Standardized formatting

Updates the pre-commit workflow and configuration to ensure only changed files in a pull request are checked.
Introduces a clear separation between local autofix hooks and CI check-only hooks.
Updated hooks versions.

NOTE : Since pre-commit hooks were actively used in #38 no particular "Apply lint" PR is required as of now.

Workflow improvements:

• The .github/workflows/format.yml workflow now detects changed files in a pull request and only runs pre-commit checks on those files, reducing unnecessary work and speeding up CI.
• The workflow uses updated versions of actions/checkout and actions/setup-python, and now runs on Python 3.12.

Pre-commit configuration enhancements:

• The .pre-commit-config.yaml file now clearly separates hooks that can autofix files (run locally) from those that only check (run in CI), using the stages field to control when each hook runs.
• Adds new CI-only (manual stage) hooks for ruff-check and ruff-format, ensuring that CI checks do not modify files but only report issues.
• Adds or updates hooks for checking merge conflicts, YAML, TOML, and pyproject validation, specifying their appropriate stages for local and CI runs.