chore: switch to poetry 1.2

[Panaetius]

Moves everything over to work with poetry 1.2.0b3. This is a beta version but we've waited long enough for a proper 1.2 release and the non-deterministic lock files are taking a lot of time and are a nuisance.

Switches extras for dependency groups where it makes sense (so now it's e.g. poetry install --with all instead of pip install .[all]). Only toil is still a proper extra.

~Note, poetry's plugin system is currently not really supported from pip, see https://github.com/python-poetry/poetry/issues/5701 I've added a plugin on our side that downloads templates on poetry build but this doesn't work when installing through pip because of this issue. Since we use poetry build for creating packages, this would only affect installing from a local repository, which I think we can live with for now.~ I added back the old makefile way of doing things, it just works better. Otherwise we'd hafr to make a separate package for the plugin that we install first.

closes #2921 closes #2553