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Ruff + 3.13 version bump (#243)

* Update settings.json

* Ran ruff formatting

* Trimmed dependencies

* Update extensions.json

* Add 3.13 tests and stuff

* Drop 3.8 (it's EOL)

* Bump min python version and copyright year

* Update pyproject.toml

* Remove shebangs (not needed)

* Delete .flake8

* Autoformat all yml files

* Update CONTRIBUTING.md

* Remove old dependency and update migration guide

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