chore: nightly skills sync

[github-actions]

Automated skills sync

Components updated:

• Proteina-Complexa
• aggregate payload
• compliance backfill
• nvMolKit

Failed to sync:

• KERMT (NVIDIA-BioNeMo/KERMT): agent/skills empty or missing

Cards backfilled from compliance.d (upstream still owes a skill-card.md):

• open-models-skills/kermt/kermt-infer
• open-models-skills/kermt/kermt-monitor
• open-models-skills/kermt/kermt-pretrain-scratch
• open-models-skills/kermt/kermt-continue-pretrain
• open-models-skills/kermt/kermt-finetune
• open-models-skills/kermt/kermt-setup
• open-models-skills/kermt/kermt-add-cmim-pretrain
• open-models-skills/kermt/kermt-embed
• open-models-skills/proteina-complexa/complexa-target
• open-models-skills/proteina-complexa/complexa-setup
• open-models-skills/proteina-complexa/complexa-sweep
• open-models-skills/proteina-complexa/complexa-evaluate-pdbs
• open-models-skills/proteina-complexa/complexa-design

Upstream now ships its own card — delete these compliance.d entries:

• compliance.d/library-skills/nvmolkit-usage/skill-card.md

Sourced content changes + any pruning are shown in the diff. Native
skills (NIM, workflows, parabricks, genomics, cuEquivariance) are untouched.
Review the diff and merge — nothing merges unattended.

[greptile-apps]

Confidence Score: 3/5

[Low impact] Nightly sync of skill documentation and evaluation metadata.

The PR does not appear safe to merge until the nvMolKit signature and aggregate publication artifacts are regenerated against the refreshed content.

Findings

1.  Signature resources do not match ▶
2.  Documentation map links are broken ▶

Summary

The automated sync refreshes nvMolKit and Proteina-Complexa skill content and backfills publication cards for KERMT and Proteina-Complexa. Two previously reported nvMolKit publication-integrity failures remain unresolved:

• The library signature does not match the current SKILL.md.
• The aggregate benchmark, card, and signature remain stale relative to the refreshed aggregate payload.

_{Reviews (19) · Last reviewed commit: "chore: sync skills from source repos" · Reviewed by Greptile}

[greptile-apps]

Documentation map links are broken

The new links to INFERENCE.md, CONFIGURATION_GUIDE.md, EVALUATION_METRICS.md, and SEARCH_METADATA.md resolve relative to this directory, but none of those files exists. Readers following the documentation map therefore receive file-not-found errors instead of the promised guidance; the mirrored plugin file contains the same broken links.

[greptile-apps]

Signature resources do not match

The new signature bundle records SKILL.md with SHA-256 31375d..., but the current file hashes to 39ec45.... It also requires a BENCHMARK.md that is absent from this directory. Consumers verifying this skill against the bundle will reject it because the signed resources are missing or do not match.