Chores needed for a clear code base structure

We did release the `2.1.0` I guess we can do some cleaning on the package management to make code base structure a bit more clear? Here are things I think we can do, let me know if you think there are any risk that will bring the risk of break apps.

- [x] #550
- [x] #595
- [x] Using `pyproject.toml`, this will happened only after the package is out from app registry.
- [ ] Move modules to folder (but should make sure the old module import still work for backward compatibility).
- [ ] Rename the default branch `master` -> `main`

@yakutovicha @danielhollas do you agree or have more things that we can do?