Refactor the `kotaemon/pipelines` module to `kotaemon/indices`. Create the VectorIndex.
Note: currently I place `qa` to be inside `kotaemon/indices` since at the moment we only have `qa` in RAG. At the same time, I think `qa` can be an independent module in `kotaemon/qa`. Since this can be changed later, I still go at the 1st option for now to observe if we can change it later.
* add rerankers in retrieving pipeline
* update example MVP pipeline
* add citation pipeline and function call interface
* change return type of QA and AgentPipeline to Document
