chore: bump pyo3 to 0.28.2 and quick-xml to 0.39.2

[nephi-dev]

Summary

• Bump pyo3 from 0.26.0 to 0.28.2
• Bump quick-xml from 0.38.3 to 0.39.2
• Add from_py_object attribute to SearchType and Node PyO3 classes (required by pyo3 0.28)
• Add pass_filenames: false to cargo fmt and cargo clippy pre-commit hooks to prevent filenames being passed to those commands
• Bump crate version from 2.4.0 to 2.4.1

Test plan

• Build succeeds with maturin develop
• Existing Python tests pass
• Pre-commit hooks run without errors

🤖 Generated with Claude Code