chore: enable ruff UP006/UP007, replace legacy typing imports

[TKaltofen]

Summary

• Enables ruff rules UP006 and UP007 in pyproject.toml to enforce modern type annotation syntax
• Auto-fixes 2169 violations across 294 files: replaces List[X] with list[X], Dict[K,V] with dict[K,V], Optional[X] with X | None, Union[X,Y] with X | Y
• Adds ruff check . to tox commands so lint rules are enforced alongside format, mypy, and bandit
• Removes 10 now-unnecessary # type: ignore comments in node_centrality and forecasting modules

Closes #234

Test plan

• ruff check . passes with zero violations
• mypy --strict passes (572 source files, 0 errors)
• Full tox pytest run: 2191 passed, 124 skipped (13 pre-existing failures unrelated to this change)
• ruff format clean (3 files reformatted by auto-fix)