UV-first benchmark workflow, CLI entrypoints, and HPC docs polish

[SergeiNikolenko]

Summary

• introduce a UV-managed project layout (pyproject.toml, uv.lock) with extras for annotation, similarity, lint, and test
• add bento CLI wrappers in src/bento for legacy scripts (annotate-ligands, compute-pocket-similarity, map-annotations, check-env)
• add environment validation logic (src/bento/envcheck.py) and a script bridge (scripts/check_env.py)
• improve repo documentation and contribution materials (README, docs/reproducibility.md, docs/hpc.md, .github/CONTRIBUTING.md, CONTRIBUTING.md)
• add SLURM templates and CI workflow for lint/test checks
• modernize legacy script config/env handling and add tests for CLI/config/annotation mapping/env checks

Validation

• uv sync --no-editable --extra lint --extra test
• uv run ruff check .
• uv run ruff format --check .
• uv run pytest -q
• Server run on Lobachevsky:
  • uv sync --frozen --no-editable --extra lint --extra test --extra annotation --extra similarity
  • uv run bento check-env --profile annotation
  • uv run bento check-env --profile similarity --glosa-dir ~/tools/glosa_v2.2

Notes

• similarity profile now validates javac and AssignChemicalFeatures.class in addition to glosa, java, and g++.
• on Lobachevsky, similarity check reports missing javac and missing AssignChemicalFeatures.class until JDK/compiler setup is completed in GLoSA directory.