Merge branch 'qa'

Merge branch 'qa'

PLEIADES v2.0 - Major Architecture Overhaul

- Complete project restructure with modern src/ layout
- Migration from Poetry to Pixi for dependency management
- Legacy code preserved in legacy/ directory
- Comprehensive test suite (1078 tests, 78% coverage)
- Modern Python packaging standards
- Enhanced SAMMY integration with JSON mode support

Merge pull request #11 from lanl/10-provide-the-option-to-specify-the…

…-output-folder-other-than-within-the-repository

10 provide the option to specify the output folder other than within the repository