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Cookiecutter update (#292)

### What kind of change does this PR introduce?

* Added support and CI builds for Python3.13
* Removed several unnecessary dependencies listed in `pyproject.toml`
* Migrates `optional-dependencies` to `dependency-groups`
* Sets token-based workflows to run within an `automation` environment
* Updates dependencies
* `pre-commit` has been replaced by `prek`
* `Makefile` now handles some dependency installation logic
* Configuration issues in `tox.toml` have been resolved

### Does this PR introduce a breaking change?

Yes. 

- Many dependencies that are implicitly installed and never called but
listed in the `pyproject.toml` have been removed. Many of these
dependencies are bundled and only called within the `xscen` codebase.
- The new method for installing dependencies is to either use the
`Makefile` commands or the new command invocation.
- `tox` has been undergoing significant overhaul to its configuration
language. The previous config settings were not working as intended, but
it now implements most features from the `ini` format in the `toml`
spec. There are likely some neat new goodies that we can make use of for
specialized testing.
- `ESMF_VERSION` no longer requires a preceding `v` when using `tox`.

### Other information:

`dependency-groups` are a way to ensure that development-time
dependencies are not published with distributions of packages, which is
great for packages that do not bundle code, or for preventing end-users
from installing tools they will never require when using the package.

Example invocation:
```
$ pip install --group lint,test
```
A dependency-group is only available when examining the source code of
the library and allows developers to only install the dependencies
without needing to install the library itself (great for linting). It
also supports installing the library or nesting of other
dependency-groups/optional-dependencies, if desired. Testing and other
miscellaneous development librar... (continued)

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