pyproject.toml: Move certain tool.ruff settings to tool.ruff.lint

[0cjs]

tool.ruff.{select,isort,ignore,per-file-ignores} will soon be deprecated in favour of putting these under tool.ruff.lint. (See reverted PR #3214 for the complaint that appears in a more recent version of ruff.) Change these now to avoid complaints later.

• [x] ran the linter to address style issues (tox -e fix)
• [x] wrote descriptive pull request text
• [n/a] ensured there are test(s) validating the fix
• [n/a] added news fragment in docs/changelog folder
• [n/a] updated/extended the documentation