Add RFdiffusion-to-LigandMPNN workflow and direct app-backed nodes

[y1zhou]

Summary

• Adds workflow-compatible RFdiffusion and LigandMPNN app functions, including shared CLI-argument builders and workflow-safe output contracts.
• Adds rfd_ligandmpnn workflow to fan out RFdiffusion trajectories/designs and run LigandMPNN design nodes in parallel for each generated scaffold.
• Updates workflow runtime/core nodes so remote workflow nodes submit real app function calls directly, process remote results through node hooks, and avoid the old extra per-node runner layer.
• Adds inline zstd byte support for small workflow archives and materializes inline outputs once under each attempt directory with ledger JSON rewritten to durable VolumePath storage.
• Adds workflow --dry-run DAG printing, compact DAG labels, workflow CLI coverage, and updated app/workflow agent docs and skills.

Details

• RFdiffusion outputs remain volume-backed and LigandMPNN outputs are returned as small inline zstd tarballs for workflow materialization.
• LigandMPNN redesign residues are inferred from RFdiffusion .trb/PDB outputs so fixed contig residues are not passed as designable positions.
• Workflow app composition now uses included app handles and app dependency metadata instead of deployed-app lookup strings.
• The workflow ledger no longer stores base64 inline byte payloads in SQLite; it stores the materialized app-result JSON after inline bytes are converted to workflow-volume paths.