make jax_tools slightly less annoying: non-breaking versions

couple small issues:

• direct initialize to Traj / Batch etc? If not easy, at least cast
• double check serialization? might be some issues
• traj_len, batch_size

make nix easier:

• add a check to nix venv creation that ./venv is in gitignore
• possible to move to official nix packages instead of venv-ing?
• move to pypi pinocchio now that v3 is out?

make install easier:

• pyproject.toml with optional deps
• flake.nix using poetry2nix
• migrate jaxCuda to poetry2nix
• migrate to poetry 2.0.0 so we can just use pep-621 / pep-631 compliant metadata