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

Convert legacy light pages (auth, callback, shared, blast) and components to native dark tokens

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

feat(frontend): HUD glass design system + clay components

fix: remove opacity:0 flicker from all pages

Security, crash fixes, demo prep, dead code removal

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

named exports, any->unknown, theme toggle (light/dark), dark mode fixes, error extractor, deleted pipline/ typo dir

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

Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow

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

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