWORDS.has(term));
 }
 
-function extractLinkedIssueNumbers(text: string, repoFullName: string): number[] {
-  const numbers = [...text.matchAll(/\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+#(\d+)\b/gi)].map((match) => Number(match[1]));
-  // GitHub also auto-closes via the fully-qualified `KEYWORD owner/repo#N` form (e.g. Renovate/Dependabot bodies).
-  // Count it only when owner/repo case-insensitively equals THIS repo — a reference to a different repo closes an
-  // issue elsewhere, not here, so it must not spoof a same-repo link. Same `\b`-anchored keywords as above (#1988).
-  const target = repoFullName.toLowerCase();
-  for (const match of text.matchAll(/\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+([\w.-]+\/[\w.-]+)#(\d+)\b/gi)) {
-    if (match[1]!.toLowerCase() === target) numbers.push(Number(match[2]));
-  }
-  return [...new Set(numbers.filter((value) => Number.isInteger(value) && value > 0))];
-}
-
 function outcomeSuccessPatterns(history: ContributorOutcomeHistory): OutcomePattern[] {
   const patterns: OutcomePattern[] = [];
   for (const outcome of history.repoOutcomes) {

test/unit/backfill.test.ts

@@ -254,8 +254,14 @@ describe("GitHub backfill", () => {
             nodes: [{ __typename: "PullRequest", mergedAt: "2026-05-24T00:00:00Z", labels: { nodes: [{ name: "bug" }] }, body: "Fixes #1" }],
           },
           r_JSONbored_gittensory_open: {
-            issueCount: 2,
-            nodes: [{ __typename: "PullRequest", updatedAt: "2026-04-01T00:00:00Z", labels: { nodes: [{ name: "ci" }] }, body: "" }],
+            issueCount: 3,
+            nodes: [
+              { __typename: "PullRequest", updatedAt: "2026-04-01T00:00:00Z", labels: { nodes: [{ name: "ci" }] }, body: "" },
+              { __typename: "PullRequest", updatedAt: "2026-04-02T00:00:00Z", labels: { nodes: [{ name: "ci" }] }, body: "Fixes #2" },
+              // REGRESSION: no `body` field at all (GitHub omits it, not just an empty string) -- exercises
+              // the `node.body ?? ""` nullish fallback the unlinkedPullRequests count feeds into.
+              { __typename: "PullRequest", updatedAt: "2026-04-03T00:00:00Z", labels: { nodes: [{ name: "ci" }] } },
+            ],
           },
           r_JSONbored_gittensory_issues: {
             issueCount: 12,
@@ -270,7 +276,7 @@ describe("GitHub backfill", () => {
     expect(result).toMatchObject({ repoCount: 1, updatedRepoStats: 1, warnings: [] });
     expect(authHeaders).toContain("Bearer public-token");
     expect(await listContributorRepoStats(env, "JSONbored")).toMatchObject([
-      { repoFullName: "JSONbored/gittensory", pullRequests: 50, mergedPullRequests: 47, openPullRequests: 2, issues: 12, unlinkedPullRequests: 1 },
+      { repoFullName: "JSONbored/gittensory", pullRequests: 50, mergedPullRequests: 47, openPullRequests: 3, issues: 12, unlinkedPullRequests: 2 },
     ]);
   });
 

test/unit/db-parsers.test.ts

@@ -38,8 +38,8 @@ describe("database row parser hardening", () => {
   it("caps linked issues extracted from attacker-controlled PR bodies and reports overflow", () => {
     const body = Array.from({ length: MAX_LINKED_ISSUE_NUMBERS + 25 }, (_, index) => `Fixes #${index + 1}`).join("\n");
 
-    expect(extractLinkedIssueNumbers(body)).toEqual(Array.from({ length: MAX_LINKED_ISSUE_NUMBERS }, (_, index) => index + 1));
-    expect(extractLinkedIssueNumbersWithOverflow(body)).toEqual({
+    expect(extractLinkedIssueNumbers(body, "owner/repo")).toEqual(Array.from({ length: MAX_LINKED_ISSUE_NUMBERS }, (_, index) => index + 1));
+    expect(extractLinkedIssueNumbersWithOverflow(body, "owner/repo")).toEqual({
       numbers: Array.from({ length: MAX_LINKED_ISSUE_NUMBERS }, (_, index) => index + 1),
       overflow: true,
     });
@@ -48,13 +48,37 @@ describe("database row parser hardening", () => {
   it("deduplicates linked issues before applying the extraction cap", () => {
     const body = [`Fixes #1`, ...Array.from({ length: MAX_LINKED_ISSUE_NUMBERS }, (_, index) => `Resolves #${index + 1}`)].join("\n");
 
-    expect(extractLinkedIssueNumbers(body)).toEqual(Array.from({ length: MAX_LINKED_ISSUE_NUMBERS }, (_, index) => index + 1));
-    expect(extractLinkedIssueNumbersWithOverflow(body).overflow).toBe(false);
+    expect(extractLinkedIssueNumbers(body, "owner/repo")).toEqual(Array.from({ length: MAX_LINKED_ISSUE_NUMBERS }, (_, index) => index + 1));
+    expect(extractLinkedIssueNumbersWithOverflow(body, "owner/repo").overflow).toBe(false);
   });
 
   it("returns no linked issues when the cap is zero or negative", () => {
-    expect(extractLinkedIssueNumbers("Fixes #1\nCloses #2", 0)).toEqual([]);
-    expect(extractLinkedIssueNumbers("Fixes #1", -5)).toEqual([]);
+    expect(extractLinkedIssueNumbers("Fixes #1\nCloses #2", "owner/repo", 0)).toEqual([]);
+    expect(extractLinkedIssueNumbers("Fixes #1", "owner/repo", -5)).toEqual([]);
+  });
+
+  it("recognizes the fully-qualified `Fixes owner/repo#N` closing syntax when owner/repo matches this repo (#3862)", () => {
+    expect(extractLinkedIssueNumbers("Closes owner/repo#42", "owner/repo")).toEqual([42]);
+    // Case-insensitive, matching GitHub's own repo-name matching.
+    expect(extractLinkedIssueNumbers("Fixes Owner/Repo#7", "owner/repo")).toEqual([7]);
+    // A DIFFERENT repo's qualified reference must not spoof a same-repo linked issue.
+    expect(extractLinkedIssueNumbers("Resolves other/repo#99", "owner/repo")).toEqual([]);
+    // Bare and qualified forms mix freely and dedupe together.
+    expect(extractLinkedIssueNumbers("Fixes #1\nCloses owner/repo#1\nResolves owner/repo#2", "owner/repo")).toEqual([1, 2]);
+  });
+
+  it("REGRESSION (#3862): a stored PR using ONLY the qualified `Closes owner/repo#N` form is not flagged as unlinked", async () => {
+    const env = createTestEnv();
+    await upsertPullRequestFromGitHub(env, "owner/repo", {
+      number: 5,
+      title: "Qualified-form closing reference",
+      state: "open",
+      user: { login: "contributor1" },
+      labels: [],
+      body: "Closes owner/repo#42",
+    });
+    const stored = await getPullRequest(env, "owner/repo", 5);
+    expect(stored?.linkedIssues).toEqual([42]);
   });
 
   it("returns empty arrays from D1 raw() when a select has no rows", async () => {
@@ -393,15 +417,15 @@ describe("database row parser hardening", () => {
     await upsertPullRequestFromGitHub(env, "owner/repo", { number: 10, title: "Too many claims", state: "open", user: { login: "bob" }, head: { sha: "a1" }, labels: [], body });
     const claimed = await getPullRequest(env, "owner/repo", 10);
     expect(claimed?.linkedIssues).toHaveLength(MAX_LINKED_ISSUE_NUMBERS);
-    expect(extractLinkedIssueNumbersWithOverflow(claimed?.body ?? "").overflow).toBe(true);
+    expect(extractLinkedIssueNumbersWithOverflow(claimed?.body ?? "", "owner/repo").overflow).toBe(true);
 
     const resynced = await upsertPullRequestFromGitHub(env, "owner/repo", { number: 10, title: "Too many claims", state: "open", user: { login: "bob" }, head: { sha: "a1" }, labels: [] });
     expect(resynced.body).toBe(body);
     expect(resynced.linkedIssues).toHaveLength(MAX_LINKED_ISSUE_NUMBERS);
 
     const stored = await getPullRequest(env, "owner/repo", 10);
     expect(stored?.body).toBe(body);
-    expect(extractLinkedIssueNumbersWithOverflow(stored?.body ?? "").overflow).toBe(true);
+    expect(extractLinkedIssueNumbersWithOverflow(stored?.body ?? "", "owner/repo").overflow).toBe(true);
     expect(stored?.linkedIssues).toHaveLength(MAX_LINKED_ISSUE_NUMBERS);
   });
 

test/unit/enrichment-wire.test.ts

@@ -717,17 +717,17 @@ describe("resolveReesAnalyzers", () => {
 
 describe("resolveEnrichmentLinkedIssueNumbers", () => {
   it("prefers explicit linkedIssues over body parsing", () => {
-    expect(resolveEnrichmentLinkedIssueNumbers([7], "Fixes #42")).toEqual([7]);
+    expect(resolveEnrichmentLinkedIssueNumbers([7], "Fixes #42", "owner/repo")).toEqual([7]);
   });
 
   it("parses Fixes #N from the PR body when linkedIssues is empty", () => {
-    expect(resolveEnrichmentLinkedIssueNumbers([], "Fixes #42\nCloses #99")).toEqual([42, 99]);
-    expect(resolveEnrichmentLinkedIssueNumbers(undefined, "Resolves #3")).toEqual([3]);
+    expect(resolveEnrichmentLinkedIssueNumbers([], "Fixes #42\nCloses #99", "owner/repo")).toEqual([42, 99]);
+    expect(resolveEnrichmentLinkedIssueNumbers(undefined, "Resolves #3", "owner/repo")).toEqual([3]);
   });
 
   it("returns an empty list when neither source yields issue numbers", () => {
-    expect(resolveEnrichmentLinkedIssueNumbers([], "no issue refs")).toEqual([]);
-    expect(resolveEnrichmentLinkedIssueNumbers(undefined, undefined)).toEqual([]);
+    expect(resolveEnrichmentLinkedIssueNumbers([], "no issue refs", "owner/repo")).toEqual([]);
+    expect(resolveEnrichmentLinkedIssueNumbers(undefined, undefined, "owner/repo")).toEqual([]);
   });
 });