[abhijeetgangan]

Summary

• Bump GitHub Actions to checkout v6, setup-python v6, setup-uv v8.2.0, upload-pages-artifact v5, deploy-pages v5, stale v10, codecov-action v7 and prek-action v2; setup-uv is pinned exactly because v8 no longer publishes an @v8 tag.
• Bump ruff to 0.17.1, drop its target-version in favour of requires-python, and ignore CPY001 and PLR0917.
• Bump codespell to 2.4.3 and markdownlint-cli to 0.49.1, and run the pre-commit-hooks checks as prek builtin hooks.
• Keep ty at 0.0.48: 0.0.90 skips [tool.ty.overrides] for files with PEP 723 script headers and fails on examples/ and docs/.
• SimState raises a ValueError for descending, interleaved or gapped system_idx; descending indices used to pass silently and the others raised a RuntimeError.
• calc_kT, calc_kinetic_energy and the cell-filter masses sum per system with index_add, so they no longer assume atoms are sorted by system.
• HeatFluxAutoCorrelation runs the model once per update instead of twice.
• Typing tidy-ups: deduplicated __all__, Self | None return types, a generic CorrelationCalculator, keyword cutoff= for vesin, and simpler truncate and load_states checks.

Checklist

Before a pull request can be merged, the following items must be checked:

• Doc strings have been added in the Google docstring format.
• Run ruff on your code.
• Tests have been added for any new functionality or bug fixes.