Add python 3.13, Remove python 3.8

[sneakers-the-rat]

Sibling of: linkml/linkml#2358
Fix: linkml/linkml#2370

does what it says on the tin.

Currently linkml/linkml#2358 is failing because there's a from typing import re statement in here, so i also removed that.

I added the upgrade ruff rules and one to check for unused imports just to automate the update, and i figure why the heck not leave them in here i would actually really like to at least isort stuff in here if not give it the same linting rules as upstream.

Other stuff

• Removed the monkeypatch to allow arbitrary kwargs in dataclasses - if we want to keep this in then someone else re-implement it, but the basis for doing that was removed in python 3.13 and it seems like the thing it was supposed to do (report line numbers from instantiation errors) is better done at yaml loading time rather than object instantiation time to me, since the only time it would work anyway is after yaml has been loaded with the loader that would be able to report the error in the first place.
• The tox files have never worked for me with poetry, and it doesn't look like they've been used in a long time anyway (still using whitelist_externals rather than allowlist_externals ) so i fixed them to just work with normal standards-compliant installation rather than wrestle with accursed poetry, but i can take that out if it's not wanted.
• added an __all__ to linkml_runtime.linkml_model because importing '*' from it makes linters complain.
• fix pydantic deprecation warnings like dict -> model_dump and parse_obj -> model_validate, which i swear i have done like 20 times but it keeps showing up somehow lol
• add a __test__ = False flag to TestEnvironment so pytest doesn't try to treat it like a test.