Refactor: single package, typed r_brics, more lint rules

[anmorgunov]

This PR encompasses a significant refactoring effort focused on modernizing the codebase, improving structure, and enhancing developer tooling.

Key changes include:

• Python 3.12 Upgrade: Updated the project and dependencies to support Python 3.12.
• Dependency & Tooling Updates:
  • Adopted uv for dependency management.
  • Updated pyproject.toml with project metadata, refined dependencies, and linting configurations.
  • Streamlined pre-commit hooks, leveraging ruff --fix.
  • Added new dependencies required by the updates.
• Code Refactoring & Structure:
  • Standardized import statements across the entire project.
  • Improved file organization by moving modules (gui, fragmentation) into the core fragmentretro package.
  • Moved type definitions to fragmentretro.typing.
  • Updated rBRICS module with type hints and better namings
  • Introduced a base FragmentRetroError for unified error handling.
• Documentation & Configuration:
  • Updated mkdocs.yml for improved documentation site generation (theme, navigation, metadata).
  • Adjusted documentation content (.md files) to reflect code changes.
• Logging: Moved logging setup from pyproject toml to the logging_config file to avoid issues when publishing to pypi

These changes aim to improve maintainability, adopt modern Python practices, and enhance the overall developer experience.

[anmorgunov]

issues that need to be manually addressed:

• docstring for check_connected_subgraph in fragmenter_base mentions check_subgraph arg, but that arg is not specified/used