Manifest.json logic is clunky

[TanGentleman]

The steps should be modularized and made more clear.

1. When creating config object, make sure rag_settings respect RagSchema in classes.py
2. When RAG mode is true, first read manifest.json.
3. If collection_name is present, replace fields in rag_settings and load vectorstore 3*. If collection not present, create vectorstore from documents
4. Create retriever and rag_chain
5. Update manifest if needed (if 3*)