[EXP] Update the benchmark code (#71)

* chore(hnsw): reorder imports to satisfy ruff I001

* chore: sync changes; fix Ruff import order; update examples, benchmarks, and dependencies

- Fix import order in packages/leann-backend-hnsw/leann_backend_hnsw/hnsw_backend.py (Ruff I001)

- Update benchmarks/run_evaluation.py

- Update apps/base_rag_example.py and leann-core API usage

- Add benchmarks/data/README.md

- Update uv.lock

- Misc cleanup

- Note: added paru-bin as an embedded git repo; consider making it a submodule (git rm --cached paru-bin) if unintended

* chore: remove unintended embedded repo paru-bin and ignore it

Fix CI: avoid missing .gitmodules entry by removing gitlink and adding to .gitignore.

* ci: retrigger after removing unintended gitlink (paru-bin)

* feat(benchmarks): add --batch-size option and plumb through to HNSW search (default 0)

* feat(hnsw): add batch_size to LeannSearcher.search and LeannChat.ask; forward only for HNSW backend

* chore(logging): surface recompute and batching params; enable INFO logging in benchmark

* feat(embeddings): add optional manual tokenization path (HF tokenizer+model) with mean pooling; default remains SentenceTransformer.encode

* fix micro bench and fix pre commit

* update readme

---------

Co-authored-by: yichuan-w <yichuan-w@users.noreply.github.com>

apps/base_rag_example.py

@@ -299,7 +299,6 @@ class BaseRAGExample(ABC):
         chat = LeannChat(
             index_path,
             llm_config=self.get_llm_config(args),
-            system_prompt=f"You are a helpful assistant that answers questions about {self.name} data.",
             complexity=args.search_complexity,
         )