chore: unify linting and formatting with Ruff

[Yunnglin]

Summary

• replace flake8, YAPF, and double-quote-string-fixer with Ruff 0.16.4
• centralize Python linting and import sorting under Ruff E, F, W, and I rules
• configure Ruff formatting with 120-character lines, single quotes, spaces, and LF endings
• preserve the existing lint scope for tests and vendored code through explicit exclusions and per-file ignores
• apply the Ruff formatting baseline to all maintained Python source files in scope
• update CI and contributor documentation to match the unified toolchain

B, SIM, and Q are intentionally not enabled in this PR. B and SIM introduce additional policy and semantic refactoring beyond an equivalent migration, while Ruff documents quote lint rules as potentially conflicting with the formatter.

Validation

• pre-commit validate-config
• make lint
• ruff check .
• ruff format --check .
• normalized AST comparison across all 518 reformatted Python files
• /mnt/nas2/anaconda3/envs/eval/bin/python -m pytest tests/cli/test_all.py::TestRun::test_ci_lite -v -s -p no:warnings

Closes #1631

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