promote: resolution-determinism stack (fork #64/#67/#68/#69/#70) - #92
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…70 Brings org dev src to fork dev src for the resolution-determinism stack (org was current through fork #60 / org #91). Ports the 14 differing src files (making org src == fork src) plus the 17 src-coupled test files + refmet freeze fixtures. Studies-coupled tests and the entire studies/ tree stay fork-only, as does the fork-specific prose-figure/off-category-audit guard (both assert the studies tree exists). Bundled (per the batching policy) since the changes are entangled in shared files (certificate.py/mapper.py/kestrel annotators) and cannot be cleanly separated: - fork #64: Kestrel search sends schema field names category/prefix (server-side filtering) - fork #67: resolver deterministic majority tie-break (_stable_majority) - fork #68: RefMet availability surfacing + bounded batch resilience - fork #69: deterministic Kestrel candidate order (stable_result_order) - fork #70: pinned /match freeze as authoritative RefMet source + refmet_source provenance All Greptile 5/5 on the fork. Offline gate green in this worktree (817 passed, 0 failed); ruff/black/pyright clean on src. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Promotes the resolution-determinism src stack from the fork (trentleslie/biomapper2), all Greptile 5/5 there, to org
dev. Org dev was current through fork #60 (org #91); this brings the remaining src gap.Scope
Ports the 14 differing src files (org
src/becomes identical to forksrc/) + 17 src-coupled test files + refmet freeze fixtures.studies/and studies-coupled tests stay fork-only.Bundled because the changes are entangled in shared files (
certificate.py,mapper.py, the Kestrel annotators) and cannot be cleanly separated:category/prefix(restores server-side filtering)_stable_majority)voted/no_match/unavailable) + bounded batch resiliencestable_result_order, exact-tie broken on CURIE)/matchfreeze as authoritative RefMet source +refmet_source/refmet_snapshot_versionprovenance; breaker out of the default path when a freeze is present, byte-identical when absentSafety
REFMET_SNAPSHOT_PATHset → live/matchpath unchanged), so deploying this to org dev without a freeze changes nothing until a snapshot is configured.Live validation (done on the fork)
Cold-cache A/B on fork dev: with the freeze, retinol + 4 SCFAs resolve deterministically (identical across runs and batch sizes, retinol=CHEBI:12777); without it, 84/200 rows flip node between two cold runs (retinol CHEBI:12777↔CHEBI:132246). Artifacts:
determinism_proof_20260908.🤖 Generated with Claude Code