[arena-ai-coding-agent]

Summary of Changes

1. Refusal of Deferred ILR Bases:

   • AnalysisConfig.DEFERRED_ILR_BASIS defines the deferred bases ("phylogenetic", "sequential_binary_partition", "balance_dendrogram").
   • Refused at NormalizationConfig construction and in prepare_analysis_table instead of warn-and-substitute.
   • context_help("normalization.ilr_basis") rewritten to document that only the default Helmert basis is implemented and others are deferred (Issue feat(analysis): ILR basis — phylogenetic ILR (PhILR), sequential binary partition (SBP), balance dendrogram  #20).

2. Balance Row Labelling & Integrity:

   • Relabels ILR rows to balance_1..balance_n-1.
   • Records ILR provenance and diagnostics in diagnostics.checks["ilr"].
   • Prevents all-zero-taxa healing from restoring original taxon labels onto balance rows.

3. CI Test Suite Fix:

   • Updates prepare_analysis_table keeps counts and hands over the offset test in test/unit/test_scaling.jl to use a 4-sample fixture (table_4), satisfying the min_samples_per_group=2 requirement (>= 2 * 2 = 4 samples).
   • Adds unit tests for deferred basis refusal and balance row labelling.
   • Updates RCall usage to rcopy(reval(...)).

4. Documentation & Outreach:

   • Adds docs/owner-review-2026-09-25.md (with CC-BY-SA-4.0 SPDX header) and CHANGELOG entry.

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