docs(genetics): pattern-recognition hand-off + integration plan + headstone (for a domain expert new to the stack)#501
Conversation
…dstone
Three artifacts for a genetics-domain researcher who knows their domain cold
but has not seen this stack:
1. docs/GENETIC_RESEARCH_VIA_STACK.md (237 lines)
The "wow that's potential" doc. Eight pattern matches from genetics domain
to shipped substrate primitives, each grounded in file:line:
- Sequence sketches (MinHash) ↔ CAM-PQ 48-bit fingerprint (PR #210; 94%
of Jina 1024-D on SimLex-999)
- Genomic coordinates ↔ HHTL nibble-trie (lance-graph-contract::hhtl)
- chromosome→arm→band→gene ↔ CLAM 3-level 16-way tree (ndarray::hpc::clam)
- Novel-variant detection ↔ CHAODA anomaly score on LFD distribution
(ndarray::hpc::clam.rs:1493-1560; Ishaq et al. 2021)
- minimap2 minimizers ↔ bgz17 11/17 X-Trans stride (BGZ17_ELEVEN_SEVENTEEN
_RATIONALE.md; provable anti-moiré bound)
- Bayesian variant evidence ↔ Friston entropy×energy plane (PR #491/#494;
ρ(entropy, accuracy) = −0.78 measured in ndarray #218)
- Cancer cascade simulation ↔ MailboxSoA + CounterfactualMailbox
(mailbox_soa.rs + counterfactual.rs; SPAWN_DISSONANCE_THRESHOLD = 0.55)
- do-calculus on driver mutations ↔ Pearl-2³ mask in CausalEdge64
(high_heel.rs:202; pearl_junction)
Plus the architecture diagram, the shipped-vs-proposed table, the dynamics
axis as the unique substrate contribution (counterfactual lanes preserved),
the first cargo command that proves it (CHAODA tests on main), and the
one-paragraph pitch.
2. .claude/plans/genetic-research-substrate-integration-v1.md (213 lines)
The HOW. Ten deliverables (D-GEN-1..10) + three gating probes:
- D-GEN-1: adapter-genetics-experimental crate scaffold (~1 day)
- D-GEN-2: FASTA/VCF parsers via noodles-* (~3 days)
- D-GEN-3: k-mer → CAM-PQ fingerprint (~half-day)
- D-GEN-4: reference genome NodeGuid addressing mint (~1 day)
- D-GEN-5: GO/Reactome/ClinVar TtlHydrators (~1 week)
- D-GEN-6: §14 oracle adapter for variant caller comparison (~3 days)
- D-GEN-7: KRAS G12D 1024-cell counterfactual fan-out (~2 weeks, FLAGSHIP)
- D-GEN-8: DeepNSM genetic-language reader probe (~1 week)
- D-GEN-9: Histology splat extension with genomic profile (~3 days)
- D-GEN-10: §14 oracle benchmark against GIAB truth set (~1 week)
- Probes: PROBE-CHAODA-1000G, PROBE-KRAS-COUNTERFACTUAL-DET, PROBE-CAM-
PQ-VS-BLAST
5-phase sequencing; minimum viable hand-off at end of P1; flagship at D-GEN-7.
§0 anti-invention guardrail + no-new-enum-variant contract test (#500)
enforced throughout.
3. .claude/handovers/2026-06-16-genetic-research-headstone-exploration.md
(293 lines) — the WHAT-COMPLETE-LOOKS-LIKE doc.
Headstone shape mirroring 3DGS-Cesium-BindSpace4-headstone-exploration.md:
- Purpose: preserve the architectural synthesis
- Capstone thesis: one block of prose (bioinformatics ships pipelines;
the substrate ships a SHAPE)
- Four-layer architecture from a geneticist's vantage
- Why bioinformatics pipelines alone are not enough
- Why building genomics tooling from scratch is not enough
- 8 invariants the adapter inherits from the substrate
- 9 conditions for "complete"
- Era closes (per-tool pipeline silos; no counterfactual preservation;
trained-classifier-only outlier detection) vs. era opens (one SPO
graph; counterfactual lanes; CHAODA unsupervised; Pearl-2³ native;
Friston entropy×energy calibration; same-math-at-all-scales splat
extension; §14 oracle cross-pipeline equivalence)
The three artifacts compose: epiphany doc tells the geneticist WHY; plan
tells them HOW; headstone tells them WHAT COMPLETE LOOKS LIKE.
Predecessor: .claude/plans/3DGS-genetics-4x4-fanout-plan.md (static
representation; this PR extends with dynamics + counterfactual lanes).
https://claude.ai/code/session_01VysoWJ6vsyg3wEGc5v7T5v
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| Per the substrate's §0 anti-invention guardrail (lance-graph #496) and the no-new-variant contract test (#500): | ||
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| 1. **No new `ValueSchema` enum variant.** Genetic-research rows ride `Full` or `Compressed` presets; specialisation is via `classid → ClassView` mint. | ||
| 2. **No new `EdgeCodecFlavor` enum variant.** Use `CoarseResidue` for genomic edges (the 1-byte palette + signed-4-bit residue is sufficient for sequence-similarity edges; ICC 0.97–0.99 measured on ndarray #218). |
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This plan explicitly selects EdgeCodecFlavor::CoarseResidue, but the repo already records TD-COARSERESIDUE-NO-VALUE-TENANT in .claude/board/TECH_DEBT.md: CoarseResidue needs a per-dimension residue in the value slab and currently has no ValueTenant, so pairing it with the Full/Compressed presets leaves the residue unaddressable or colliding with another tenant. Following this “locked” decision would make the genetics adapter pick an unresolved storage shape before the documented operator decision is made; mark this as blocked or use a flavor with an existing storage path until that debt is resolved.
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Both real bugs; addressed in cd53ab5.
On the CoarseResidue lock: confirmed TD-COARSERESIDUE-NO-VALUE-TENANT at .claude/board/TECH_DEBT.md:40 ("the EdgeCodecFlavor enum rode #495 / 920671d (entropy-ladder D-EL-1); #496 only adds the ValueSchema/FULL-default on top. The #495 AGENT_LOG claim that 'signed-CoarseResidue is a first-class tenant' was aspirational — no such tenant exists in VALUE_TENANTS"). Pairing CoarseResidue with Full/Compressed would have left the signed-4-bit residue unaddressable.
§0 rule 2 now reads:
Genomic edges ride
Pq32x4(TurbovecResiduetenant has shipped storage) orCoarseOnly(1-byte palette, no separate residue slab).CoarseResidueis BLOCKED until the operator mints its dedicatedValueTenant(TD-COARSERESIDUE-NO-VALUE-TENANT,.claude/board/TECH_DEBT.md:40) — pairing it withFullorCompressedtoday leaves the signed-4-bit residue unaddressable.
D-GEN deliverables route through Pq32x4 (TurbovecResidue tenant has shipped storage) or CoarseOnly (palette only) until the tech-debt entry is resolved by an operator-minted tenant. Commit: cd53ab5.
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| ### D-GEN-5: GO / Reactome / ClinVar `TtlHydrator`s | ||
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| **What:** add three `TtlHydrator` implementations to `lance-graph-ontology::OntologyRegistry`: |
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There is no TtlHydrator type or trait in crates/lance-graph-ontology; the shipped pattern is MetaStructureHydrator/OwlHydrator plus exported hydrate_*() glue functions in hydrators/mod.rs. Because this line asks future work to add three TtlHydrator implementations, it sends D-GEN-5 down a non-existent API path and risks inventing a new substrate abstraction despite the plan’s no-new-primitives guardrail.
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Confirmed — TtlHydrator does not exist; addressed in cd53ab5.
The shipped API per crates/lance-graph-ontology/src/hydrators/mod.rs:1-57 is Pattern D — Meta-Structure Hydration: OwlHydrator + MetaStructureHydrator types plus hydrate_*() glue functions (hydrate_dolce / hydrate_owltime / hydrate_provo / hydrate_qudt / hydrate_schemaorg / hydrate_skos / hydrate_fibo_fnd / hydrate_fibo_be / hydrate_odoo / hydrate_zugferd / hydrate_skr03 / hydrate_skr04). Per the mod.rs preamble: "Each per-ontology hydrator is data + ~50 LOC of glue, never a bespoke crate."
D-GEN-5 now proposes hydrate_go() / hydrate_reactome() / hydrate_clinvar() glue over the shipped OwlHydrator / MetaStructureHydrator, mirroring the proven shape of hydrate_dolce / hydrate_provo / hydrate_skos. No new trait, no new bespoke crate.
The companion mentions in docs/GENETIC_RESEARCH_VIA_STACK.md §3 and .claude/handovers/2026-06-16-genetic-research-headstone-exploration.md (Layer 0 / 1, "Why building from scratch is not enough", "What complete looks like") have been brought into line with this shape. Commit: cd53ab5.
Two corrections per Codex review on the genetic-research artifacts: (1) EdgeCodecFlavor::CoarseResidue is blocked, not usable. Plan §0 rule 2 previously locked genomic edges onto CoarseResidue. Per TD-COARSERESIDUE-NO-VALUE-TENANT (.claude/board/TECH_DEBT.md:40), the enum variant exists but no ValueTenant in VALUE_TENANTS addresses its signed-4-bit residue slab; pairing it with Full or Compressed today leaves the residue bytes unaddressable. Rule 2 now routes genomic edges through Pq32x4 (TurbovecResidue tenant has shipped storage) or CoarseOnly (1-byte palette, no separate residue slab), and explicitly flags CoarseResidue as BLOCKED pending the operator-minted tenant. (2) TtlHydrator does not exist; shipped API is Pattern D. D-GEN-5 previously proposed three new "TtlHydrator" implementations. The shipped API per crates/lance-graph-ontology/src/hydrators/mod.rs:1-57 is Pattern D - Meta-Structure Hydration: OwlHydrator + MetaStructureHydrator types plus hydrate_*() glue functions (hydrate_dolce / hydrate_owltime / hydrate_provo / hydrate_qudt / hydrate_schemaorg / hydrate_skos / hydrate_fibo_fnd / hydrate_fibo_be / hydrate_odoo / hydrate_zugferd / hydrate_skr03 / hydrate_skr04). Each per-ontology hydrator is "data + ~50 LOC of glue, never a bespoke crate" per the mod.rs preamble. D-GEN-5 now proposes hydrate_go() / hydrate_reactome() / hydrate_clinvar() glue over the shipped types, mirroring the proven shape of hydrate_dolce / hydrate_provo / hydrate_skos. No new trait, no new bespoke crate. Both findings were the exact failure mode the operator has been catching me on: naming an existing primitive incorrectly OR proposing a non-existent substrate abstraction despite the plan's own no-new-primitives guardrail. Files touched: - .claude/plans/genetic-research-substrate-integration-v1.md (3 edits) - docs/GENETIC_RESEARCH_VIA_STACK.md (2 edits) - .claude/handovers/2026-06-16-genetic-research-headstone-exploration.md (4 edits) https://claude.ai/code/session_01VysoWJ6vsyg3wEGc5v7T5v
…oaOwner cherry-pick + LanceVersionScheduler + SurrealMailboxView (D-PG-6) Lands four tasks from the shortest-unblocking-path list surfaced after PR #497-#501 + the AdaWorldAPI/surrealdb fork bump (lance/lance-index =7.0.0, lancedb =0.30.0, ndarray exact-rev). All four meet at the single contract trait `MailboxSoaView`, closing the cascade in one commit (E-UNBLOCK-CASCADE-1). ## Task 3 — `NiblePath::{from_guid_prefix, prefix}` (zero-dep, foundational) Ontology-side keystone follow-up of PR #498's `classid → ReadMode` LE contract. The 20-nibble `classid(8) | HEEL(4) | HIP(4) | TWIG(4)` prefix overflows the 16-nibble MAX_DEPTH: the deterministic fold drops the canon-reserved high u16 of classid (root-first pack: `classid_lo(4) | HEEL(4) | HIP(4) | TWIG(4)`), returning None when the fold would be lossy. `prefix(d)` is the O(1) ancestor view; `prefix(d).is_ancestor_of(self)` holds for every d ≤ self.depth (the routing-cache view of a deeper class path). +7 tests in `hhtl::tests`; contract lib 619 → 632 green. ## Task 2 — `impl MailboxSoaView + MailboxSoaOwner for MailboxSoA<N>` Cherry-pick of jolly-cori-clnf9 commit 463d71b (integrated-cognitive-planner-v1 §2 Seam #3, +149 LOC). Adds `pub phase: KanbanColumn` field + zero-copy repr(transparent) slice impls (edges_raw, meta_raw) + the in-RAM Rubicon driving-loop test (`test_in_ram_driving_loop_walks_rubicon_to_commit`). The contract spine (#437/#439) now drives an actual loop end-to-end — no surreal, no ractor bus needed for the in-process case. +1 driving-loop test; cognitive-shader-driver lib 85 → 86 green. ## Task 1 — `LanceVersionScheduler` over `VersionedGraph::versions()` D-MBX-9-IN core impl (the CI-gated twin of the contract slice shipped 2026-05-31). Lives in `crates/lance-graph/src/graph/scheduler.rs`. Wraps a `VersionedGraph` + inner `VersionScheduler<S = NextPhaseScheduler>` and exposes: - `drive_once(view, exec)` — read current Lance version, lower to a move - `drive_at_latest(view, exec)` — fold `versions().last()` into a move - `current_dataset_version()` — typed `DatasetVersion` over nodes head Closes `E-SUBSTRATE-IS-THE-SCHEDULER`'s OUT-direction end-to-end. The OUT direction stays propose-not-dispose (R1): returned `KanbanMove` is for the caller's `MailboxSoaOwner::try_advance_phase` to apply. +5 tests with real on-disk tempdir Lance (no mocks). ## Task 4 — `SurrealMailboxView<'a>` (D-PG-6 contract slice) Read-only `MailboxSoaView` adapter the SurrealQL projection populates via `from_columns(...)` — pure zero-copy borrow over the kv-lance scan's byte buffers. Imports `MailboxSoaView` but NOT `MailboxSoaOwner` (compile-time enforcement of `kanban.rs:1-21` "surreal=project-read-only, callcenter=commit"). `read_via_kv_lance()` returns the new typed `SurrealContainerError::BlockedColdBuild` until the surrealdb fork dep in `Cargo.toml` is uncommented — kept off by default to avoid the ~10 min cold surrealdb build for contributors who don't need it. The contract surface is available today; the integration is one Cargo.toml edit + a SurrealQL projection body in `view.rs`. +4 tests; new `lance-graph-contract` dep in surreal_container/Cargo.toml; BLOCKED(C) marker flipped to RESOLVED. ## What this unblocks - **D-MBX-9-IN-impl** — SHIPPED (the contract trait now has a Lance-backed implementor). - **D-MBX-A6-P3** — still queued, BUT Seam #3 (the in-RAM loop) is now in-tree; a downstream session can wire the emit-side without depending on the unmerged jolly branch. - **D-PG-6 (Rubicon kanban VIEW)** — contract slice SHIPPED; impl-side gated on `BlockedColdBuild` flip-on (one Cargo.toml uncomment + projection body). - **Identity-architecture v1 §3 P-SCOPE-CLASSIFY** — solved (the bijection-width fix is deterministic + ancestor-preserving + falsifiable by tests). ## Tests + clippy - lance-graph-contract: **632** (+7 hhtl) - cognitive-shader-driver: **86** (+1 driving-loop) - lance-graph::scheduler: **5** (new module, real Lance tempdir) - surreal_container::view: **4** (new module) All clippy `-D warnings` clean on the new files. Pre-existing lints in lance-graph-ontology / lance-graph-planner / ndarray_bridge.rs are out of session scope. ## Board hygiene (mandatory rule) - LATEST_STATE.md — Contract Inventory PREPEND for the new types. - EPIPHANIES.md — E-UNBLOCK-CASCADE-1: three independent landings converge on one trait surface, closing four queued deliverables in one commit. - AGENT_LOG.md — task-by-task summary with test counts. https://claude.ai/code/session_01Xzyc27Nx3f8WC5KzwfWfjx
…oaOwner cherry-pick + LanceVersionScheduler + SurrealMailboxView (D-PG-6) Lands four tasks from the shortest-unblocking-path list surfaced after PR #497-#501 + the AdaWorldAPI/surrealdb fork bump (lance/lance-index =7.0.0, lancedb =0.30.0, ndarray exact-rev). All four meet at the single contract trait `MailboxSoaView`, closing the cascade in one commit (E-UNBLOCK-CASCADE-1). ## Task 3 — `NiblePath::{from_guid_prefix, prefix}` (zero-dep, foundational) Ontology-side keystone follow-up of PR #498's `classid → ReadMode` LE contract. The 20-nibble `classid(8) | HEEL(4) | HIP(4) | TWIG(4)` prefix overflows the 16-nibble MAX_DEPTH: the deterministic fold drops the canon-reserved high u16 of classid (root-first pack: `classid_lo(4) | HEEL(4) | HIP(4) | TWIG(4)`), returning None when the fold would be lossy. `prefix(d)` is the O(1) ancestor view; `prefix(d).is_ancestor_of(self)` holds for every d ≤ self.depth (the routing-cache view of a deeper class path). +7 tests in `hhtl::tests`; contract lib 619 → 632 green. ## Task 2 — `impl MailboxSoaView + MailboxSoaOwner for MailboxSoA<N>` Cherry-pick of jolly-cori-clnf9 commit 463d71b (integrated-cognitive-planner-v1 §2 Seam #3, +149 LOC). Adds `pub phase: KanbanColumn` field + zero-copy repr(transparent) slice impls (edges_raw, meta_raw) + the in-RAM Rubicon driving-loop test (`test_in_ram_driving_loop_walks_rubicon_to_commit`). The contract spine (#437/#439) now drives an actual loop end-to-end — no surreal, no ractor bus needed for the in-process case. +1 driving-loop test; cognitive-shader-driver lib 85 → 86 green. ## Task 1 — `LanceVersionScheduler` over `VersionedGraph::versions()` D-MBX-9-IN core impl (the CI-gated twin of the contract slice shipped 2026-05-31). Lives in `crates/lance-graph/src/graph/scheduler.rs`. Wraps a `VersionedGraph` + inner `VersionScheduler<S = NextPhaseScheduler>` and exposes: - `drive_once(view, exec)` — read current Lance version, lower to a move - `drive_at_latest(view, exec)` — fold `versions().last()` into a move - `current_dataset_version()` — typed `DatasetVersion` over nodes head Closes `E-SUBSTRATE-IS-THE-SCHEDULER`'s OUT-direction end-to-end. The OUT direction stays propose-not-dispose (R1): returned `KanbanMove` is for the caller's `MailboxSoaOwner::try_advance_phase` to apply. +5 tests with real on-disk tempdir Lance (no mocks). ## Task 4 — `SurrealMailboxView<'a>` (D-PG-6 contract slice) Read-only `MailboxSoaView` adapter the SurrealQL projection populates via `from_columns(...)` — pure zero-copy borrow over the kv-lance scan's byte buffers. Imports `MailboxSoaView` but NOT `MailboxSoaOwner` (compile-time enforcement of `kanban.rs:1-21` "surreal=project-read-only, callcenter=commit"). `read_via_kv_lance()` returns the new typed `SurrealContainerError::BlockedColdBuild` until the surrealdb fork dep in `Cargo.toml` is uncommented — kept off by default to avoid the ~10 min cold surrealdb build for contributors who don't need it. The contract surface is available today; the integration is one Cargo.toml edit + a SurrealQL projection body in `view.rs`. +4 tests; new `lance-graph-contract` dep in surreal_container/Cargo.toml; BLOCKED(C) marker flipped to RESOLVED. ## What this unblocks - **D-MBX-9-IN-impl** — SHIPPED (the contract trait now has a Lance-backed implementor). - **D-MBX-A6-P3** — still queued, BUT Seam #3 (the in-RAM loop) is now in-tree; a downstream session can wire the emit-side without depending on the unmerged jolly branch. - **D-PG-6 (Rubicon kanban VIEW)** — contract slice SHIPPED; impl-side gated on `BlockedColdBuild` flip-on (one Cargo.toml uncomment + projection body). - **Identity-architecture v1 §3 P-SCOPE-CLASSIFY** — solved (the bijection-width fix is deterministic + ancestor-preserving + falsifiable by tests). ## Tests + clippy - lance-graph-contract: **632** (+7 hhtl) - cognitive-shader-driver: **86** (+1 driving-loop) - lance-graph::scheduler: **5** (new module, real Lance tempdir) - surreal_container::view: **4** (new module) All clippy `-D warnings` clean on the new files. Pre-existing lints in lance-graph-ontology / lance-graph-planner / ndarray_bridge.rs are out of session scope. ## Board hygiene (mandatory rule) - LATEST_STATE.md — Contract Inventory PREPEND for the new types. - EPIPHANIES.md — E-UNBLOCK-CASCADE-1: three independent landings converge on one trait surface, closing four queued deliverables in one commit. - AGENT_LOG.md — task-by-task summary with test counts. https://claude.ai/code/session_01Xzyc27Nx3f8WC5KzwfWfjx
2 participants
Three artifacts for a genetics-domain researcher who knows their domain cold but has not seen this stack.
Pure docs. No code touched. No new substrate primitives.
+743 / -0over 3 files.The three artifacts compose
docs/GENETIC_RESEARCH_VIA_STACK.md.claude/plans/genetic-research-substrate-integration-v1.md.claude/handovers/2026-06-16-genetic-research-headstone-exploration.mdThe pattern recognition the epiphany doc surfaces
Eight shapes the geneticist knows ↔ eight primitives the substrate already ships, each grounded in file:line:
cam_pq/storage.rs:9+linguistic-epiphanies-2026-04-19.md:299-312lance-graph-contract::hhtl::NiblePathndarray::hpc::clam~1600 linesndarray/src/hpc/clam.rs:1493-1560crates/bgz17/src/lib.rs:53-60+BGZ17_ELEVEN_SEVENTEEN_RATIONALE.mdmailbox_soa.rs+counterfactual.rs:232pearl_junctionclassifierhigh_heel.rs:202+crate::pearl_junctionWhat the dynamics axis (the unique substrate contribution) gives
Standard tools (GATK / DeepVariant / Reactome / SCENIC / nf-core) each give part of the picture. None preserve the counterfactual branch as a persistent, query-visible substrate lane. The substrate does:
CounterfactualMailboxis the storage;revise_if_minority_winsis the update rule;InferenceType::Counterfactual(mantissa = -6) is the mechanical guarantee that counterfactual edges never leak into observed SPO.For a cancer cohort: every patient's tumor carries both its actual driver-mutation history AND the counterfactual alternatives the substrate's Friston-FEP active inference deemed worth tracking. The §14 oracle compares counterfactual lanes across patients — "this counterfactual branch was rejected in 9/10 tumors but accepted in tumor X — what's structurally different about X?" That's clinical-research signal nobody else can address natively.
Sequencing (from the implementation plan)
Minimum viable hand-off: end of P1 (~2 weeks). Flagship: D-GEN-7 (KRAS counterfactual fan-out simulation; the differentiator from every standard bioinformatics tool).
Iron rules (from §0 of the plan)
ValueSchemaenum variant — genetic-research rows rideFull/Compressedpresets viaclassid → ClassViewmint (per PR docs(plans)+test: rebaseline #497 OCR plans to #498 + gating probes (5-specialist framing) #500's contract test).EdgeCodecFlavorenum variant.ruff_cpp_spoif harvested.InferenceType::Counterfactualmantissa = -6; never written as observed SPO).predicate_count_locked_at_Nper ruff PR Claude/setup adaworld repos 4k pex #5).What this PR does NOT do
lance-graph-contract/ndarray::hpc::*/lance-graph-ontology/rubicon.crates/adapter-genetics-experimental— the plan exists; the crate is proposed, not built.3DGS-genetics-4x4-fanout-plan.md).Predecessor + related work
.claude/plans/3DGS-genetics-4x4-fanout-plan.md(2026-04 exploratory). Covers static representation: 4×4 lane interpretation (sequence coordinate / motif covariance / expression-methylation / time-lineage). This PR extends with the dynamics + counterfactual axis the static plan was missing..claude/plans/3DGS-cross-pollination-raw-field-plan.md— genetics + ultrasound + neuronal networks share the raw-field backbone.EntropyRung/Quadrant/nars_entropy) · PR Witness/meta probe family + TEKAMOLO resolver + Lo design (surreal_container) #495 (3-byte EdgeRef; reliability ⊥ causality measured) · PR Integrated cognitive planner reference map + ValueSchema presets + FULL POC default #496 (ValueSchemapresets + §0 anti-invention) · PR feat(contract): GUID decode→read-mode keystone + helix Signed360 right-size + OCR→NodeRow transcode #498 (GUID decode→read-mode keystone; helixSigned360; OCR→NodeRow transcode template) · PR docs(plans)+test: rebaseline #497 OCR plans to #498 + gating probes (5-specialist framing) #500 (rebaseline + no-new-variant contract test + gating-probes pattern).AdaWorldAPI/ruff/.claude/handovers/2026-06-16-ruff-cpp-headstone-exploration.md(relevant if htslib transcoding wanted; same headstone shape) ·AdaWorldAPI/tesseract-rs/.claude/handovers/2026-06-16-tesseract-rs-headstone-exploration.md.Test plan
cargonot invoked.lance-graphdocs(plans)+test: rebaseline #497 OCR plans to #498 + gating probes (5-specialist framing) #500's contract test pattern).Anchors
docs/GENETIC_RESEARCH_VIA_STACK.md— the pattern-recognition hand-off (file:line-grounded throughout)..claude/plans/genetic-research-substrate-integration-v1.md— 10 deliverables + 3 probes + 5-phase sequencing..claude/handovers/2026-06-16-genetic-research-headstone-exploration.md— destination-state synthesis.bardioc/SUBSTRATE_STATE_FRAMINGS.md— entropy × energy framing (cross-repo durable).OGAR/docs/CASCADE-SYNERGIES-EPIPHANY.md— Morton-cascade × palette256 × golden-helix synthesis (foundational).https://claude.ai/code/session_01VysoWJ6vsyg3wEGc5v7T5v
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