Align nvMolKit skill with BioNeMo expected representation and add evals.

[scal444]

This will be consumed by https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit

[greptile-apps]

Greptile Summary

This PR renames the skill directory from agent-skills/nvmolkit-usage/ to skills/nvmolkit-usage/, adds a portable eval suite (11 full evals + 5 trigger evals) consumed by the BioNeMo agent toolkit, and makes two unrelated C++ corrections to include paths and CCCL compatibility.

• Eval files added (skills/nvmolkit-usage/evals/): evals.json defines 11 task-level scenarios covering installation, porting, from-scratch workflows, and performance diagnosis; trigger_evals.json holds 5 entries (3 positive, 2 negative) for skill-routing tests.
• Test updates (nvmolkit/tests/test_skill.py): path constants and error messages updated; two new schema-validation tests added for both eval files.
• C++ housekeeping: fingerprint_similarity_device.cuh replaces cuda::std::min/max with cubMin{}/cubMax{} functors to unify CCCL 2.x/3.x handling; test_fmcs_primitives.cu fixes include paths to match the src/mcs/ layout.

Confidence Score: 5/5

Safe to merge — all changes are directory renames, new data files, additive tests, and two isolated C++ compatibility fixes with no behavioral change.

The cubMin{}/cubMax{} substitution in fingerprintSimilarityCanReach is semantically identical to the cuda::std::min/max it replaces, and both CCCL branches in cub_helpers.cuh correctly return the typed minimum/maximum in device code. The FMCS include path fixes align with the actual source tree layout. No logic changes touch any runtime path.

Files Needing Attention: No files require special attention.

Important Files Changed

Filename	Overview
nvmolkit/tests/test_skill.py	Path constants updated and two new tests added: schema validation for evals.json and coverage check for trigger_evals.json.
skills/nvmolkit-usage/evals/evals.json	New file: 11 portable eval definitions covering installation, porting, from-scratch workflows, performance diagnosis, and autotuning scenarios.
skills/nvmolkit-usage/evals/trigger_evals.json	New file: 5 trigger eval entries (3 positive, 2 negative) to validate skill routing decisions.
src/fingerprint_similarity_device.cuh	Replaces cuda::std::min/max with the project-local cubMin{}/cubMax{} functors from cub_helpers.cuh; semantics are preserved across CCCL versions.
tests/test_fmcs_primitives.cu	Include paths corrected to src/mcs/fmcs_cuda/ and src/mcs/mcs_common/ to reflect the actual source tree layout.
README.md	Path reference updated from agent-skills/nvmolkit-usage/ to skills/nvmolkit-usage/.
docs/agent_skill.rst	Documentation link updated to match the new skills/nvmolkit-usage/ directory path.

_{Reviews (3): Last reviewed commit: "Fix include check" | Re-trigger Greptile}

[evasnow1992]

Changes look good to me. Thank you!