NeLLi-team/sgtree: SGTree v1.0

Highlights Major refactor from monolithic script to a modular Python package (sgtree/). Added a modular Nextflow DSL2 implementation (main.nf, modules/, workflows/). Preserved core SGTree functionality across both engines: basic tree build, marker-selection mode, and --singles yes filtering. Added cross-engine regression parity tests (pixi run test-regression) validating topology, marker matrices, and RF status parity. Improved repository hygiene: standardized runtime artifacts under runs/, added cleanup task (pixi run clean-runtime), and updated docs with workflow/structure guidance. Branching Legacy pre-modular code preserved as branch sgtree-legacy. Modular Nextflow-era code available as sgtree-nf and mirrored in main. Software name remains SGTree.