Relicense to GPL (>= 2); opaque case IDs and sealed evaluator truth

[sounkou-bioinfo]

Relicenses VariantStoryBench to GPL (>= 2), in line with RGenomicsETL's policy (all copyright holders agreed), and makes the benchmark's inputs safe to hand to an engine. The history is kept.

• Licence: DESCRIPTION now reads GPL (>= 2). LICENSE carries the full GPL-2 text and is left out of the package build (.Rbuildignore), so R CMD check doesn't raise a NOTE. The README is re-rendered and NEWS records the change.
• Opaque case IDs: generated cases and fixtures get stable identifiers derived from the seed and case index, so a file name can't reveal a case's role (for example "confirmed negative"). The mapping from ID to role is kept only in the evaluator's truth.
• Sealed truth: engine inputs and evaluator truth are written to separate directories. A test checks that the engine bundle contains no truth relation or truth-derived column.
• Tests: bench_manifest_paths() now has one.
• CI: the pinned Rduckhts install stays. test-generation.R uses it for an optional round trip through four VCFs; that path was not run locally.

The opaque IDs are not a security boundary against an engine that can read this package's source. Isolation relies on giving the adapter only the engine bundle.

Checks:

• R CMD check --no-manual on the built tarball: Status OK.
• tinytest: 195 passed, 0 failed.
• make targets: all six targets complete offline from a fresh store.

Performance

No checked-in benchmark covers these changes. They rename fixture identifiers and change output directories; no data paths are measured.

Prepared with Claude 5.5 and GPT 6 Sol in Claude Code and Pi

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-28T19:55:00.636507Z	bac8a8c	PR opened

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