Add pre-commit hooks with Ruff and C++ formatting/linting support

[harryswift01]

Summary

This PR adds pre-commit hooks to SIST, covering both Python (Ruff) and C++ (clang-format, clang-tidy) linting/formatting, applies them across the existing codebase, and enforces them in CI.

Changes

Add pre-commit configuration:

• Added .pre-commit-config.yaml with ruff-check/ruff-format, general repository hygiene hooks (large file checks, merge conflict markers, YAML/TOML validation, end-of-file/trailing whitespace), rstcheck for docstrings, and a pre-push docs build gate
• Added pre-commit, ruff, pylint, and rstcheck to pyproject.toml's new pre-commit extra

Add C++ formatting and static analysis:

• Added clang-format and clang-tidy hooks, scoped so clang-tidy only runs against translation units (.cpp/.cc/.cxx/.c), not headers, since headers aren't independently compilable
• clang-tidy runs a curated check set (clang-analyzer-*, bugprone-*) rather than the full default set, to keep findings focused on genuine correctness issues rather than legacy style noise
• Added clang-format/clang-tidy to the pre-commit extra so both are pip-installable with no system dependency required
• Reformatted all existing C++ source in src/trans_three/src/trans_compete with clang-format's built-in default style

Apply hooks across the existing repository:

• Ran pre-commit run --all-files once to bring the whole repository into compliance (formatting/whitespace-only changes)

Enforce in CI and document setup:

• Added a pre-commit job to pr.yaml, gated behind needs: unit, that fails the build with a diff if any hook doesn't pass
• Documented the pre-commit setup and tooling stack in docs/source/development.rst

Impact

• No behavioural change to SIST itself, the C++ reformatting is purely cosmetic
• Verified after reformatting: both trans_three/trans_compete compile clean, tests/unit and tests/regression
• PRs will now fail CI if pre-commit checks haven't been run, closing the gap where only contributors with the hook installed locally were covered

[jimboid]

Looks good and seems to be doing the things it is meant to. Happy to merge