Fix: alignment sample sequences, reverse complement tool, BLAST program filtering, sample buttons on structure/pathway pages

Fix Phase 1 endpoints: resolve UniProt→PDB in structure viewer, use proper Reactome search, surface real backend errors in frontend

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

Guest upgrade, DB migration, settings functional, full Phase 1 feature set

Sprint 3-7: Alignment, Structure Viewer, Pathway Analysis, Utility Tools, analyze page fully live

Sprint 1-2: JWT auth middleware + UniProt dedicated page

fix: remove Lenis SmoothScrollProvider - blocks native scroll in dashboard layout

fix: animate='visible' -> animate='show' to match fadeUp variant

fix: rename lucide-react icons (LoaderCircle, CircleCheck), remove unused imports, replace Set.isSubsetOf

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

settings: mark notifications & danger zone as coming-soon, clean up unused state/imports

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

fix: Analyze button on retrieve page + sessionStorage handoff to blast wizard

fix: E-value underflow, AlphaFold step, steps_completed append, UniProt always runs

fix: use Array.from instead of Set spread for TS compatibility

fix: FASTA header text bleeding into sequence validation, add IUPAC codes U O B Z X J

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

AlphaFold 3D viewer via 3Dmol.js — pLDDT confidence coloring, style selector, spin toggle

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

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