Sync wiki: link_template is automatic from the ID (fix stale docs)
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: larger gallery images + static multi-isoform stack
Sync wiki: drop maintainer-only gallery-regeneration block
Sync wiki from main: single --out/--engine plotting, viewer GIFs, ASCII prose, updated benchmarks/figures
fetch Zenodo-only wording; plain Windows note; drop Docker/smoke; consolidate benchmark tables (1M threads×batch grid); custom-GTF stdout-only
Fix index docs: Home fetch path, drop bogus human-v115 row, 298 MB index, Plotting segments import - Home quickstart: 'fetch human --out human.idx' so the next map step's --index human.idx actually resolves (fetch defaults to ~/.cache). - Drop the fabricated 'human-v115 / ensembl_v15_human.idx' pre-built row (no such Zenodo target). - Performance: human GENCODE index is ~298 MB, not 128 MB. - Plotting: import _segments_from_dataframe from prot2exon.plot instead of the broken p2e.plot.<attr> path.
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.