Splitting .env Into YAML (High Priority)

Currently, we store all user configurations (such as graph server and LLM settings) in the `.env` file.

We need to refactor the `.env` file by splitting it and managing most user configurations with YAML.

Better to keep them in one yaml file first

**Advanced:**
Use a better/graceful way to manage `Config`(Like in `C++/Java/Go` we could read the updated config automatically by a config lib/frame -- auto refresh the memory & reload the config) --- like [Omegaconf](https://github.com/omry/omegaconf)

Also the `Config` object should be more user friendly to modify:)