feat(seo): JSON-LD structured data — Organization/WebSite graph, SoftwareApplication+HowTo homepage, BreadcrumbList across tools

feat(admet): ProTox 3.0 ML toxicity prediction — backend client + endpoint, frontend ProTox tab, restored sidebar chevron

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

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

feat(dashboard): add parallax quick-tool cards and cursor glow effect

Refine dashboard shell: neutral sign-out hover, instrument footer status line

Remove light/dark theme toggle (dark-only app), drop ThemeProvider + darkMode config, add accent-hover token

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

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

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

feat: 4-layer audit/observability system

feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update

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

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

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

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

Re-enable OAuth: restore auth pages, Providers wrapper, dashboard auth guard, landing page CTA

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

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