Add pre-commit hooks with ruff, clang-format, and line-ending enforcement

[ardiloot]

Add pre-commit hooks for automated code formatting and linting.

Configuration

• .pre-commit-config.yaml: Hook configuration
• .clang-format: C++ formatting rules (LLVM-based, C++17, 120 col)
• pyproject.toml: Ruff config, replaced flake8 with ruff

Hooks

Hook	Purpose
mixed-line-ending	Enforce LF line endings (per .gitattributes)
end-of-file-fixer	Ensure files end with single newline
trailing-whitespace	Remove trailing whitespace
ruff	Python linter (replaces flake8)
ruff-format	Python formatter
clang-format	C++ formatter (project files only)

Exclusions

• Vendored eigen-3.4.0/ excluded globally
• Cython .pyx/.pxd files excluded from ruff (unsupported)
• Per-file lint ignores for legacy test helpers and physics variable names

Commits

1. Config files (hooks, clang-format, pyproject.toml)
2. Apply formatters to entire codebase