[lint config] Update pre-commit hooks and ruff config

[C-Achard]

Add and reorganize pre-commit hooks

• Merge this BEFORE [lint apply] Add PR-only pre-commit workflow & lint all #166

• Include check-added-large-files, check-yaml, check-toml, name-tests-test (with --pytest-test-first), check-merge-conflict

• Replace setup-cfg-fmt with pyproject-fmt and add validate-pyproject.

• Bump astral-sh/ruff-pre-commit to v0.15.0.

• Enable Ruff configuration in pyproject.toml (lint rules, fix, target-version, line-length, pydocstyle convention)

• Add [tool.pyproject-fmt] settings (max_supported_python=3.12, generate_python_version_classifiers=true, table_format="long") to control pyproject.toml formatting behavior.

---

This pull request updates and expands the project's pre-commit hooks and configuration, and enables previously commented-out linting and formatting settings in pyproject.toml. The main focus is on improving code quality and consistency by introducing new checks and formatting tools.

Pre-commit hook improvements:

• Added new hooks to .pre-commit-config.yaml for checking large files, YAML and TOML syntax, test naming conventions, and merge conflicts; replaced the setup-cfg-fmt hook with pyproject-fmt and added validate-pyproject for validating pyproject.toml files.
• Updated the ruff-pre-commit hook to a newer version (v0.15.0).

Configuration enhancements:

• Enabled and configured tool.ruff and tool.ruff.lint.pydocstyle sections in pyproject.toml for linting and docstring style enforcement, and added configuration for pyproject-fmt.