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

feat(seq-tools): share colored MSA viewer across BLAST job, alignment tool, report, shared and phylo surfaces

feat(alignment): show matched/mismatched/gaps/length stats across all alignment views via shared AlignmentStatsBar

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

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(alignment): pairwise global/local alignment via BLAST hit 'Align pair' (3a)

feat: add query coverage, organism, and query accession to BLAST results

fix: remove opacity:0 flicker from all pages

Add Reactome diagrams, KEGG search, pathway enrichment (pipeline + standalone)

Security, crash fixes, demo prep, dead code removal

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

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

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

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