DX: increase test coverage to 85%

[redeboer]

Closes #615

🖱️ Developer experience

• Greatly expand the test suite across the package: new or rewritten tests for the python checks (pyproject, ruff, pytest, ty, pyright, black, mypy, pyupgrade), the env/uv, format (precommit, prettier, toml, cspell), github/workflows, nb/binder, readthedocs, and repo (poe, citation, commitlint, deprecated) modules, plus the cli, gitpod, and pixi checks.
• Rewrite the tests to use pytest-describe for grouped, readable test blocks, and add it to the test dependency group.
• Raise the coverage gate from --cov-fail-under=33 to 85 and the Codecov project target from 33% to 85% so the new coverage is enforced.
• Disable branch coverage (branch = false and branch-coverage = false) so the gate tracks line coverage only.
• Avoid writing to the real working directory from the test suite, isolating tests on disk.
• Add a doctest to __has_uv_run documenting its behaviour for both string and sequence commands.

🐛 Bug fixes

• cspell: compare against original_config.get(section_name) in _update_config_content so that newly added sections no longer raise a KeyError.
• pyright / ty: run all configuration updates through a single Executor so every update is applied in one pass instead of bailing out on the first reported change.

Squash commit messages

* DX: avoid using IO in tests directory
* DX: disable branch coverage
* DX: rewrite tests to use `pytest-describe`
* FIX: apply all `ty`/`pyright` updates in one pass
* FIX: handle new sections in `_update_config_content`