feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis

feat(results): in-app share dialog + self-normalized dotplot scoring

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

feat(seq-tools): wire motif scanner into BLAST, structure, alignment and dot-plot workflows

feat(seq-tools): motif categories & structure overlay, dot-plot scoring & features, cross-tool links

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

feat(export): add downloads to ADMET, MD, pairwise, AlphaFold, docking, pathway, plus 4 new learn topics

fix(frontend): stop polling after job completion and surface AI rate-limit retry countdown

fix(pathways): read enrichment results from projection response, add p-value and gene ratio

Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data

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

Add global/local BLAST modes, full-length pairwise alignment view, standalone pairwise tool

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

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

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

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

fix: UniProt link shows invalid URL when accession is NCBI

feat: show PDB structures, GO terms, and expanded features in UniProt panel

fix: Ramachandran tab hidden for proteins without PDB IDs + AI interpretation error

fix: add 'running' to isActive and STATUS_ORDER to prevent false 'no results' flash; show bit_score in ScoreBars

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

fix: remove opacity:0 flicker from all pages

feat: add DNA sequence output across BLAST, UniProt, sequencing, primers, and SequenceRetrieval

feat: implement 8 tool bridges (F1-F8) + audit child components

fix: default import PhyloTreeViewer in alignment, report, and PipelineResults

feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

fix: convert AlignmentView.tsx light-theme classes to dark void theme tokens

feat: add PNG/TSV/JSON/CSV/FASTA export to all 8 tool components

Fix invisible fonts in Reactome DiagramJs: isolate widget from dark-theme CSS overrides

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

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

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

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