Sync wiki from main: single --out/--engine plotting, viewer GIFs, ASCII prose, updated benchmarks/figures
Index: add mouse-vm25 pre-built index
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
Fixed Typos
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.
Clarify fetch as Zenodo-download-only in the index docs fetch read as having two meanings (download a pre-built .idx vs. wget + build an arbitrary GTF), which confused readers. Reframe section 3 as a pure Zenodo download: lead with --out so the index lands where you run, not hidden in the cache, and route non-Zenodo releases back to the manual obtain-GTF -> prot2exon index path (with the build shortcut noted once, pointing at --help).
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.