Add fetch scaffold subdirs, test coverage, and CI workflow

[gwct]

This pull request introduces a new --scaffold-subdirs option to the mafutils fetch command, allowing output files to be grouped into subdirectories named by reference scaffold instead of a flat output directory. The implementation ensures robust directory creation, error handling, and integration with both block and scaffold fetch modes. Documentation is updated to reflect the new option and recent test coverage improvements.

New Feature: Scaffold Subdirectory Output

• Added --scaffold-subdirs option to mafutils fetch, grouping output files into <output>/<scaffold>/<basename> directories for improved organization. This is supported in both block and scaffold modes, with safeguards to avoid use with --single-output. [1] [2] [3]

Implementation Details

• Introduced a shared buildOutputPath helper to generate output paths based on the scaffold_subdirs flag, and updated all relevant code paths to use it. [1] [2] [3] [4]
• Ensured all necessary scaffold subdirectories are created up front in the main process to prevent race conditions in parallel worker scenarios. [1] [2]

Command-line and API Integration

• Extended function signatures and argument passing throughout the fetch pipeline (including worker initialization and parallel execution) to propagate the new scaffold_subdirs option. [1] [2] [3] [4] [5] [6] [7]

Documentation Updates

• Updated README.md to document the new --scaffold-subdirs option.
• Enhanced DEVELOPMENT.md with details on new and existing test coverage, including tests for real-world MAF data and regression checks.

Continuous Integration

• Added a new GitHub Actions workflow (.github/workflows/tests.yml) to automatically run the test suite on pushes and pull requests to main.… test workflow