Document the _lower suffix for chain IDS that differ only by case
Document per-chain figures above four chains
Describe the "Other clusters" colour
Describe the transposed distance heatmap
Explain the capped heatmap colour scale
Document --plot-format
Document --plot-residues
Refer to the withdrawn v2.0.0 tag as the April 2026 preview
Update the wiki for the new output layout and options Rewrite Understanding Outputs for the one-folder-per-analysis layout, README.md and run.json. Replace --output-verbose with --overwrite and --distance-matrices in the command-line guide, add what the command prints and how errors are reported. Update file paths and columns in the clustering, reference, dmax, quickstart and library pages, and link the changelog from Home.
add wiki pages