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
    */

src/index.ts

@@ -325,6 +325,7 @@ export class CodeGraph {
         return { success: false, filesIndexed: 0, filesSkipped: 0, filesErrored: 0, nodesCreated: 0, edgesCreated: 0, errors: [{ message: 'Could not acquire file lock - another process may be indexing', severity: 'error' as const }], durationMs: 0 };
       }
       try {
+        const before = this.queries.getNodeAndEdgeCount();
         const result = await this.orchestrator.indexAll(options.onProgress, options.signal, options.verbose);
 
         // Re-detect frameworks now that the index is populated. The resolver
@@ -367,6 +368,15 @@ export class CodeGraph {
           this.db.runMaintenance();
         }
 
+        // The orchestrator only sees extraction-phase counts; resolution and
+        // synthesizer edges (often >50% of the graph on JVM repos) come later.
+        // Recompute against the DB so the CLI summary reports the true totals.
+        if (result.success && result.filesIndexed > 0) {
+          const after = this.queries.getNodeAndEdgeCount();
+          result.nodesCreated = after.nodes - before.nodes;
+          result.edgesCreated = after.edges - before.edges;
+        }
+
         return result;
       } finally {
         this.fileLock.release();