Sync cookiecutter-scverse v0.7.0 template (tracking #69)

[Marius1311]

The scverse-bot opened #69 to sync cookiecutter-scverse v0.7.0. The PR currently has conflicts, and more importantly, applying it wholesale would regress or rewrite a few things we've deliberately diverged on. Tracking the follow-up work here instead of force-merging the auto-sync.

The template sync touches:

• .cruft.json (template version bump)
• .github/ISSUE_TEMPLATE/bug_report.yml, .github/ISSUE_TEMPLATE/feature_request.yml
• .github/workflows/build.yaml, .github/workflows/release.yaml, .github/workflows/test.yaml
• .pre-commit-config.yaml
• .readthedocs.yaml
• docs/conf.py, docs/contributing.md
• pyproject.toml

Why we're not merging #69 directly

Several template changes require thought rather than a mechanical conflict-resolve:

1. PEP 735 [dependency-groups]. The template moves dev/test/doc to PEP 735 dependency groups. We need to keep the provider layers (openai, gemini, anthropic, all-providers, colors, gpu, tutorials) as optional-dependencies because they're install-time extras. So this is a partial adoption, not a straight copy.
2. pytest config. The template drops xfail_strict and our real_llm_query marker definition. Both must stay.
3. Python matrix. The template wants 3.11 + 3.14 stable and 3.14 pre-release. We currently run 3.11 + 3.13 stable and 3.13 pre. The bump is desirable but needs validation.
4. Sphinx -W (warnings-as-errors). The template adds -W to the docs build. Our current build emits 9 warnings (a missing bibtex key Virshup_2023 and unresolved BaseOutput cross-references). We need to fix those before enabling -W.
5. Codecov OIDC. The template switches codecov/codecov-action from token: to use_oidc: true + fail_ci_if_error: true. Requires enabling OIDC on codecov.io for the repo.
6. Pre-commit hook revs. The template lists older revs than current main (see [pre-commit.ci] pre-commit autoupdate #70 landed recently). Trivial conflict, resolved by keeping main's newer versions.
7. Misc template bits. docs/conf.py (add sphinxcontrib-katex), .readthedocs.yaml, issue templates, build/release workflow simplifications — mostly safe.

Plan — land in focused PRs

1. Fix docs warnings + enable -W in docs build. Resolve the 9 pre-existing Sphinx warnings, then adopt -W.
2. PEP 735 dependency groups for dev/test/doc. Keep provider layers as optional-dependencies. Update [tool.hatch.envs.*] accordingly. Keep xfail_strict and the real_llm_query marker.
3. Python matrix bump to 3.11/3.14. Adjust classifiers, hatch matrix, and local verification.
4. Codecov OIDC + remaining template bits. Enable OIDC on codecov.io, switch the action config, sync issue templates, .readthedocs.yaml, docs/conf.py (katex), build/release workflow simplifications, bump .cruft.json to v0.7.0.

Each PR will be scoped narrowly so CI noise is isolated and a regression is easy to roll back. Closing #69 once this is filed.