Sync wiki from main: single --out/--engine plotting, viewer GIFs, ASCII prose, updated benchmarks/figures
Architecture: drop removed test_notebooks.py
Architecture: drop reference to the local-only notebook generator
Repo reorg: parsing/, software_tests/, tutorial/{examples,reproduce_paper/{benchmarks,end_to_end}} — update all paths
fetch Zenodo-only wording; plain Windows note; drop Docker/smoke; consolidate benchmark tables (1M threads×batch grid); custom-GTF stdout-only
Point testing docs at pytest, not the removed run_tests.py The monolithic tests/run_tests.py was migrated into the pytest suite, so update Installation/Architecture/FAQ to describe pytest (modules, golden files, --update-goldens) and the pip install -e + pytest -q run.
Initial wiki — 17 pages mirrored from main repo wiki/