Fixing retrieval bugs

[GFJHogue]

I identified multiple issues in the retrieval system, that together cause the inconsistent behaviours noted in #91.

1. BM25Retrieval was relying on the default whitespace word-splitting tokenization without any additional text processing to normalize for case (BM25 case-sensitive retrieval causing failed retrievals #92) and punctuation. I added case normalization and added nltk's word tokenizer. This seems to help for cases of failed queries involving gene symbols (NFAT1).
2. The old version of langchain-chroma we were using was not properly returning Documents from SelfQueryRetriever. This appears to have been a bug that is now fixed in the version I've upgraded to here. This caused EnsembleRetriever and MergerRetriever to miss vector search results (glycolysis).
3. For reasons I still do not understand, RAG would occasionally claim no results found for the 1st message, even if identical query/rephrasing results in valid responses in all other cases. I've inserted the user's original message into chat_history only for the 1st message, which strangely seems to work as a workaround.

@heliamoh you should evaluate this branch and see if it is an acceptable minimal fix for the study-system.