chore: add benchmark npm script and stale embeddings warning

package.json

@@ -43,6 +43,7 @@
     "clean": "node -e \"require('fs').rmSync('dist',{recursive:true,force:true});require('fs').rmSync('.tsbuildinfo',{force:true})\"",
     "prepare": "npm run build:wasm && npm run build && husky && npm run deps:tree",
     "deps:tree": "node scripts/node-ts.js scripts/gen-deps.ts",
+    "benchmark": "node --experimental-strip-types --import ./scripts/ts-resolve-loader.js scripts/benchmark.ts",
     "release": "commit-and-tag-version",
     "release:dry-run": "commit-and-tag-version --dry-run",
     "version": "node scripts/node-ts.js scripts/sync-native-versions.ts && git add package.json crates/codegraph-core/Cargo.toml"

src/domain/graph/builder/stages/finalize.ts

@@ -37,6 +37,10 @@ export async function finalize(ctx: PipelineContext): Promise<void> {
     symbols._langId = undefined;
   }
 
+  // Capture a single wall-clock timestamp for the current build — used for
+  // both the stale-embeddings comparison and the persisted built_at metadata.
+  const buildNow = new Date();
+
   const nodeCount = (db.prepare('SELECT COUNT(*) as c FROM nodes').get() as { c: number }).c;
   const actualEdgeCount = (db.prepare('SELECT COUNT(*) as c FROM edges').get() as { c: number }).c;
   info(`Graph built: ${nodeCount} nodes, ${actualEdgeCount} edges`);
@@ -63,6 +67,22 @@ export async function finalize(ctx: PipelineContext): Promise<void> {
     }
   }
 
+  // Persist build metadata early so downstream checks (e.g. stale-embeddings)
+  // can read the *current* build's built_at rather than the previous one.
+  try {
+    setBuildMeta(db, {
+      engine: ctx.engineName,
+      engine_version: ctx.engineVersion || '',
+      codegraph_version: CODEGRAPH_VERSION,
+      schema_version: String(schemaVersion),
+      built_at: buildNow.toISOString(),
+      node_count: nodeCount,
+      edge_count: actualEdgeCount,
+    });
+  } catch (err) {
+    warn(`Failed to write build metadata: ${(err as Error).message}`);
+  }
+
   // Orphaned embeddings warning
   if (hasEmbeddings) {
     try {
@@ -83,6 +103,27 @@ export async function finalize(ctx: PipelineContext): Promise<void> {
     }
   }
 
+  // Stale embeddings warning (built before current graph rebuild)
+  if (hasEmbeddings) {
+    try {
+      const embedBuiltAt = (
+        db.prepare("SELECT value FROM embedding_meta WHERE key = 'built_at'").get() as
+          | { value: string }
+          | undefined
+      )?.value;
+      if (embedBuiltAt) {
+        const embedTime = new Date(embedBuiltAt).getTime();
+        if (!Number.isNaN(embedTime) && embedTime < buildNow.getTime()) {
+          warn(
+            'Embeddings were built before the last graph rebuild. Run "codegraph embed" to update.',
+          );
+        }
+      }
+    } catch {
+      /* ignore - embedding_meta table may not exist */
+    }
+  }
+
   // Unused exports warning
   try {
     const unusedCount = (
@@ -108,21 +149,6 @@ export async function finalize(ctx: PipelineContext): Promise<void> {
     /* exported column may not exist on older DBs */
   }
 
-  // Persist build metadata
-  try {
-    setBuildMeta(db, {
-      engine: ctx.engineName,
-      engine_version: ctx.engineVersion || '',
-      codegraph_version: CODEGRAPH_VERSION,
-      schema_version: String(schemaVersion),
-      built_at: new Date().toISOString(),
-      node_count: nodeCount,
-      edge_count: actualEdgeCount,
-    });
-  } catch (err) {
-    warn(`Failed to write build metadata: ${(err as Error).message}`);
-  }
-
   closeDb(db);
 
   // Write journal header after successful build