feat(branding): Synteny rebrand — new identity, signal-coded palette, and pipeline icons

feat(design): bioluminescent green+violet palette and re-tuned landing hero

feat(ui): apple-design conformance — springs for micro-interactions, reduced-motion/transparency/contrast support, typography tracking

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

Fix share links, persist wizard jobs, add AI interpretation fallback, animate landing

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

Delete legacy !important Tailwind override layer from globals.css

style(theme): Geist fonts, AA-verified text tiers, 4-band confidence tokens

chore: frontend design polish (accent palette, remove glow/gradient utils), ignore installed skill trees, add opencode skills config

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

fix: dark input/textarea/select backgrounds and focus border override

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

redesign: BioFlow AI void-dark theme — new landing page, dashboard, Three.js DNA helix, Lenis smooth scroll

dark mode: add missing CSS overrides (gradients, forms, badges, hover, bg-opacity, teal variants) + ThemeToggle on landing, auth, callback, shared pages

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

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