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/cli.py

@@ -51,7 +51,10 @@ def _index(config) -> int:
         gen = indexer.full_index()
         result: dict = {"indexed_files": 0, "total_chunks": 0, "errors": []}
         for item in gen:
-            result = item  # progress yields are dicts; final dict from return
+            if item.get("type") == "complete":
+                result = item
+            elif item.get("type") == "progress":
+                pass  # skip progress logs in result
         duration_ms = int((time.monotonic() - t0) * 1000)
         print(
             json.dumps(