fix(lbug): bump @ladybugdb/core to 0.21.2 to stop doubled rows after delete and re-copy

LadybugDB 0.21.0 and 0.21.1 return every row of a table that spans more
than one native vector twice once the incremental writeback has DETACH
DELETEd it and a COPY into an earlier table has run. NodeGroup::scan let a
morsel that ended before the group's first live row wrap an unsigned
subtraction and rescan to the end of the group (LadybugDB #1085, fixed in
0.21.2). No primary key error fires. The identity guard from #3442 stops
the run with "unexpected or duplicate ID", so a Swift edit that pulls every
importer into the write set failed on repos with more than 2048 structs.
Only unreleased main was affected: 1.6.12 ships 0.18.3.

Pin 0.21.2 in package.json, update the six @ladybugdb/core entries in the
lockfile, and move coreVersion in the vendored FTS manifest. The FTS
extension stays at 0.21.0 because no v0.21.1 or v0.21.2 artifact is
published; the pairing assertion and its unit tests pass.

Add a regression to the delete-nodes-for-files suite: 2049 structs with
CONTAINS edges are loaded, every file is deleted, the graph is loaded
again, and each id and edge must appear exactly once.

Verification (Linux, Node 22.18):
- lbug-delete-nodes-for-files: 11/11 on 0.21.2. With the 0.21.1 native
  packages swapped in, the new test fails with 4098 rows instead of 2049.
- Reporter recipe end to end on the built CLI: incremental analyze exits 0
  with no duplicate ids on a Swift-heavy fixture and on a 70-file Python
  fixture, with and without FTS. On 0.21.1 the Swift fixture exits 1.
- A 0.21.1-written database opens and reads under 0.21.2.
- prettier, eslint and typecheck:tests are clean on the changed files.
- The full lbug-db project had not finished when this was committed.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>

gitnexus/package-lock.json

@@ -23,7 +23,7 @@
       "hasInstallScript": true,
       "license": "PolyForm-Noncommercial-1.0.0",
       "dependencies": {
-        "@ladybugdb/core": "0.21.1",
+        "@ladybugdb/core": "0.21.2",
         "@modelcontextprotocol/sdk": "^1.0.0",
         "@scarf/scarf": "^1.4.0",
         "busboy": "^1.6.0",
@@ -737,9 +737,9 @@
       }
     },
     "node_modules/@ladybugdb/core": {
-      "version": "0.21.1",
+      "version": "0.21.2",
-      "resolved": "https://registry.npmjs.org/@ladybugdb/core/-/core-0.21.1.tgz",
+      "resolved": "https://registry.npmjs.org/@ladybugdb/core/-/core-0.21.2.tgz",
-      "integrity": "sha512-G0LWyn/dIqX9yHlyjpR12Rvou2o1dvCB9EkuzGa5ykCYbzur8EQhRUbi4fw3FlbckWvR6rK/tVbnFpBcRLwiHg==",
+      "integrity": "sha512-pnD1p5AaxEdmqJsLtF6bYuSmbe+pHzmaxDPNhROFOx+f7eE/AUPJFhW+rebMD6PQxK40B2NhqXbdsPCJ+FLuxg==",
       "hasInstallScript": true,
       "license": "MIT",
       "dependencies": {
@@ -748,17 +748,17 @@
         "node-addon-api": "^6.0.0"
       },
       "optionalDependencies": {
-        "@ladybugdb/core-darwin-arm64": "0.21.1",
+        "@ladybugdb/core-darwin-arm64": "0.21.2",
-        "@ladybugdb/core-darwin-x64": "0.21.1",
+        "@ladybugdb/core-darwin-x64": "0.21.2",
-        "@ladybugdb/core-linux-arm64": "0.21.1",
+        "@ladybugdb/core-linux-arm64": "0.21.2",
-        "@ladybugdb/core-linux-x64": "0.21.1",
+        "@ladybugdb/core-linux-x64": "0.21.2",
-        "@ladybugdb/core-win32-x64": "0.21.1"
+        "@ladybugdb/core-win32-x64": "0.21.2"
       }
     },
     "node_modules/@ladybugdb/core-darwin-arm64": {
-      "version": "0.21.1",
+      "version": "0.21.2",
-      "resolved": "https://registry.npmjs.org/@ladybugdb/core-darwin-arm64/-/core-darwin-arm64-0.21.1.tgz",
+      "resolved": "https://registry.npmjs.org/@ladybugdb/core-darwin-arm64/-/core-darwin-arm64-0.21.2.tgz",
-      "integrity": "sha512-TEFYNqBdbIojf1t29p3esgRhMDm56lD5eK91dwWFZJTVWAZoGXn+yLKs0NUQgj3lW2ZquuRTLZGglPhFEsDL1Q==",
+      "integrity": "sha512-xJrPBfdh+i51SVuPlj0qgve2HQloCqPomMh01RHKpRKl/pmrwj7dU+wnK+PDVb1OCAq5MAjt8SOiChvY89Wfiw==",
       "cpu": [
         "arm64"
       ],
@@ -769,9 +769,9 @@
       ]
     },
     "node_modules/@ladybugdb/core-darwin-x64": {
-      "version": "0.21.1",
+      "version": "0.21.2",
-      "resolved": "https://registry.npmjs.org/@ladybugdb/core-darwin-x64/-/core-darwin-x64-0.21.1.tgz",
+      "resolved": "https://registry.npmjs.org/@ladybugdb/core-darwin-x64/-/core-darwin-x64-0.21.2.tgz",
-      "integrity": "sha512-w9p3oKrqeMOeWpX3xdCc/hQJHfrZtpB9We+Ir+0qyls68dSQoeXXR1GZYzzTElOtxr4OM5USwYbVyxADx+CMZg==",
+      "integrity": "sha512-zF+iONU8WOtzj9OLNr1CewQMcoJ+gwO3TJ0H4Lz+TA9D7JEdcTiHcdIQD4HQoJKEnKOwhL33MkWBdst8SfcV0g==",
       "cpu": [
         "x64"
       ],
@@ -782,9 +782,9 @@
       ]
     },
     "node_modules/@ladybugdb/core-linux-arm64": {
-      "version": "0.21.1",
+      "version": "0.21.2",
-      "resolved": "https://registry.npmjs.org/@ladybugdb/core-linux-arm64/-/core-linux-arm64-0.21.1.tgz",
+      "resolved": "https://registry.npmjs.org/@ladybugdb/core-linux-arm64/-/core-linux-arm64-0.21.2.tgz",
-      "integrity": "sha512-TodWmzOHxmmKvXXo9buBXGeyolxf/NqBUbo/LcR/tuMViKhGH8TBzIXi8DfVVwmsJ+CQCU065TvXgv2JoHAlZg==",
+      "integrity": "sha512-t/Z2ESuwx6RaEruZzGFrPHX19PEz5vKRVCm5fmSr85DqLd8/W5KWcw4f/RUpQtHdU2gdYLKkBur8yEpn36wNZA==",
       "cpu": [
         "arm64"
       ],
@@ -795,9 +795,9 @@
       ]
     },
     "node_modules/@ladybugdb/core-linux-x64": {
-      "version": "0.21.1",
+      "version": "0.21.2",
-      "resolved": "https://registry.npmjs.org/@ladybugdb/core-linux-x64/-/core-linux-x64-0.21.1.tgz",
+      "resolved": "https://registry.npmjs.org/@ladybugdb/core-linux-x64/-/core-linux-x64-0.21.2.tgz",
-      "integrity": "sha512-hCcLYv8ds0x4fkTaRkuc4f75KLdH9e0EV51ne6uBNdQSY7kyc0RgSoUG3utUGfFDMMkfgIJAeIxQY4ck9jQiXg==",
+      "integrity": "sha512-U4cAfkmPjixDURzyrkYG9NTzjEJpitaTOOATGWLTl78coc3oLpIil71wN+y2e0UuM4yd7450iLTyzL2QFzUazg==",
       "cpu": [
         "x64"
       ],
@@ -808,9 +808,9 @@
       ]
     },
     "node_modules/@ladybugdb/core-win32-x64": {
-      "version": "0.21.1",
+      "version": "0.21.2",
-      "resolved": "https://registry.npmjs.org/@ladybugdb/core-win32-x64/-/core-win32-x64-0.21.1.tgz",
+      "resolved": "https://registry.npmjs.org/@ladybugdb/core-win32-x64/-/core-win32-x64-0.21.2.tgz",
-      "integrity": "sha512-nBS1XSRJfpexdlhkezmEiRtkUt2qEDp4zBjIhH+oxgRdD7UsRz1Jyit8foJuZAmUsoQGukN5LO+YeyDU2WZTyA==",
+      "integrity": "sha512-O4rQve2RcXPbEPv222N2OwM5p6TgWYeQ0vT+BlhBfo8cOxvFrXkI45gl6qbH5tKlBdGDLV2ijKyrb1hoAFx4Zg==",
       "cpu": [
         "x64"
       ],

gitnexus/package.json

@@ -67,7 +67,7 @@
     "version": "node scripts/sync-plugin-manifests.mjs"
   },
   "dependencies": {
-    "@ladybugdb/core": "0.21.1",
+    "@ladybugdb/core": "0.21.2",
     "@modelcontextprotocol/sdk": "^1.0.0",
     "@scarf/scarf": "^1.4.0",
     "busboy": "^1.6.0",

gitnexus/test/integration/lbug-delete-nodes-for-files.test.ts

@@ -566,3 +566,82 @@ withTestLbugDB('embedding-row-dml-vector-gate', (handle) => {
     }, 120_000);
   });
 });
+
+/**
+ * Delete-all-then-recopy of a table that spans more than one native vector.
+ *
+ * @ladybugdb/core 0.21.0 and 0.21.1 returned every row of such a table twice
+ * once the incremental writeback had DETACH DELETEd it and a COPY into an
+ * earlier table had run: `NodeGroup::scan` let a morsel that ended before the
+ * group's first live row wrap an unsigned subtraction and rescan to the end of
+ * the group (LadybugDB #1085, fixed in 0.21.2). No primary-key error fires, so
+ * the only symptom was `Graph identity reconciliation failed … duplicate ID`
+ * on repos with more than 2048 symbols of one label (Swift structs in the
+ * report that found it), and 2×-inflated counts for anything that scanned.
+ *
+ * The statement order below is the one `runFullAnalysisInner` issues: delete the
+ * write set's rows, then COPY File before the symbol tables.
+ */
+withTestLbugDB('delete-recopy-multi-vector-table', (handle) => {
+  describe('deleteNodesForFiles then loadGraphToLbug on a multi-vector table', () => {
+    // One native vector holds 2048 rows; 2049 is the smallest table that spans two.
+    const STRUCT_COUNT = 2049;
+    const STRUCTS_PER_FILE = 64;
+    const fileOf = (i: number): string => `Sources/S${Math.floor(i / STRUCTS_PER_FILE)}.swift`;
+
+    const buildStructGraph = () => {
+      const nodes: TestNodeInput[] = [];
+      const rels: TestRelInput[] = [];
+      const files = new Set<string>();
+      for (let i = 0; i < STRUCT_COUNT; i++) {
+        const fp = fileOf(i);
+        if (!files.has(fp)) {
+          files.add(fp);
+          nodes.push({ id: `File:${fp}`, label: 'File', name: path.basename(fp), filePath: fp });
+        }
+        const id = `Struct:${fp}:S${i}`;
+        nodes.push({
+          id,
+          label: 'Struct',
+          name: `S${i}`,
+          filePath: fp,
+          startLine: 1,
+          endLine: 3,
+        });
+        rels.push({ sourceId: `File:${fp}`, targetId: id, type: 'CONTAINS' });
+      }
+      return { graph: buildTestGraph(nodes, rels), filePaths: [...files] };
+    };
+
+    it('returns each struct and its edge exactly once after the rows were deleted and re-copied', async () => {
+      const { loadGraphToLbug, deleteNodesForFiles, executeQuery } =
+        await import('../../src/core/lbug/lbug-adapter.js');
+      const storagePath = path.dirname(handle.dbPath);
+      const structIds = async (): Promise<string[]> =>
+        ((await executeQuery('MATCH (n:Struct) RETURN n.id AS id')) as Array<{ id: string }>).map(
+          (r) => String(r.id),
+        );
+      const containsEdges = async (): Promise<number> => {
+        const rows = (await executeQuery(
+          `MATCH (:File)-[r:CodeRelation]->(:Struct) WHERE r.type = 'CONTAINS' RETURN count(r) AS c`,
+        )) as Array<{ c: number | bigint }>;
+        return Number(rows[0]?.c ?? 0);
+      };
+
+      const { graph, filePaths } = buildStructGraph();
+      await loadGraphToLbug(graph, '/tmp/repo', storagePath);
+      expect(new Set(await structIds()).size).toBe(STRUCT_COUNT);
+
+      // Every file is in the write set, as when a Swift edit pulls in all importers.
+      await deleteNodesForFiles(filePaths);
+      expect(await structIds()).toEqual([]);
+
+      await loadGraphToLbug(graph, '/tmp/repo', storagePath);
+
+      const ids = await structIds();
+      expect(ids).toHaveLength(STRUCT_COUNT);
+      expect(new Set(ids).size).toBe(STRUCT_COUNT);
+      expect(await containsEdges()).toBe(STRUCT_COUNT);
+    }, 120_000);
+  });
+});

gitnexus/vendor/lbug-fts/manifest.json

@@ -1,5 +1,5 @@
 {
-  "coreVersion": "0.21.1",
+  "coreVersion": "0.21.2",
   "extensionVersion": "0.21.0",
   "filename": "libfts.lbug_extension",
   "officialRepo": "https://extension.ladybugdb.com/",