fix(cli): include resolution + synthesizer edges in indexAll report (#413)

The orchestrator's per-file counter only sees extraction-phase edges, so the `X nodes, Y edges` line printed after `codegraph init -i` / `codegraph index` undercounts the graph — often by more than half on repos with heavy cross-file resolution (mall: 20 047 reported vs 45 629 actually in the DB).

Snapshot (nodes, edges) before/after the full pipeline in `indexAll` and write the true delta back to the result. New lightweight `QueryBuilder.getNodeAndEdgeCount()` is one round-trip with no per-kind breakdowns. `indexFiles` (no resolution) and `sync` (uses `nodesUpdated`, not `nodesCreated`) are unaffected.

Regression test added: `__tests__/integration/full-pipeline.test.ts > reports edgesCreated including resolution + synthesizer phases`.

src/db/queries.ts

@@ -1445,6 +1445,19 @@ export class QueryBuilder {
   // Statistics
   // ===========================================================================
 
+  /**
+   * Lightweight (nodes, edges) count snapshot. Used around an index/sync
+   * run to compute true additions across extraction + resolution +
+   * synthesis — the per-phase counter in the orchestrator only sees
+   * extraction's contribution, which is why the CLI summary under-reported
+   * the edge count (resolution + synthesizer edges were invisible).
+   */
+  getNodeAndEdgeCount(): { nodes: number; edges: number } {
+    return this.db
+      .prepare('SELECT (SELECT COUNT(*) FROM nodes) AS nodes, (SELECT COUNT(*) FROM edges) AS edges')
+      .get() as { nodes: number; edges: number };
+  }
+
   /**
    * Get graph statistics
    */