Sync wiki from main: single --out/--engine plotting, viewer GIFs, ASCII prose, updated benchmarks/figures
Notebooks: consolidate atlas+ClinVar, redesigned analyses; perf threads {1,2,4,8,16}; drop removed-notebook links
Repo reorg: parsing/, software_tests/, tutorial/{examples,reproduce_paper/{benchmarks,end_to_end}} — update all paths
Point Performance page at validation/software_comparison notebooks; add walkthrough nbviewer link The combined proteintogenome_comparison.ipynb is being split into validation.ipynb (accuracy) + software_comparison.ipynb (speed); repoint the accuracy and speed sections accordingly. Add a walkthrough nbviewer link on the Tutorials page since its interactive viewers don't render on GitHub.
Restructure wiki into a sequential 7-section workflow Install -> Building an index -> Mapping -> Plotting -> Tutorials and notebooks -> Performance and benchmarking -> Reference. Merge the old scattered pages (Genome-onboarding + Custom-proteins -> Index; Output-modes + Input-format -> Mapping; Performance-and-RAM + Validation + Benchmarks -> Performance and benchmarking); drop the standalone Quickstart and CLI-reference. Update all CLI to the four-command form (index / map / fetch / plot) and the fetch-defaults-to-Zenodo model. Sidebar lists each section's subsections.