feat(theme): dual light/dark mode with Apple light theme, toggle, and theme-aware viewers

fix(seq-tools): stop auto-scrolling on job completion, fix structure highlight & AlphaFold viewer loading

Refine design system: semantic color tokens, tiered motion, denser result cards, VinaLog toolbar

fix(frontend): clear stale results, prefill-only bridges, and results-ready banners

feat(frontend): roll design-system classes across all dashboard pages + fix sidebar toggle alignment

feat: improve phylo tree viz — branch length labels, bigger nodes, hub labels, tooltips, ML recommendation

feat: instrument 7 tool pages with usage audit trail

feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes