fix(indexer): use upsert_chunks return value for chunk count

Previously total_chunks counted from process_file return (num_chunks)
which could differ from actual stored count if upsert silently failed.
Now using stored count returned by upsert_chunks.

Also fixes cli._index to skip progress yields when building result.

python/obsidian_rag/indexer.py

@@ -184,8 +184,8 @@ class Indexer:
                 for e, v in zip(enriched, vectors):
                     e["vector"] = v
                 # Store
-                upsert_chunks(table, enriched)
-                total_chunks += num_chunks
+                stored = upsert_chunks(table, enriched)
+                total_chunks += stored
                 indexed_files += 1
             except Exception as exc:
                 errors.append({"file": str(filepath), "error": str(exc)})