DisMech compact evidence vocabulary + typed citation sidecar

.claude/board/LATEST_STATE.md

@@ -1,3 +1,115 @@
+## 2026-08-20 — branch `claude/lance-graph-stage-3-recovery-2wrdbd` — DisMech compact evidence vocabulary + citation sidecar
+
+### Current Contract Inventory — 1 new zero-dep module
+
+- **`lance_graph_contract::dismech_evidence`** (new):
+  - `DismechTopology` — the four measured `causal_link_type` states, 2 bits,
+    `from_source`/`as_source`/`to_bits_2`/`from_bits_2`, plus
+    `source_knows_intermediates()` / `mediator_unresolved()` which separate the
+    3,978-edge ORACLE population from the 4,539-edge RESTRAINT CONTROL.
+  - `Supports` (4, 2 b), `EvidenceSource` (5, 3 b) — round-tripped exhaustively.
+  - `CitationNamespace` (PMID/DOI/ORPHA/NCT/CGGV/URL), `CitationKey`
+    (`Identified{namespace,id}` | `ContentAddressed(ContentId)`),
+    `BibliographyRecord{key, title: ContentId}`.
+- **SOURCE-SIDE ONLY — deliberately does NOT reference `CausalEdge64`.** The
+  durable causal overlay must not become a pile of hot reasoning registers
+  (operator ruling); `DismechTopology -> CE64 bits 59..60` happens at
+  HYDRATION, in the consumer, as a 1:1 read of `to_bits_2()`.
+- **Every parse FAILS CLOSED.** `UNKNOWN` is a value the corpus asserts 408
+  times, so minting it from a parse failure would forge an assertion the source
+  never made — pinned by
+  `unrecognised_topology_fails_closed_and_never_becomes_unknown`.
+- **Citation identity never derives from the title** — pinned by
+  `reference_identity_survives_a_title_rewording`, the falsifier that matters
+  for an LLM-generated corpus. Where no stable identifier exists,
+  `CitationKey::ContentAddressed` says so explicitly rather than synthesising a
+  bibliographic id.
+
+### Gates
+
+`lance-graph-contract` **1178/1178** (7 new); `cargo fmt` clean; `cargo clippy
+--all-targets --no-deps -D warnings` clean.
+
+### NOT frozen by this PR (measurement says do not)
+
+The endpoint codebook and the DisMech-local identity scheme stay OPEN until the
+unprefixed population is probed — 63.6% of unprefixed endpoints are still
+unresolved and the tail contains three different KINDS (provenance leakage,
+mechanism propositions, lexical variants). Full numbers:
+`E-DISMECH-CORPUS-CENSUS-1`. Also open: phenotype resolution must be scoped to the EXISTING `Domain::Phenomenology` (HP is its populated vocabulary, not a new domain — see the ⊘ correction on that entry)
+(23.7% of resolved phenotype labels are HP/MONDO-ambiguous), and
+`phenotypes[].category` at 261 distinct exceeds the 255 `Codebook` cap.
+
+---
+## 2026-08-20 — branch `claude/lance-graph-stage-3-recovery-2wrdbd` — S3.0 CLOSED AS NOT-NEEDED (no new type); #973 retraction + two overclaim corrections
+
+### Contract Inventory — NO CHANGE
+
+**This PR adds no type, no module, no bit, no tenant, no layout version.** It
+is a retraction + audit. `crates/lance-graph-contract/src/lib.rs` is byte-clean
+against `main`.
+
+### What was withdrawn, and why
+
+A first draft of this recovery PR reintroduced #973's `CausalLiteral`
+(`4 × u16`, 8 bytes) with corrected prose. **The operator stopped it before
+merge, and was right on four counts** — all now recorded as
+`E-A-LOCAL-DERIVATION-CANNOT-OVERRULE-A-MEASURED-COUNTEREXAMPLE-1` instance 2:
+
+1. **Wrong universality.** Its own test asserted `TREATED_WITH` — the structure
+   is GENERIC. Causality is a predicate family / qualification, never universal
+   identity.
+2. **`4 × u16` is not absolute.** MedCare-rs `ONTOLOGY_BAKE_STATE.md`:182:
+   *"real OBO ids run past `u16` (MONDO:0700092 = 700,092)."* The V3 rail
+   already solves this.
+3. **A WordNet overclaim.** #875 was cited as an "EXACT structural encoding"; its
+   own W5 gate reports **256 cells, occupancy median 255, over 65,292 leaves** —
+   a locality/search prior, never an identity encoding.
+4. **`routing_prefix()` was unearned.** Lexicographic prefix over concatenated
+   ordinals, labelled an "HHTL locality projection", with no consumer and no
+   measurement.
+
+### The question that closed the slot
+
+> **WHAT EXACT INFORMATION CANNOT BE EXPRESSED BY THE ADDRESSING THAT ALREADY
+> EXISTS?**
+
+**Nothing demonstrable.** `identity_quad::IdentityQuad` (operator-RATIFIED
+2026-08-17) already carries **four exact external identities as `4 × u24` in one
+96-bit V3 facet** behind a `classid(4)`, refuse-don't-truncate, bake-time
+crosswalk resolution. It strictly dominates the withdrawn type. Siblings:
+`ogar_elk::ClassAddr` (`u32 + u32`, a pre-bake join key by its own doc),
+`canonical_node::NodeGuid` + HHTL, the V3 OBO rail.
+
+Per the operator's rule — no concrete falsifier ⇒ **no new absolute-address
+type.** S3.0 is closed as NOT-NEEDED, not filled because a plan had a slot.
+
+### The genuinely open addressing gap (different, not fixed here)
+
+`ClassId = u16` (`class_view.rs:54`) is near-exhausted for **relations** —
+MedCare-rs `CLAUDE.md` #10: *"cannot address a relation — 11 prefixes, 8 of 280
+ids over the ceiling."* A classid-mint capacity question for OGAR/lance-graph;
+to be raised with the operator in session, not patched from a consumer.
+
+### Where the work actually is
+
+| | ADDRESS | HYDRATED SoA | TRAVERSAL |
+|---|---|---|---|
+| Bible / Rosetta | yes | **NO** | partial / context |
+| OSM | yes | yes | overlay / junction |
+| MedCare ontology | yes | yes | **YES, Stage 1** |
+| DisMech oracle | source | structured | causal oracle |
+
+The empty column is not ADDRESS. Next: **hydrate epistemic / causal nodes →
+reason over them → think about the reasoning**, with the DisMech oracle
+experiment as the gate (hide mechanism intermediates → hydrate the addressed
+neighbourhood → let NARS/recipes recover candidates → compare against DisMech
+truth).
+
+Full audit: `.claude/handovers/2026-08-20-s3-0-cold-start-recovery-audit.md`.
+Stage-2/2.5/2.6 (#971) untouched; #970's CE64 layout untouched.
+
+---
 ## 2026-08-20 — lance-graph #971 (MERGED, `2cbe62d`, head `d627f5c`) — Stage 2 carves + Stage 2.5 census + Stage 2.6a V3 invariance + CE64 ⇄ V3 losslessness
 
 Six commits, four stages. The per-stage Contract Inventory and results are in

.claude/board/STATUS_BOARD.md

@@ -1,3 +1,33 @@
+## stage-3 — RE-SCOPED 2026-08-20: S3.0 closed as NOT-NEEDED; the ladder's empty column is HYDRATION, not ADDRESS
+
+PR #973 (S3.0 address, first attempt) closed unmerged. Its retraction PR then
+attempted a corrected `CausalLiteral` and was **stopped before merge by the
+operator** — four unearned claims, recorded in
+`E-A-LOCAL-DERIVATION-CANNOT-OVERRULE-A-MEASURED-COUNTEREXAMPLE-1`. No new
+address type is minted: `IdentityQuad` (4 × u24 in one V3 facet, ratified
+2026-08-17) already carries exact four-component identity, and no falsifier
+showed existing addressing insufficient.
+
+| D-id | Deliverable | Status |
+|---|---|---|
+| S3.0 | exact literal address | **CLOSED — NOT NEEDED** (use `IdentityQuad` / `ClassAddr` / V3 rail) |
+| S3.0b | qualified causal regime | Queued |
+| S3.1 | hydrate `CausalMeta` + `EpistemicMeta` over EXISTING addresses | **Next** |
+| S3.1b | EntropyWork · BasinSet · Attention; `RowFocusMask × WideFieldMask` | Queued |
+| S3.2 | V3 / CE64 leg from the hydrated node | Queued |
+| S3.3 | `ResolvedPredicate`; unknown fails CLOSED; explicit composition | Queued |
+| S3.4 | DisMech ORACLE experiment — hide intermediates, hydrate neighbourhood, NARS recovers, compare vs truth | **the gate** |
+| S3.5 | NARS evidence mass: raw/source/HEEL/effective, deterministic W+/W− | Queued |
+| S3.6 | JC measurement per predicate × cohort × horizon × instrument | Queued |
+| S3.7 | `ReasoningEpisode`; measure the 17 confidence-mute kernels | Queued |
+| S3.8 | potholes, first_possible vs first_derived, strict historical replay | Queued |
+| S3.9 | Meta / Rubicon → OGAR-loco; Pearl qualification earned by receipts | Queued |
+
+**Open, and NOT an S3 deliverable:** `ClassId = u16` near-exhausted for
+relations (MedCare-rs commitment #10) — an OGAR/lance-graph classid-mint
+capacity question for the operator.
+
+---
 ## preparation-arc plan wave — 2026-08-19 (operator: "integration plans for all open arcs")
 
 Five plans, each PROPOSED (no code — the reset charter's audit-first order

.claude/handovers/2026-08-20-s3-0-cold-start-recovery-audit.md

@@ -0,0 +1,192 @@
+# S3.0 Cold-Start Recovery Audit — 2026-08-20
+
+**Outcome: no new address type. S3.0 as specified is WITHDRAWN.**
+This PR retracts #973's overclaim, corrects a WordNet overclaim this session
+itself introduced, and records why the S3.0 address slot needs no new type.
+
+## A. MERGED substrate truth
+
+- **PR #970** [MERGED, `781c3b9b`]: CE64 v2 layout final. Bits 59-60 =
+  `TrustTexture` (canonical) + ADDITIVE `CausalTopology` reading over the same
+  bits. Bits 61-63 = spare + ADDITIVE `ReasoningBand`, explicit
+  `with_reasoning_band()` only, never auto-derived. Deprecated v1 `temporal`
+  (52-63) is NOT valid v2 chronology; version-gate edges of unknown
+  provenance. Confirmed in `crates/causal-edge/src/layout.rs`.
+- **PR #971** [MERGED]: Stage-2/2.5/2.6a frozen baseline. `InferenceType` is a
+  LOSSY compat projection of the 4-bit signed mantissa (8/16 states corrupted,
+  incl. `pack_v2` default `0 -> +1`) — carry the raw nibble. CE64<->V3
+  bit-identical modulo dedup'd SPO + deprecated temporal. Capability !=
+  reachability measured.
+- **PR #973** [REJECTED, closed unmerged]: nothing on `main`.
+
+## B. MEASURED substrate truth
+
+1. **`identity_quad::IdentityQuad`** [MERGED, operator-RATIFIED 2026-08-17,
+   `ISS-IDENTITY-QUAD-WIDE-CARVING-HOME`]. **Four external identity spaces,
+   `4 × u24` contiguous, in ONE 96-bit V3 facet payload** via
+   `LegacyOutlier::WideTriple`, behind a `classid(4)`. Refuses rather than
+   truncates (`QuadError::OrdinalTooLarge`, `MAX_ORDINAL = 2^24 - 2`);
+   codebooks refuse rather than saturate (`CodebookError::TooLarge`). Its
+   stated purpose is resolving a crosswalk ONCE at bake time so a read is a
+   fixed-offset register read — no join, no crosswalk walk.
+2. **`ogar_elk::ClassAddr`** [MERGED]: `classid: u32 + identity: u32` — 8
+   bytes for ONE node, and its own doc is explicit that it is a pre-bake
+   **join key**, "not an ABI address, and deliberately not documented as one".
+3. **Real OBO identities exceed `u16`** [MEASURED, MedCare-rs
+   `docs/ONTOLOGY_BAKE_STATE.md`:182]: *"real OBO ids run past `u16`
+   (MONDO:0700092 = 700,092) and one V3 field cannot hold that."* The
+   substrate ALREADY solved this: the V3 rail splits a 24-bit CURIE numeric as
+   `family:identity = (num >> 16, num & 0xFFFF)`, read via
+   `obo_store::row_addr`. Corpus scale: MONDO 32,095 · HP 19,836 ·
+   UBERON 14,975 · PATO 1,887, and relations cross families.
+4. **`ClassId = u16` is near-exhausted for RELATIONS** [MEASURED, MedCare-rs
+   `CLAUDE.md` commitment #10 + `RAIL_OFFENE_POSTEN.md`]: *"`ClassId = u16`
+   cannot address a relation — 11 prefixes, 8 of 280 ids over the ceiling."*
+   That is a real open gap — and it is a **classid-mint capacity** question
+   owned by OGAR/lance-graph, NOT something a new literal type fixes.
+5. **WordNet #875/#876** [MERGED, MEASURED] — see §C2 for the corrected
+   reading. Also #876: a consumer can be structure-blind to an address's
+   hierarchy without that meaning the address lacks structure.
+6. **TEKAMOLO #839/#844** [MERGED, live code]: one 16-byte content-blind
+   register, several simultaneous ClassView-selected readings
+   (`G3D4`/`G4D3`/`G6D2`/`24×i4`). Capability lands as a new READING.
+7. **24×i4 anaphora #850** [MEASURED, 7,657 real German relative clauses,
+   88.01% in-window]: a local representation exhausting cleanly marks a TYPE
+   boundary — switch reading, never widen the pointer.
+
+## C. REJECTED claims
+
+### C1. #973's `E-THE-LITERAL-CANNOT-LIVE-IN-THE-PATH-IT-ROOTS-1` — RETRACTED
+
+#973 measured correctly that a `domain·S·P·O` at `u16` each is exactly 16
+nibbles = `NiblePath::MAX_DEPTH`, zero slack. It then promoted that local fact
+about ONE sequential depth-limited router path into an implied global claim
+that exact identity cannot live in HHTL addressing and evidence must
+"ref-escape" out of address space. The three counterexamples in §B5-B7 were
+never consulted. The arithmetic survives; the inference does not.
+
+### C2. This session's OWN WordNet overclaim — RETRACTED
+
+The first draft of this recovery PR said #875 proved a *"full-width 4-ary HHTL
+fold of real WordNet ancestry is an EXACT structural encoding"*. **That is
+false, and #875's own numbers say so:** W5 reports *256/256 cells used,
+occupancy min 29 / median 255 / max 1270* over **65,292 leaves**. That is
+~255 leaves per cell — emphatically NOT injective, not an identity encoding.
+
+What #875 actually measured is a **deterministic, taxonomy-informed HHTL
+locality / search prior**: shared-address-levels vs LCA-depth corr +0.494 (vs
+−0.036 shuffled), out-of-cell band recall 0.763 vs 0.031 random = 24.71×, and
+a 2.47-hop sub-nibble distinction the 16-ary router cannot address. A
+discriminating prior that deliberately does NOT cover everything — #875 itself
+dropped its cover guard as inert for exactly this reason.
+
+So the Bible/Rosetta + WordNet composition is:
+`frozen verse identity × quasi-absolute taxonomy-informed semantic coordinate
+× witness/qualia planes` — **not** evidence that 256 HHTL cells uniquely
+identify a lexicon. Corrected in the PR body, EPIPHANIES, and this audit;
+the module doc carrying it is deleted with the type.
+
+### C3. `CausalLiteral` was the wrong universal type — WITHDRAWN
+
+Two independent defects:
+
+- **Wrong name / wrong universality.** Its own test asserts
+  `CausalLiteral(7, 100, 43, 200)` as `TREATED_WITH` — demonstrating the
+  structure is generic, not causal. `ASSOCIATED_WITH` / `TREATED_WITH` /
+  `CAUSES` / `MEDIATES` / `PART_OF` are exact predicate identities over one
+  generic literal substrate. Causality is a **predicate family /
+  qualification**, never universal identity. If a primitive were needed it
+  would be `ExactLiteralAddr(D,S,P,O)`.
+- **`4 × u16` is NOT absolute, and cannot be.** A `u16` subject cannot hold
+  MONDO:0700092 = 700,092 (§B3). The type would have silently mis-addressed
+  the single largest ontology in the MedCare bake. Calling it "absolute
+  identity" was a second global overclaim in the same PR that retracted one.
+
+## D. Salvageable
+
+- The nine tests' SHAPE (injectivity sweep, component-isolation matrix,
+  many-sources-one-literal, unbound sentinel) is good discipline and should be
+  reused by whatever type actually lands — but it belongs on
+  `IdentityQuad`/`ClassAddr`-based composition, not on a new 4×u16 plane.
+- The retraction of C1 and the two process findings.
+- `routing_prefix()` is REMOVED, not merely deferred — see §G.
+
+## E. The development ladder (operator-requested matrix)
+
+|                    | ADDRESS | HYDRATED SoA | TRAVERSAL |
+|--------------------|---------|--------------|-----------|
+| Bible / Rosetta    | yes     | **NO**       | partial / context |
+| OSM                | yes     | yes          | overlay / junction |
+| MedCare ontology   | yes     | yes          | **YES, Stage 1** |
+| DisMech oracle     | source  | structured   | causal oracle |
+
+**The column that is empty is not ADDRESS.** Address is solved three times
+over (`ClassAddr`, the V3 rail, `IdentityQuad`, `NodeGuid`/HHTL). The missing
+work is: **hydrate epistemic / causal nodes → reason over them → think about
+the reasoning.**
+
+### The question S3.0 had to answer, and its answer
+
+> **WHAT EXACT INFORMATION CANNOT BE EXPRESSED BY THE ADDRESSING THAT ALREADY
+> EXISTS?**
+
+**Nothing that this session could demonstrate.** `IdentityQuad` (classid + 4 ×
+u24, ratified 2026-08-17) strictly dominates the withdrawn 4×u16 type on every
+axis: wider (handles real OBO ids, which u16 does not), already V3-carving
+conformant (rides a sanctioned reading rather than minting a parallel identity
+plane), already refuse-don't-truncate, already bake-time-join-resolving.
+
+There is therefore **no concrete falsifier showing existing addressing is
+insufficient**, and per the operator's rule no new absolute-address type is
+minted. The S3.0 slot in the Stage-3 plan is closed as NOT-NEEDED rather than
+filled because the plan had a slot.
+
+**The one genuinely open addressing gap found** is different and is NOT this:
+`ClassId = u16` is near-exhausted for RELATIONS (§B4). That is a classid-mint
+capacity question for OGAR/lance-graph, to be raised with the operator in
+session — not something a new literal type addresses.
+
+## F. Next target (per operator §6)
+
+```
+  EXISTING absolute address  (ClassAddr / V3 rail / IdentityQuad / NodeGuid)
+          |
+     hydrate node
+          |
+   CausalMeta + EpistemicMeta
+          |
+   EntropyWork · BasinSet · Attention
+          |
+   RowFocusMask × WideFieldMask
+          |
+      V3 / CE64  ->  NARS  ->  ReasoningEpisode  ->  Meta/Rubicon  ->  OGAR-loco
+```
+
+**DisMech as the oracle experiment:** hide known mechanism intermediates →
+hydrate the addressed ontology neighbourhood → let NARS/recipes recover
+candidates → compare against DisMech truth. Grounded: `dismech-rs`
+`graph::build_causal_graph` is a real transcode of the upstream Python
+resolver, falsified at **1,995 diseases / 33,458 edges** against the private
+`medcare-dismech` measurement (33,328, within 0.4%), and 1,903 committed
+`pathographs/MONDO_*.json` exist as ground truth. Not started this session.
+
+## G. `routing_prefix()` — REMOVED
+
+Concatenating D/S/P/O nibbles into a `NiblePath` yields deterministic
+**lexicographic** prefixes. It was labelled an "HHTL locality / cohort
+projection" — but no consumer exists and no measurement establishes that it
+preserves HHTL *semantic* locality. `NiblePath` is built for the `subClassOf`
+Abstammung tree, where a prefix is an ancestry claim; a lexicographic prefix
+over concatenated ordinals carries no such guarantee. Calling it one was a
+third unearned claim. Removed with the type; if it returns it needs a real
+consumer and a measurement first.
+
+## H. Falsifiers that would reopen S3.0
+
+1. A concrete case where `IdentityQuad` (4 × u24 + classid) provably cannot
+   express an exact proposition identity the substrate needs.
+2. A measured need for a 4th component space beyond `IdentityQuad`'s four
+   slots — noting its own doc says a fifth identifier space is a **second
+   facet**, never a wider field.
+3. Resolution of the `ClassId = u16` relation-capacity gap requiring a new
+   addressable relation identity (a classid-mint question first).