chore: add benchmark npm script and stale embeddings warning

Add `npm run benchmark` script to make benchmark execution discoverable
instead of requiring manual `node --import ./scripts/ts-resolve-loader.js`
invocation.

Warn users when embeddings predate the last graph rebuild so they know
to re-run `codegraph embed` for fresh search results.

Impact: 1 functions changed, 8 affected

Author: carlos-alm

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

@@ -83,6 +83,34 @@ export async function finalize(ctx: PipelineContext): Promise<void> {
     }
   }
 
+  // Stale embeddings warning (built before last 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();
+        const now = Date.now();
+        if (embedTime < now && !Number.isNaN(embedTime)) {
+          const prevBuildAt = getBuildMeta(db, 'built_at');
+          if (prevBuildAt) {
+            const prevBuildTime = new Date(prevBuildAt).getTime();
+            if (embedTime < prevBuildTime) {
+              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 = (