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Cookiecutter update (#65)

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

* Updates the cookiecutter template to include the latest changes:
    * Updated GitHub Workflows to use more secure actions/connections
    * Replaced `pre-commit` with `prek`. Updates pre-commit hooks
    * GenAI contributions guidelines have been added to project files
* `dependency-groups` are now used for managing
development/testing/documentation dependencies (PEP 735)
    * General development/documentation dependency updates.
    * Makefile recipes now handle some dependency management commands
    * `tox.toml` now uses `dependency-groups` and Makefile
* `pytest` has been updated to v9.0. Now uses TOML-based configuration
spec
* Linting tools now include `vulture`, `deptry`, `yamllint`, and
`codespell`
* `pre-commit` hooks have been updated.
* Python 3.14 builds are now enabled.

### Does this PR introduce a breaking change?

Yes.

- Development dependencies now use the new `dependency-groups` system
(requires `pip >=25.2`).
- `tox` now relies on the Makefile for command definitions.
- `prek` replaces `pre-commit`. `prek` is a drop-in replacement that
runs much faster and uses fewer resources. Existing `pre-commit` will
continue to work, but new environments will install this by default
going forward.

### Other information:

This PR includes the changes from the AI Policy set to `standard`. If we
want to use the `strict` or `No AI policy` settings, I can update this
manually.

`_copy_without_render` in `.cruft.json` is a workaround to not have to
raw-escape jinja templates when drafting workflows in the cookiecutter.
Seems to be working as designed, so that's nice.

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