Enable remaining Ruff rules

[njzjz-bot]

Closes #316

Summary

• Upgrade the Ruff pre-commit hooks to v0.16.0 and run both lint fixes and formatting.
• Enable the requested D, UP, C4, TID251, TID253, T20, B904, N804, N805, and I rule sets.
• Apply the resulting modernization, import, docstring, and exception-chaining fixes across the codebase.
• Preserve dflow runtime artifact compatibility through a documented typing.List alias, because current pydflow rejects the equivalent PEP 585 list type.

Validation

• ruff check .
• ruff format --check dpgen2 tests docs/conf.py
• python -m compileall -q dpgen2 tests
• PYTHONPATH=tests pytest -q tests/op tests/fp tests/exploration tests/entrypoint with the unavailable optional fpop tests and the known collection script excluded: 153 passed
• Broader suite with the same exclusions: 237 passed, 1 skipped; 22 integration tests require unavailable MinIO or localhost HTTP services
• pre-commit itself is not installed in this environment; the Ruff hook commands were run directly

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh