fix: extraction, multi-hop traversal, and aggregate result shape (BR-ADV-FEATURES-BUN)

Three advanced-API correctness fixes, all reproducible on Node (not Bun-specific):

- Entity/concept extraction returned []. SmartExtractor combined agreeing signals
  with a weighted sum compared against an absolute 0.60 gate, so a confident
  low-weight signal lost selection to a mediocre high-weight one that then failed
  the gate, dropping the whole result. Select and gate on a normalized weighted
  average instead. The public `confidence` option now controls the threshold (was
  a dead hardcoded 0.60), and the embedding-signal timeout is raised 100ms -> 2000ms
  so the neural signal is not silently dropped on slower runtimes.

- Multi-hop find({ connected }) returned only the 1-hop neighbour. executeGraphSearch
  ignored depth/via; it now delegates to the depth-aware neighbors() BFS.

- find({ aggregate }) hid groupKey/metrics/count under .metadata, so callers
  expecting AggregateResult saw empty rows. Expose those fields at the top level.

Adds real-embedding regression tests in tests/integration/advanced-apis-regression.test.ts.

src/neural/signals/EmbeddingSignal.ts

@@ -43,7 +43,10 @@ export interface EmbeddingSignalOptions {
   minConfidence?: number // Minimum confidence threshold (default: 0.60)
   checkGraph?: boolean   // Check against graph entities (default: true)
   checkHistory?: boolean // Check against historical data (default: true)
-  timeout?: number       // Max time in ms (default: 100)
+  timeout?: number       // Max time in ms (default: 2000). A real transformer embed of a single
+                         // candidate is commonly 50–200ms (cold/under load higher); the previous
+                         // 100ms default silently timed out, dropping the neural signal entirely —
+                         // which alone left concept extraction (no regex fallback) returning nothing.
   cacheSize?: number     // LRU cache size (default: 1000)
 }
 
@@ -110,7 +113,7 @@ export class EmbeddingSignal {
       minConfidence: options?.minConfidence ?? 0.60,
       checkGraph: options?.checkGraph ?? true,
       checkHistory: options?.checkHistory ?? true,
-      timeout: options?.timeout ?? 100,
+      timeout: options?.timeout ?? 2000,
       cacheSize: options?.cacheSize ?? 1000
     }
   }