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

refactor(icons): migrate lucide-react to @phosphor-icons/react, remove dep

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

fix: remove opacity:0 flicker from all pages

Polish: restyle blast/dashboard/jobs/history/results pages to dark theme, fix Loader2 icons, update result components

full dark migration: CSS overrides for all legacy classes, framer-motion animations across every page/component, rebrand to Bio Nexus

design.md + rules.md compliance: dark theme, teal palette, pulsing dot, Pydantic models, api.ts routing, config fixes, db/max_hits threading, Supabase migration 004

Core pipeline testability: progress callback, rate limiter 429, history table

Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1)