[arena-ai-coding-agent]

Summary

• Multiplicative Replacement (Martín-Fernández 2003): Implemented exact count-scale multiplicative replacement in Execution.prepare_analysis_table. Preserves total sample depth ($\sum x_{ij}^* = \sum x_{ij}$) and subcompositional ratios between all non-zero components ({aj}^/x_{bj}^ = x_{aj}/x_{bj}$). (Refs feat(analysis): Advanced zero handling — glmGamPoi dispersion, Bayesian multiplicative replacement, multiplicative replacement with delta  #21)
• Bayesian Multiplicative Replacement (Martín-Fernández 2015): Implemented Dirichlet prior posterior replacement preserving sample depth. (Refs feat(analysis): Advanced zero handling — glmGamPoi dispersion, Bayesian multiplicative replacement, multiplicative replacement with delta  #21)
• TSS Offsets for NB_GLM (Issue feat(analysis): TSS/CSS/RSS offsets — exact normalization with DESeq2-style offsets, not alias to relative  #16): Implemented exact Total Sum Scaling offsets for nb_glm. Keeps raw counts in prepared (preserving integer negative binomial properties) and sets offset = log(lib_sizes) instead of fractional scaling. (Refs feat(analysis): TSS/CSS/RSS offsets — exact normalization with DESeq2-style offsets, not alias to relative  #16)
• Epistemic Claims with Receipts: Added Standpoint, TaxonWarrant, ProjectionY, and SHA-256 Receipt verification in src/core/epistemic.jl, with encode_avec_fibre / parse_avec_fibre for the avec_fibre column. Aligns directly with EpistemicTypes.jl and echo-types.
• Zero Observation Disambiguation: Added disambiguate_zero distinguishing certified biological absence (Val(:true_absence)) from observation limit (Val(:undetected)), connecting to absolute-zero and Issue feat(analysis): Occupancy models — presence/absence with imperfect detection, zero-inflated NB, hurdle models  #18.
• Original R Pipeline Protected: DADA2, SWARM, VSEARCH, and R runtime scripts remain strictly isolated and untouched.

Tests & Hygiene

• check-spdx.sh: OK (279 files covered)
• check-format.sh: OK (326 files checked)
• check-blob-hygiene.sh: OK
• New comprehensive unit tests added to test/unit/test_execution.jl and test/unit/test_analysis_config.jl.

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