fix(graph): migrate inline anchors atomically with grounds_to moves

src/graph/runtime.ts

@@ -310,6 +310,13 @@ export function persistMovedGroundings(
     const scaffoldFile = relative(config.projectRoot, filePath).replaceAll("\\", "/");
     let dirty = false;
     const pendingMoves = new Map<string, { previous: GroundedSource; newId: string }>();
+    // Per-node migration is atomic (#128): a node grounded both in
+    // grounds_to and as an inline mex:// anchor must migrate through ONE
+    // resolution. The grounds_to pass records its resolution per old id so
+    // the anchor pass can follow it even when the store has already lost
+    // the old node's rows (no baseline, no fingerprint, no alias) — instead
+    // of skipping the anchor and leaving GROUNDING_GONE behind.
+    const migratedNodes = new Map<string, string>();
     for (const grounding of groundings) {
       const aliasedNode = runtime.graph.getNode(grounding.node);
       if (aliasedNode) {
@@ -320,6 +327,7 @@ export function persistMovedGroundings(
         const fingerprint = runtime.reconciler.getFingerprint(aliasedNode.id);
         if (fingerprint) grounding.fingerprint = serializeFingerprint(fingerprint);
         moveGroundingBaseline(scaffoldFile, oldId, grounding.node, runtime, pendingMoves, grounding);
+        migratedNodes.set(oldId, grounding.node);
         dirty = true;
         moved += 1;
         continue;
@@ -336,13 +344,21 @@ export function persistMovedGroundings(
       const fingerprint = runtime.reconciler.getFingerprint(resolution.nodeId);
       if (fingerprint) grounding.fingerprint = serializeFingerprint(fingerprint);
       moveGroundingBaseline(scaffoldFile, oldId, grounding.node, runtime, pendingMoves, grounding);
+      migratedNodes.set(oldId, grounding.node);
       dirty = true;
       moved += 1;
     }
     const groundedContent = dirty ? writeGroundings(content, groundings) : content;
     let anchoredContent = groundedContent;
     const anchors = findMexAnchors(anchoredContent);
     for (const anchor of [...anchors].reverse()) {
+      const migratedId = migratedNodes.get(anchor.nodeId);
+      if (migratedId !== undefined) {
+        if (migratedId === anchor.nodeId) continue;
+        anchoredContent = rewriteMexAnchor(anchoredContent, anchor, migratedId);
+        moved += 1;
+        continue;
+      }
       const aliasedNode = runtime.graph.getNode(anchor.nodeId);
       if (aliasedNode) {
         if (aliasedNode.id === anchor.nodeId) continue;

test/graph-integration.test.ts

@@ -404,6 +404,107 @@ describe("code-graph grounding integration", () => {
     ]);
   }, 20_000);
 
+  it("migrates an inline anchor atomically when grounds_to and the anchor share a moved node (#128)", async () => {
+    const { root, scaffold, config } = fixture();
+    const source = join(root, "src", "service.ts");
+    writeFileSync(source, "export function calculateTotal(items: number[]): number {\n  return items.reduce((a, b) => a + b, 0);\n}\n");
+
+    const engine = createGraphEngine({ rootDir: root });
+    await engine.build();
+    const node = engine.searchNodes("calculateTotal").find((entry) => entry.kind === "function")!;
+    engine.close();
+
+    // Ground the node BOTH in frontmatter and as an inline anchor — the shape
+    // the stack.md template encourages.
+    let runtime = await loadGroundingRuntime(config);
+    const fingerprint = runtime!.reconciler.getFingerprint(node.id);
+    writeFileSync(scaffold, writeGroundings(readFileSync(scaffold, "utf-8"), [{
+      node: node.id,
+      fingerprint: serializeFingerprint(fingerprint!),
+    }]) + `\n[\`calculateTotal()\`](mex://${node.id})\n`);
+    refreshGroundingBaselines(config, [scaffold], runtime!);
+    runtime!.close();
+
+    // Move the function to another file with an identical body, replace the
+    // original, and rebuild: the old node id vanishes from the store entirely.
+    const movedSource = join(root, "src", "moved.ts");
+    writeFileSync(movedSource, readFileSync(source, "utf-8"));
+    writeFileSync(source, "export const unrelated = 1;\n");
+    const rebuilt = createGraphEngine({ rootDir: root });
+    await rebuilt.build();
+    const movedNode = rebuilt.searchNodes("calculateTotal").find((entry) => entry.kind === "function")!;
+    expect(movedNode.id).not.toBe(node.id);
+    rebuilt.close();
+
+    runtime = await loadGroundingRuntime(config);
+    const moved = persistMovedGroundings(config, [scaffold], runtime!);
+    runtime!.close();
+
+    expect(moved).toBe(2); // grounds_to entry + inline anchor, one resolution
+    const persistedContent = readFileSync(scaffold, "utf-8");
+    expect(persistedContent).not.toContain(`mex://${node.id}`);
+    expect(persistedContent).toContain(`mex://${movedNode.id}`);
+    expect(extractGroundings(persistedContent)[0].node).toBe(movedNode.id);
+
+    // The next check must not report the anchor as gone.
+    const report = await runDriftCheckWithGraphStatus(config, { graphWarning: () => {} });
+    expect(report.issues.filter((issue) => issue.code === "GROUNDING_GONE")).toHaveLength(0);
+  }, 20_000);
+
+  it("migrates the inline anchor from the grounds_to resolution even when the store lost the old node's rows (#128)", async () => {
+    const { root, scaffold, config } = fixture();
+    const source = join(root, "src", "service.ts");
+    writeFileSync(source, "export function calculateTotal(items: number[]): number {\n  return items.reduce((a, b) => a + b, 0);\n}\n");
+
+    const engine = createGraphEngine({ rootDir: root });
+    await engine.build();
+    const node = engine.searchNodes("calculateTotal").find((entry) => entry.kind === "function")!;
+    engine.close();
+
+    let runtime = await loadGroundingRuntime(config);
+    const fingerprint = runtime!.reconciler.getFingerprint(node.id);
+    writeFileSync(scaffold, writeGroundings(readFileSync(scaffold, "utf-8"), [{
+      node: node.id,
+      fingerprint: serializeFingerprint(fingerprint!),
+    }]) + `\n[\`calculateTotal()\`](mex://${node.id})\n`);
+    refreshGroundingBaselines(config, [scaffold], runtime!);
+    runtime!.close();
+
+    const movedSource = join(root, "src", "moved.ts");
+    writeFileSync(movedSource, readFileSync(source, "utf-8"));
+    writeFileSync(source, "export const unrelated = 1;\n");
+    const rebuilt = createGraphEngine({ rootDir: root });
+    await rebuilt.build();
+    const movedNode = rebuilt.searchNodes("calculateTotal").find((entry) => entry.kind === "function")!;
+    rebuilt.close();
+
+    // A store where the old node's rows are already gone (the reporter's
+    // post-move state): no grounded-source row, no fingerprint row, and no
+    // compatibility alias. Without per-node atomic migration the anchor pass
+    // finds no baseline and silently skips, leaving GROUNDING_GONE behind.
+    const db = openSqlite(join(root, ".mex", "graph.db"));
+    try {
+      db.prepare("DELETE FROM _mex_grounded_source WHERE node_id = ?").run(node.id);
+      db.prepare("DELETE FROM node_fingerprints WHERE node_id = ?").run(node.id);
+      db.prepare("DELETE FROM node_aliases WHERE alias_id = ?").run(node.id);
+    } finally {
+      db.close();
+    }
+
+    runtime = await loadGroundingRuntime(config);
+    const moved = persistMovedGroundings(config, [scaffold], runtime!);
+    runtime!.close();
+
+    expect(moved).toBe(2);
+    const persistedContent = readFileSync(scaffold, "utf-8");
+    expect(persistedContent).not.toContain(`mex://${node.id}`);
+    expect(persistedContent).toContain(`mex://${movedNode.id}`);
+    expect(extractGroundings(persistedContent)[0].node).toBe(movedNode.id);
+
+    const report = await runDriftCheckWithGraphStatus(config, { graphWarning: () => {} });
+    expect(report.issues.filter((issue) => issue.code === "GROUNDING_GONE")).toHaveLength(0);
+  }, 20_000);
+
   it("keeps legacy checks running when the graph engine fails to load", async () => {
     const { scaffold, config } = fixture();
     writeFileSync(scaffold, writeGroundings(readFileSync(scaffold, "utf-8"), [{