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

Restore DNA helix as full-window landing hero background, drop fake HUD readout

Add next/core-web-vitals ESLint config, fix unescaped entities

Polish tool pages: fix dead bg-glass-card classes, contrast on teal, confidence band tokens, RNA badge

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

Redesign landing: asymmetric hero with instrument-window helix, bento features, route-style pipeline, restrained motion

Delete legacy !important Tailwind override layer from globals.css

Convert legacy light pages (auth, callback, shared, blast) and components to native dark tokens

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

feat(docking): show full AutoDock Vina log by default, no scroll cap

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

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(docking): Vina full-detail — parse 1.2.7 log (RMSD l.b./u.b., version, seed), RMSD table + run-config UI (3e)

feat(uniprot,domains): reviewed/organism filters + debounce/fast-path, PROSITE raw-sequence scan UI (3c,3d)

feat(alignment): multi-method MSA (clustalo/muscle/kalign/mafft/tcoffee) with method selector (3b)

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

feat(md): verified force field/solvent menu (ff14SB/ff15ipq/ff19SB/amberfb15/CHARMM36 x OBC1/OBC2/GBN2) with alanine-dipeptide createSystem startup probe; explicit errors for invalid combos; dynamic frontend menu

fix(blast): honor program/db/max_hits params, accept DNA queries, poll cap 65 min

fix(frontend): clear stale results, prefill-only bridges, and results-ready banners

fix(md): don't abandon long jobs after 5 min + trim workload

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

feat(md): clay simulation-parameter controls (force field, solvent, run length)

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

feat(md): temperature/KE, Rg and SASA traces; fix OpenMM in deployed image

feat(md): real OpenMM production runs with accurate Ca RMSD

fix: increase axios timeout for long-running endpoints and fix Render config

feat: cross-feature auto-fill bridges — data flows between all tools via sessionStorage

fix: add optional score property to Domain type for TSV export

feat: expanded Domain & Motif Analysis with all features and cross-project links

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: StructureComparison re-fetches on every render due to audit dep

perf: parallelize post-BLAST steps + fast_mode Swiss-Prot toggle

fix: BLAST reliability - API key, exponential backoff, retry, error tracking

feat: live pipeline status progression — worker pushes status to Supabase at each step

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

feat: ADMET 3a/3b split — mark RDKit descriptors as production, toxicity/ADMET as rule-based heuristic

fix: ADMET import error + MD secondary structure accuracy

feat: industrial-grade ADMET + detailed MD/function results

fix: stale job polling + 5min timeout + backend staleness guard

fix: extract string from rate-limit error object to prevent React crash

fix: OpenMM via micromamba + BioPython structural fallback, real error messages

feat: scientifically accurate MD simulation with OBC2 solvent, Kabsch RMSD, per-residue RMSF

Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

Phase 0a: SSRF protection + auth on docking/sequencing, worker design doc

Fix color scheme switching, vina log parsing, icon dedup, dead code