refactor: modernize type hints and project configuration

[ilypopv]

📝 Summary

This PR modernizes the codebase by adopting PEP 604 union types (|) and Annotated for Typer CLI arguments. It also improves project maintainability by
adding a comprehensive .gitignore and updating project metadata in pytest.toml.

🛠 Type of Change

• Refactoring

🔍 Key Changes

• Type Hint Modernization: Replaced legacy Optional[T] and Union[A, B] syntax with modern Python 3.10+ pipe operators (T | None and A | B) across
  all modules.
• Typer Refactoring: Updated CLI argument definitions to use Annotated[...] for better type safety and cleaner parameter defaults.
• Project Configuration:
  • Added a robust .gitignore covering Python environments, IDEs (PyCharm/VSCode), and large data artifacts (CSV, Parquet, Models).
  • Bumped version to 1.1.3 in pyproject.toml.
  • Updated author contact information and added pythonpath = ["."] for better testing integration.
• Code Quality & Robustness:
  • Refined error handling in pipeline.py to catch specific OSError instead of broad Exception.
  • Cleaned up unused variables in unit tests using the underscore prefix convention.
  • Standardized shebangs and import orders across entry-point scripts.

🧪 How Has This Been Tested?

• Verified that existing unit tests in tests/test_units.py pass after refactoring variable names.
• Manual verification of CLI argument parsing via typer to ensure Annotated implementation does not alter command-line behavior.

[codecov]

Codecov Report

❌ Patch coverage is 93.75000% with 1 line in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
krakenparser/pipeline.py	66.66%	1 Missing ⚠️

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