docs: add --diversity flag to gotree prune docs and generate example SVGs

[Copilot]

gotree prune --diversity was implemented but absent from the documentation. This adds full documentation coverage and the generated example images.

Changes

• docs/commands/prune.md

  • Updated option 3 description to explain --diversity behaviour: closest tip pairs are iteratively identified and one randomly removed to maximise diversity of retained tips; clarifies how --random and -r interact

  • Added --diversity to the Flags usage block

  • Added example: keeping 4 diversity-maximising tips from a 20-tip tree

    gotree generate yuletree --seed 10 -l 20 -o outtree1.nw
    gotree prune -i outtree1.nw --random 4 --diversity --seed 10 -r -o pruned.nw
    gotree draw svg -w 200 -H 200 -i outtree1.nw -o commands/prune_8.svg
    gotree draw svg -w 200 -H 200 -i pruned.nw   -o commands/prune_9.svg

• docs/commands/prune_8.svg — 20-tip input tree (new)

• docs/commands/prune_9.svg — 4-tip diversity-pruned output tree (new)

---

🔒 GitHub Advanced Security automatically protects Copilot coding agent pull requests. You can protect all pull requests by enabling Advanced Security for your repositories. Learn more about Advanced Security.