Residue eval redesign: expansion-head control arm (B), paired chain bootstrap, within-zone position analysis, contamination gate, readout-capacity ladder

Preflight: a residue_decoder checkpoint cannot shrink on head swap, so stop demanding it

Lock each model/dataset directory against concurrent writers and guard the final rename

Swarm external retrieval: parallel GPU embedding jobs with CPU-only scoring

Use full sequences with model-specific retrieval limits

Add benchmark-aligned remote retrieval calibration

Run ESM2-650M as 2h head plus 8h end-to-end

Add end-to-end ESM2-650M fine-tuning baseline

Add retrieval-preserving joint decoder finetuning

Add decoder-only progress probe and baseline comparison

Prevent ESM residue probe host-memory OOM and add resume

NetSurfP-3.0 auto-download (atomic+validated), corrected 68-col layout (no SS3 block, RSA@55, phi/psi@65-66, disorder polarity), dataset-name resolution, prefetch step in submit scripts, RUNBOOK

ResidueDecoderHead + span masking + --sequence-head wiring; NetSurfP loader, leakage-free residue probe, compression audit, preflight gate and submit scripts

Fix residue-head position overflow, best.pth tracking, and unattended SLURM chain safety