Host images in the wiki repo + relative paths: fixes intermittent/broken images (was proxied from raw.githubusercontent via camo, rate-limited)
Sync wiki: per-section output crops in Mapping; auto linkout + Static/Interactive table in Plotting; public viewer source in Python-API; two-route flow diagram
Sync wiki from main: single --out/--engine plotting, viewer GIFs, ASCII prose, updated benchmarks/figures
Repo reorg: parsing/, software_tests/, tutorial/{examples,reproduce_paper/{benchmarks,end_to_end}} — update all paths
Mapping: trim column-4 note, one unified Feature-TSV column table; move query-BED-building to FAQ
Updated Mapping (markdown)
Fixed Typos
Add "The same in Python:" lead-in before mirrored Python blocks In Mapping.md the per-output-mode Python snippets followed the CLI command with no separating text, reading as if both had to be run. Add a short lead-in so each Python block clearly shows the equivalent, not an additional step.
Add CLI subcommands to section titles + custom-proteins TSV docs - Append (prot2exon index/fetch), (prot2exon map), (prot2exon plot) to the Index/Mapping/Plotting page titles and sidebar entries. - Document the append_custom_proteins.py Input TSV, column table, and run command in Index.md, matching the current script (semicolon blocks, --in/stdout, --source-tag).
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.