arborist/docs/warrant-substrate-cookbook.md

# Warrant substrate cookbook

Architecture reference for the open-licensed textbook substrate
that backs every claim-pack record in arborist. Written
2026-05-10 after the day-long push from 18/92 → 92/92 claim-pack
warrant-chain coverage. Intended for future blackops shifts so
they don't have to re-derive the substrate map from bench
journals.

## What this cookbook is

When a Q&A answer cites a claim-pack record (axiom or theorem),
the runtime walks a chain:

```
answer cite
    ↓
claim-pack record_root (g4-generated 2025)
    ↓
derivations row (process_id, citation, src_root, proof_blob)
    ↓
surface chunk_root (open-licensed textbook)
    ↓
Merkle inclusion proof → document_root
    ↓
audit_events chain entry (sha256-linked)
```

The "open-licensed textbook" at the second-to-last step is the
**substrate**. This document maps which substrate covers which
pillar, what license + ingest path each uses, and the discipline
patterns that keep the chains audit-clean.

## Pillar-by-pillar substrate map

Eight pillars in the claim-pack source (`#000029`);
<!--AUTOCOUNT:db-where:*:documents?source_type=claim_pack-->92<!--/AUTOCOUNT-->
records total. As of 2026-05-10, every record resolves to at
least one substrate in `~/.arborist/crawl/textbook_*.db`.

### Pillar I — Logic (13 records)

| Substrate | License | Source | Covers |
|---|---|---|---|
| Russell *Introduction to Mathematical Philosophy* (1919) | PD | PG #41654 single-page HTML | natural numbers, classes, descriptions, types, propositional functions |
| Russell *Principles of Mathematics* (1903) | PD content + CC-BY-SA-4.0 typesetting | Klement single-page HTML | class theory, relations, paradox derivation, magnitudes |
| De Morgan *First Notions of Logic* (1839) | PD | PG #67017 single-page HTML | AEIO propositions, syllogism, hypothetical reasoning |
| Boole *Investigation of the Laws of Thought* (1854) | PD | PG #15114 LaTeX-source via `textbook_tex` | propositional Boolean algebra, "elective symbols" |
| Software Foundations Vol 1 *Logical Foundations* | MIT | softwarefoundations.cis.upenn.edu BFS | natural deduction (Logic.v): excluded middle, double negation, existential introduction, vacuous quantification |
| Whitehead-Russell *Principia Mathematica Vol 1* (1910, partial) | PD | PG #78050 single-page HTML | preface + intro + chs I-III; theory of types in narrative form |

Modern citations (Mendelson, Enderton) are aliased per #000041 to
combinations of these substrates depending on the specific axiom.

### Pillar II — Set theory (10 records)

| Substrate | License | Source | Covers |
|---|---|---|---|
| Cantor *Contributions to the Founding of the Theory of Transfinite Numbers* (Jourdain 1915) | PD | Wikisource Article 1 only | cardinal arithmetic, equivalence, addition / multiplication / exponentiation, finite cardinals |
| Russell *Principles of Mathematics* (1903) | PD content + CC-BY-SA-4.0 typesetting | Klement HTML | Russell's Paradox derivation, class theory |
| Whitehead-Russell *PM Vol 1* (partial) | PD | PG #78050 | type theory narrative |

Modern Jech citations alias to these. Note: Cantor's Article 2
(operations on ordered sets) is not transcribed on Wikisource; the
Article 1 transcription covers cardinal-arithmetic axioms but not
ordinal axioms. PM *24+ formal type theory is not in PG #78050
(only preface + intro + chs I-III), so the **Russell's Paradox
Resolution** record matches via lexical fallback against narrative
discussion rather than the actual *24 formalism — honest soft
match, not a strict primary binding.

### Pillar III — Arithmetic (13 records)

| Substrate | License | Source | Covers |
|---|---|---|---|
| Peano *Arithmetices Principia, Nova Methodo Exposita* (1889) | CC-BY-SA-4.0 (Verheyen + Nahas English transl.) | mdnahas/Peano_Book GitHub LaTeX via `textbook_tex` | Peano arithmetic axioms (zero, successor, induction) |
| Dedekind *Essays on the Theory of Numbers* (Beman 1901) | PD | PG #21016 LaTeX via `textbook_tex` | Dedekind cuts construction of reals + chains-and-induction definition of natural numbers |
| Russell *Introduction to Mathematical Philosophy* (1919) | PD | PG #41654 HTML | natural numbers, definition of number, induction (informal) |
| Software Foundations Vol 1 *Logical Foundations* | MIT | upenn BFS | Coq induction proofs, lists, polymorphism |

Landau + Gödel citations alias to these. Note: Peano writes
symbolically (`0 ∈ N`); the cascade's parenthetical-phrase variant
+ OR-fallback variant land hits via SF-LF / Russell IMP /
Dedekind for axiom records that cite "Axiom of Zero" /
"Distinctness of Zero" / "Injectivity of Successor" / etc. (the
direct phrase doesn't appear in Peano's text).

### Pillar IV — Geometry (18 records)

| Substrate | License | Source | Covers |
|---|---|---|---|
| Hilbert *Foundations of Geometry* (Townsend 1902) | PD | PG #17384 LaTeX via `textbook_tex` | every Hilbert axiom (incidence, betweenness, congruence, parallels, continuity) |

This pillar resolves directly — the Hilbert citation in claim-pack
records IS the textbook in shard. 11/18 match unaliased; 7/18
match via term-aliases (#000042) bridging the 1902 Townsend
vocabulary vs modern ("connection" vs "incidence", "Group III:
Axiom of Parallels" vs "Euclidean Parallel Postulate", "space
axiom" vs "Non-Triviality", "first theorem of congruence" vs
"Side-Angle-Side"). Pillar IV is the cleanest demonstration that
the substrate-binding works end-to-end.

### Pillar V — Probability (5 records)

| Substrate | License | Source | Covers |
|---|---|---|---|
| Grinstead-Snell *Introduction to Probability* | GFDL-1.3 | Dartmouth PDF → `pdftotext -layout` → localhost-HTML → `arborist ingest --source html` | Kolmogorov axiomatized probability spaces, sample spaces, conditional probability, Bayes, expected value, large numbers |
| Laplace *A Philosophical Essay on Probabilities* (Truscott + Emory 1902) | PD | PG #58881 single-page HTML | pre-Kolmogorov narrative treatment: expected value, conditional probability, additivity |

Kolmogorov 1933 itself is URAA-blocked in US until 2058
(Kolmogorov d.1987 → life+70). Grinstead-Snell is the closest
open-licensed equivalent. The PDF→localhost-HTML pipeline (see
Ingest patterns below) was first proven on this textbook.

### Pillar VI — Classical mechanics (5 records)

| Substrate | License | Source | Covers |
|---|---|---|---|
| Newton *Principia* (Motte 1729) | PD | Wikisource HTML BFS depth=3 max=120 from /1729/ root | three laws of motion + universal gravitation |

Goldstein-Poole-Safko citations alias to Newton. Newton 1729 vocab
(`Lex Tertia`, `quantity of motion`, `every action`) differs from
modern; 4 term-aliases registered in #000042 for completeness
(some lift via cascade, some don't matter — cascade picks other
discriminators).

The shard was rebuilt 2026-05-10 — the original `crawl_url` at
`/The_Mathematical_Principles_of_Natural_Philosophy` (no edition
specifier) followed Wikisource sidebar links instead of book
content. New manifest entry pins the (1729) edition root +
explicit `urls` for Axioms / Definitions / Rules of Reasoning
subpages. Recrawl produced 120 docs / 779 chunks (was 60 / 289 of
mostly nav cruft).

### Pillar VII — Combinatorics (14 records)

| Substrate | License | Source | Covers |
|---|---|---|---|
| Bogart *Combinatorics Through Guided Discovery* | GFDL-1.3 | bogart.openmathbooks.org BFS | introductory: sum/product, binomial, inclusion-exclusion, pigeonhole |
| Levin *Discrete Mathematics: An Open Introduction* (3rd ed) | CC-BY-SA-4.0 | discrete.openmathbooks.org BFS | intermediate: stars-and-bars, hockey-stick, generating functions intro |
| Keller-Trotter *Applied Combinatorics* | CC-BY-SA-4.0 | appliedcombinatorics.org BFS (38-min crawl-delay) | advanced: generating functions, partitions, Polya enumeration |

Stanley + Brualdi + Knuth combinatorics citations alias to all
three substrates per source_ref string (14 unique compound strings
each get three substitute rows; pillar VII has 42 alias rows total
of the 54 in `citation_aliases`).

Note: Keller-Trotter has `Crawl-Delay: 20` in robots.txt, so a
full BFS at depth=2 max=80 takes ~27-38 minutes. Background-task
the crawl with a generous timeout.

### Pillar IX — Lambda calculus + abstract algebra (14 records)

| Substrate | License | Source | Covers |
|---|---|---|---|
| Programming Language Foundations in Agda (PLFA — Wadler/Kokke/Siek) | CC-BY-4.0 | plfa.github.io BFS | untyped + simply-typed lambda calculus, β/α/η reduction, Confluence/Church-Rosser, fixed point |
| Software Foundations Vol 1 *Logical Foundations* | MIT | upenn BFS | Coq induction, lambda calculus, Imp.v sequence/conditional/while-loop |
| Judson *Abstract Algebra: Theory and Applications* | GFDL-1.3 | judsonbooks.org PreTeXt BFS | groups, rings, fields, Galois theory, Boolean lattices, Cayley + orbit-stabilizer |

Barendregt + Dummit-Foote + Böhm-Jacopini citations alias to
these. PLFA is the lambda-calculus core; SF-LF doubles as a logic
substrate (pillar I) AND a structured-programming substrate
(Böhm-Jacopini Imp.v); Judson is the abstract-algebra primary
substitute.

## Ingest patterns

Five proven patterns. Pick whichever matches your source.

### A. HTML single URL (`urls` in manifest)

For PG eBooks with a single-page HTML edition (Russell IMP, De
Morgan, Laplace) or Wikisource transcriptions (Cantor Article 1).
Manifest entry:

```jsonl
{"id":"foo","urls":["https://...html"], ...}
```

Make target: `make textbook ID=foo`. Calls `arborist ingest
--source html --urls-from <file>`.

### B. HTML BFS crawl (`crawl_url` + `crawl_depth` + `crawl_max`)

For multi-chapter HTML books (PreTeXt: Bogart, Levin, KT, Judson;
Wikisource book-length texts: Newton, Aristotle Prior/Posterior;
LibreTexts: Grinstead-Snell). Manifest entry:

```jsonl
{"id":"foo","crawl_url":"https://...","crawl_depth":2,"crawl_max":80, ...}
```

Make target: `make textbook ID=foo`. Calls `arborist crawl --seed-url
... --depth ... --max-pages ... --ingest`.

Robots.txt `crawl-delay` is honored. Plan timeouts: appliedcombinatorics
20s × 80 pages = 27-38 min; plfa.github.io ~5 min; opendatastructures
~1 min.

### C. LaTeX-source (`tex_url`)

For PG eBooks with no HTML edition (Hilbert, Boole, Dedekind) or
GitHub-hosted LaTeX (Peano). Manifest entry:

```jsonl
{"id":"foo","tex_url":"https://.../foo.tex","license":"PD", ...}
```

Make target: dedicated per-book like `make textbook-hilbert` (the
generic `make textbook` route doesn't handle `tex_url`). Calls
`arborist ingest --source textbook_tex --url ...`. Pipeline strips
PG-style preamble + tabular/figure envs; substitutes `\to` → →,
`\neg` → ¬, `\forall` → ∀.

Limitation: `paracol` multi-column macros (Peano) leak some
residue (`gobble 1cm`, `0.5cm`, `paracol3`) but substantive prose
extracts cleanly. If the source uses heavy custom macros, expect
some noise.

### D. PDF → localhost-HTML → html-source

For sources that have a PDF but no clean HTML (Grinstead-Snell
Dartmouth PDF; Bayes 1763 Royal Society scan; Frege Begriffsschrift
Internet Archive). Pattern:

```bash
curl -sLo /tmp/foo.pdf https://...
pdftotext -layout /tmp/foo.pdf /tmp/foo.txt
mkdir -p /tmp/serve
{ echo '<html><head><title>...</title></head><body><pre>';
  cat /tmp/foo.txt;
  echo '</pre></body></html>'; } > /tmp/serve/foo.html

cd /tmp/serve && python3 -m http.server 8765 &
SRV_PID=$!
sleep 2
arborist --db ~/.arborist/crawl/textbook_foo.db ingest \
  --source html --url "http://localhost:8765/foo.html"
kill $SRV_PID
```

Then run the title backfill (see Discipline patterns below).

### E. Direct chunk insertion (Python API)

For one-off cases where none of A-D fit. Walk
`arborist.document.Document` + `arborist.store.connect` to insert
manually. Used when wrapping non-standard sources.

## Discipline patterns

### Title-from-author backfill

**Empirical defect:** HTML and `textbook_tex` ingest pipelines
take document titles from `<title>` tags or URLs. Wikisource and
Project Gutenberg HTML pages do NOT include author surname in
`<title>`. Resolver's `_shard_matches_citation` REQUIRES the
cited author's surname to appear in the shard's title-haystack;
silently fails for alias-resolved chains where the substitute
author isn't self-evident in the shard.

**Source-side fix shipped** (#000031 follow-up B-2, commit
`551c969` 2026-05-10): the HTML, `textbook_tex`, and crawler
ingest paths now accept an `--author` flag that augments the
title at insert time: `arborist ingest --source html --author
"Bertrand Russell"` → title becomes `"Introduction to
Mathematical Philosophy | Project Gutenberg, by Bertrand
Russell"` with no SQL UPDATE required. The relevant Makefile
targets (`make textbook-*`) wire `--author` for every textbook
in the substrate. Use the `--author` flag for all new ingests.

**Legacy fix-up for already-ingested shards that pre-date
B-2**: SQL UPDATE on `documents.title` after the fact:

```python
import sqlite3
c = sqlite3.connect(shard_path)
c.execute(
    "UPDATE documents SET title = title || ', by <author surname>' "
    "WHERE title NOT LIKE '%<author surname>%'"
)
c.commit()
```

For HTML BFS shards with many docs (Judson 39, Bogart 51, Levin
51, KT 79, PLFA 58, SF-LF 33), append-suffix pattern. For
single-doc shards (Russell IMP, Russell PoM, Cantor, Dedekind,
Peano, Laplace, Grinstead-Snell), full title overwrite. As of
2026-05-10 every shard in `~/.arborist/shards/` already carries
the augmented titles — this section is preserved as the
runbook for any future re-ingest of a corpus that pre-dates
2026-05-10 source-side wiring.

### Audit discipline on aliases

Per #000041 / #000042: every alias row carries `decision_by`
(non-empty, audit-fail-closed) + `decision_rationale` (free
text — caveats, peer-vs-primary distinction, partial-coverage
warnings).

CLI refuses to register without `--by`. Format convention:

```
arborist alias citation add ORIGINAL \
    --substitute SUB --author AUTHOR --title TITLE \
    --by "fox 2026-05-10" \
    --rationale "honest sentence about WHY this substitute covers the cited axioms"
```

The rationale is the load-bearing field for an audit reviewer.
"Russell IMP covers Mendelson's propositional axioms but not
his incompleteness chapters" is honest. "Russell IMP covers
Mendelson" is not.

### Multi-substitute aliases

When one cited proprietary work is best covered by N peer
substrates, register N rows (same `original_ref`, different
`substitute_ref`). Resolver tries each; first hit wins.
Examples: Mendelson → {Russell IMP, De Morgan, Boole, Russell
PoM, SF-LF}. Stanley/Brualdi/Knuth (per source_ref) → {Bogart,
Levin, KT}.

### Cascade tuning (`_build_record_query_cascade`)

Two helpers added 2026-05-10:

1. `_phrase_from_parenthetical(theorem_name)` — extracts
   discriminator from trailing parenthetical when one exists.
   "Kolmogorov's First Axiom (Non-Negativity)" → `"non
   negativity"`. The original `_phrase_for_axiom` was stripping
   parentheticals; many substrates used the parenthetical content
   as the actual term.
2. **Content-tokens OR-join (top 3)** — soft fallback after the
   AND-join (top 5). When AND zeroes out (substrate doesn't have
   all 5 tokens together), OR-of-3 reliably surfaces matching
   chunks. The +14 record unlock at 84% → 100%.

Full cascade order, tightest → loosest:

1. title-phrase
2. parenthetical-phrase (NEW)
3. content-tokens AND-join (top 5)
4. content-tokens OR-join (top 3) (NEW)
5. legacy single-token / discriminating-token query

## Honest tier breakdown

The <!--AUTOCOUNT:db-where:*:documents?source_type=claim_pack-->92<!--/AUTOCOUNT--> chains have three quality tiers:

- **Direct primary (~25 records)** — citation matches the literal
  textbook ingested. Hilbert pillar IV (18), Goldstein → Newton
  (3), Stanley → Bogart for the records Bogart genuinely covers.
  Chain is "the cited primary IS in the shard."
- **Substrate substitution (~50 records)** — citation alias to a
  peer-level open work that covers overlapping axioms. Audit row
  carries `decision_rationale` explaining honesty. Reviewer can
  re-judge.
- **Soft-fallback match (~17 records)** — OR-of-top-3 content
  tokens surfaced *some* chunk in the substrate that shares
  vocabulary. The chunk *contains* relevant terms; whether it
  *proves* the axiom is a separate, weaker claim. Heuristic-grade.

The schema doesn't currently distinguish these tiers. Audit
reviewers walk `citation_aliases` (<!--AUTOCOUNT:db-rows:citation_aliases-->74<!--/AUTOCOUNT--> rows live as of 2026-05-10) + read
`decision_rationale` fields to grade each chain. If tier
distinction becomes load-bearing, add a `tier ∈ {primary,
substitute, soft}` column to `derivations`.

## Audit-trail integrity

Every alias row + every derivation insertion writes one row in
`audit_events` with `event_hash = sha256(prev || canonical(body))`.
Verify chain integrity:

```bash
make chain-check-shards   # 0 per shard = intact
```

The `audit_events` chain ensures: if any alias row is later
modified or removed, the chain breaks at that point and downstream
verification fails. Tampering is detectable.

## What this doesn't yet do

The substrate is in place; the **render layer doesn't read it**.
Q&A answers citing claim-pack records still display
`ANCHOR-WARRANTED` on the four-rung ladder. #000031 Phase 3 wires
the render layer to consult `derivations` and promote to
`EVIDENCE-WARRANTED`. ~50-100 LOC in
`arborist.cli._render_audit_label`. Not done.

The `process_id` on alias-resolved derivations is currently
`warrant-resolver-v1` (DIRECT) rather than `warrant-resolver-v1+alias`.
The `via_alias` flag is set only by term-alias query expansion in
`resolve_chunks`, not by citation-alias substitute-Citation
injection in `warrant_resolve`. Audit trail is correct in
`citation_aliases` table itself; just under-attributed in
derivation rows. ~15 LOC fix.

Per-record tier classification (primary / substitute / soft)
isn't in the schema. Reviewers infer from `citation_aliases` rows
+ `decision_rationale` text. Could be promoted to a column if the
distinction becomes load-bearing for downstream consumers.

## Re-running the substrate build

Most steps are idempotent at the DB layer (content-addressed
inserts; same source content → same `document_root` → no-op).
Network refetches happen but inserts dedupe.

```bash
# Bulk: all four 2026-05-09 base-knowledge additions
make textbooks-base-knowledge

# Per-book convenience targets
make textbook-bogart           textbook-keller-trotter   textbook-levin
make textbook-aristotle-prior  textbook-aristotle-posterior
make textbook-newton           textbook-morin
make textbook-judson           textbook-cantor           textbook-demorgan
make textbook-russell-imp      textbook-russell-pom
make textbook-laplace          textbook-pm               textbook-grinstead-snell
make textbook-hilbert          textbook-boole            textbook-peano
make textbook-dedekind         textbook-plfa             textbook-sf-lf

# Title-from-author backfill (one-off SQL — see "Discipline" above
# for the per-shard script)

# Run resolver
arborist warrant-resolve --use-aliases --write
# → 92 / 92 (100%) under the 18-substrate + 74-citation-alias
#       + 13-term-alias state (counts as of 2026-05-10)
```

## Adjacent: live-corpus → bench-fixture harvest

The textbook substrate above gives the cookbook a static surface
— 18 hand-curated, license-validated, deterministically ingested
sources. A parallel pattern landed 2026-05-10 in `ff1752c` under
#000037 → #000025 that does the opposite: **grow bench fixtures
from live corpus state, not hand-curation**. Worth documenting
here because the discipline patterns (attribution metadata,
determinism via stratification, fail-loud regen) carry across
both surfaces.

### Pattern

```
#000037 Phase 1 controller (arborist/substrate/prometheus.py)
  emits FalsificationFixtureProposal records when
  witness_divergence (n_unverified / n_quotes) >= 0.5
    ↓
bench/scripts/harvest_falsification_proposals.py reads qa.db,
  filters live providence_cache rows, stratifies top-20 per
  audit_mode (HYBRID + UNGROUNDED), writes JSONL
    ↓
bench/fixtures/5f/falsification-harvested-v1.jsonl
  (<!--AUTOCOUNT:fixture-rows:bench/fixtures/5f/falsification-harvested-v1.jsonl-->41<!--/AUTOCOUNT--> rows = 1 _meta header + 40 fixtures)
    ↓
tests/test_bench_batteries.py:test_5f_falsification_harvested_pack_*
  exercises every test run; error_detection_rate == 1.0
  by construction (every harvested row IS a falsification)
```

### Three discipline patterns reused from the textbook substrate

1. **Attribution metadata on every derived artifact** — same
   discipline as `derivations.proof_blob` carrying inclusion
   proofs back to source chunks. Each harvested fixture row
   carries `_harvest_meta` with `cache_key`,
   `witness_divergence` at harvest time, `audit_mode_at_harvest`,
   `harvested_from`, `harvest_threshold`, and `source_ticket:
   "#000037 §13 step 11"`. Regeneration provenance auditable.

2. **Determinism via sort-and-cap** — same discipline as
   citation-alias cascade tuning's "top 5 AND-join then top 3
   OR-join" structure. The harvester sorts top-by-cache_key per
   audit_mode bucket + caps at 20 per mode. Same `qa.db` state →
   byte-identical fixture file across regenerations.

3. **Pin the metadata contract in tests** —
   `test_5f_falsification_harvested_pack_runs_clean` asserts
   every row carries the meta. Same shape as the cookbook
   appendix's discipline pins: a future regeneration that drops
   attribution fires a test failure, not a silent regression.

### Where to use this pattern

Anywhere a controller emits Proposal records that should become
real fixtures. The recipe:

- Define the Proposal dataclass on the controller side (see
  `arborist/substrate/prometheus.py:FalsificationFixtureProposal`).
- Write a harvester script under `bench/scripts/` that reads
  the source state (`qa.db`, `~/.arborist/shards/*.db`),
  filters + stratifies, and emits a JSONL fixture pack.
- Pin the metadata contract in `tests/test_bench_batteries.py`
  (or the equivalent battery test file).
- Wire `make <battery>-harvest` so regen is one command.

The 18-textbook substrate is the static foundation; the
harvested-fixture pattern is how that foundation gets exercised
against current corpus state on every test run. Both live in
this cookbook because the discipline rules — attribution,
determinism, fail-loud — are identical.

---

## References

- `#000031` — surface-ingest cited textbooks
- `#000041` — citation-aliases table + <!--AUTOCOUNT:db-rows:citation_aliases-->74<!--/AUTOCOUNT--> live rows
- `#000042` — term-aliases table + <!--AUTOCOUNT:db-rows:term_aliases-->13<!--/AUTOCOUNT--> live rows (5 arithmetic + 4 classical-physics + 4 geometry)
- `#000038` — Phase 4 content acquisition (still-blocked
  proprietary candidates: Hilbert-Ackermann 1928, Mendelson,
  Enderton, Jech, Goldstein, Barendregt, Stanley, Brualdi, Knuth;
  the substrate substitution pattern is the workaround)
- `#000037` — Prometheus-Σ recursive falsification controller;
  source of the `FalsificationFixtureProposal` records the
  harvest pattern consumes
- `#000025` — 5F battery; sink for the harvested falsification
  fixtures (§11 Phase 1f)
- `bench/scripts/harvest_falsification_proposals.py` — harvester
  script (266 LOC) reading qa.db + emitting stratified fixtures
- `bench/fixtures/5f/falsification-harvested-v1.jsonl` —
  current harvested pack (regenerate via `make bench-5f-harvest`)
- `bench/results/full-warrant-resolution-2026-05-10.md` — the
  bench journal that closed 84% → 100%
- `bench/fixtures/textbooks/manifest-v1.jsonl` — license-validated
  manifest of every textbook in the substrate
- `arborist/qa/warrant_resolver.py` —
  `_build_record_query_cascade` + `_phrase_for_axiom` +
  `_phrase_from_parenthetical` + `resolve_chunks`
- `arborist/qa/aliases.py` — citation + term alias schema +
  CLI add/list/remove

## Appendix — test-coverage cross-reference (2026-05-10)

Per-discipline regression-guard test files. Each test file pins
contract phrases / numerical invariants so a future PR that
silently drops a discipline rule fires a unit-test failure rather
than waiting for bench-time STRICT-rate drift to surface it.

### Citation-alias / term-alias mechanism (#000041 + #000042)

- `tests/test_aliases.py` — <!--AUTOCOUNT:tests:tests/test_aliases.py-->28<!--/AUTOCOUNT--> tests covering
  `add_citation_alias` / `add_term_alias` audit-fail-closed
  (empty `decision_by` raises ValueError), domain isolation
  (same term different domain stays distinct), lowercase
  normalization (Term/Term/Geometry → all lowercased on
  insert), bidirectional `lookup_term_aliases`,
  `expand_query_with_term_aliases` quoted-phrase preservation,
  fail-closed on unreachable DB, parenthesis-as-token tokenizer
  contract (OR-expansion round-trip), and `list_term_aliases`
  filter-by-domain / term-substring.

### Warrant-resolver chain (#000031 Phase 1+2+3)

- `tests/test_warrant_resolver.py` — <!--AUTOCOUNT:tests:tests/test_warrant_resolver.py-->23<!--/AUTOCOUNT--> tests covering citation
  parsing (3 patterns: "Title by Author", multi-author Oxford
  comma, semicolon-separated multi-cite); cascade builder
  (5-query variants: title-phrase, parenthetical-phrase,
  AND-top-5, OR-top-3, legacy); `via_citation_alias` floor
  propagation through ResolutionMatch (B-1 attribution fix).
- `tests/test_warrant_chain.py` — <!--AUTOCOUNT:tests:tests/test_warrant_chain.py-->9<!--/AUTOCOUNT--> tests covering
  `warrant_chain_lookup` (process_id LIKE filter, missing-table
  fail-closed, +alias variant matching), `has_warrant_chain`
  empty-set short-circuit, verifier suppression of
  WARRANT_MISSING when chain present, verdict-field
  `warrant_proven_claim_idxs` always present (schema guarantee).

### Textbook ingest license-discipline gate

- `tests/test_textbooks_manifest.py` — <!--AUTOCOUNT:tests:tests/test_textbooks_manifest.py-->43<!--/AUTOCOUNT--> tests covering every
  license token in `_ALLOWED_LICENSES` (parametrized 12-token
  sweep), placeholder rows allowed without URLs, disallowed
  license + emit URLs raises, CLI dispatch, return-code
  contract (0 ok / 2 missing-arg / 3 license-fail / 4
  unknown-id), and the live manifest itself validates clean.

### Cascade tuning (#000040 + parenthetical/OR-fallback)

- `tests/test_warrant_resolver.py::_phrase_from_parenthetical`
  — extracts `"non negativity"` from
  "Kolmogorov's First Axiom (Non-Negativity)"; the discriminator
  is INSIDE the parenthetical that earlier resolver versions
  stripped. Pinned so a future "simplify the cascade" PR can't
  silently regress.

### Substrate-paper-spec'd primitives (#000012 + #000018 + #000034 + #000037)

- `tests/test_anchor_prg.py` — <!--AUTOCOUNT:tests:tests/test_anchor_prg.py-->31<!--/AUTOCOUNT--> tests for φ_PRG HMAC-SHA-512
  expansion (#000035 Phase 1). Covers KAT regression, hand-formula
  (first-block matches direct ``hmac.new``), prefix-extending
  closure invariant, output-length monotonicity per dim_h.
- `tests/test_phi_alignment_probe.py` — **<!--AUTOCOUNT:tests:tests/test_phi_alignment_probe.py-->23<!--/AUTOCOUNT--> tests** (was 14;
  +9 from `a4b3056` 2026-05-10 pattern backfill) for φ_linear
  Hessian-alignment probe (#000034 Phase 1a). Covers KAT
  regression, hand-formula (uniform baseline), monotonicity in
  W concentration + dim_h, closure (a_top + a_bot ≡
  full-spectrum on dense decomposition), Lanczos eigenvalue
  ordering invariant.
- `tests/test_t3_bound_calculator.py` — **<!--AUTOCOUNT:tests:tests/test_t3_bound_calculator.py-->83<!--/AUTOCOUNT--> tests** (was 51;
  +2 from `581ad90` 2026-05-10 KAT-fixture-gap closure) for the
  T3 per-window covert-channel bound calculator (#000036 §11);
  pins the closed-form B1/B2/B3 formulas, monotonicity in each
  input, recommendation-text mode transitions, and the §11
  worked-example bit-for-bit (with doc-calibration update
  surfaced through the test).
- `tests/test_fork_score.py` — <!--AUTOCOUNT:tests:tests/test_fork_score.py-->31<!--/AUTOCOUNT--> tests for v8 ForkScore
  (#000012 Phase 1a); pins SIGNAL_FLOOR (5pp) + HARD_REGRESSION_FLOOR
  (5pp), score = sum-of-breakdown closure, security_risk inert
  under default iota=0 (opt-in), NEG_INF_REGRESSION hard-reject.
- `tests/test_substrate_fork_score.py` — <!--AUTOCOUNT:tests:tests/test_substrate_fork_score.py-->27<!--/AUTOCOUNT--> tests covering the
  ``arborist substrate score`` CLI surface (renamed from
  ``test_v8_fork_score.py`` in `a4058a4` per the 2026-05-10
  v-prefix retirement). Adapter tests + 4 in-process CLI tests
  via ``build_parser()`` + 1 real subprocess invocation
  catching entry-point / sys.argv drift the in-process tests
  miss.
- `tests/test_weights.py` — <!--AUTOCOUNT:tests:tests/test_weights.py-->16<!--/AUTOCOUNT--> tests for WeightSet defaults
  (each weight value pinned to its docstring rationale; PR that
  flips alpha=1.0→0.5 fires this test), greek-letter and
  Python-safe key aliases, frozen-dataclass invariant.
- `tests/test_pi_star_protocol_and_registry.py` — <!--AUTOCOUNT:tests:tests/test_pi_star_protocol_and_registry.py-->21<!--/AUTOCOUNT--> tests for
  `PiStar` Protocol contract + registry mutation discipline
  (no public unregister; `name@version` content-pinned).
- `tests/test_prometheus.py` — <!--AUTOCOUNT:tests:tests/test_prometheus.py-->42<!--/AUTOCOUNT--> tests for the Prometheus-Σ
  recursive-falsification controller (#000037 Phase 1, commits
  `f625cac` + `f9f5ae4`). Verifier-style discipline (NOT
  calculator pattern — it's a state machine, not closed-form
  math): pins §16.2 named contracts (17), boundary veto-class
  cases (5), §14 exception-matrix dispatch including row 4
  Hermes-saturation guard, §13 step 11 falsification-fixture
  proposal, §15 weight-tunable entropy + memory gates,
  ESCALATE > QUARANTINE > REJECT priority ordering.
- `tests/test_prometheus_audit.py` — <!--AUTOCOUNT:tests:tests/test_prometheus_audit.py-->25<!--/AUTOCOUNT--> tests for the
  `controller_events` sibling table (#000037 Phase 2, commits
  `a786d6d` initial + `43380b1` QA-runner wiring + `cc72784`
  controller-events inspector CLI). Pins migration idempotency,
  no-chain-mutation invariant (advisory writes never enter
  `audit_events.event_hash` preimage), `(event_kind, body_hash)`
  UNIQUE dedupe contract, query paths for the three event kinds
  (`controller_decision`, `controller_difficulty`,
  `controller_budget_allocation`), QA-runner advisory non-
  blocking on bad verdict, and the `arborist controller-events`
  inspector CLI surface (kind / organism-prefix filters, JSON
  output, graceful skip on non-arborist sqlite files).

### Q&A / verifier scaffolding

- `tests/test_qa_progress.py` — <!--AUTOCOUNT:tests:tests/test_qa_progress.py-->31<!--/AUTOCOUNT--> tests for the Progress
  emitter (env / TTY / cli-override precedence; truthy/falsy
  spelling matrix; fail-closed on missing `.isatty`).
- `tests/test_qa_prompts.py` — <!--AUTOCOUNT:tests:tests/test_qa_prompts.py-->20<!--/AUTOCOUNT--> tests pinning load-bearing
  system prompts (worked-example presence, two-pointer cap,
  pointer-mode no-quote-instruction discipline,
  JSON-mode first-char-`{` / last-char-`}` rule); a silent
  prompt edit that drops a critical instruction would otherwise
  surface only as a STRICT-rate drop in bench.

### Concept-relations write-side

- `tests/test_concepts_extract.py` — <!--AUTOCOUNT:tests:tests/test_concepts_extract.py-->28<!--/AUTOCOUNT--> tests for synonym /
  IDF / FTS5-titles extractors (`_title_tokens` stopword
  + length-floor + dedupe; `EXTRACTORS` registry contract;
  `link_reciprocity_synonym` idempotency + self-overlap
  exclusion; `backfill_documents_fts` NULL-title skip).

### Unit-test density vs production-code size

| domain | LOC tested | test LOC | test/code ratio |
|---|---|---|---|
| aliases.py | 512 | 469 (<!--AUTOCOUNT:tests:tests/test_aliases.py-->28<!--/AUTOCOUNT--> tests) | 0.92 |
| warrant_resolver.py | ~800 | ~430 (combined) | 0.54 |
| warrant_chain.py | 89 | 320 (<!--AUTOCOUNT:tests:tests/test_warrant_chain.py-->9<!--/AUTOCOUNT--> tests) | 3.6 |
| t3_bound_calculator.py | 249 | 446 (<!--AUTOCOUNT:tests:tests/test_t3_bound_calculator.py-->83<!--/AUTOCOUNT--> tests) | 1.79 |
| fork_score.py | 386 | 609 (<!--AUTOCOUNT:tests:tests/test_fork_score.py-->31<!--/AUTOCOUNT--> tests) | 1.58 |
| weights.py | 73 | 180 (<!--AUTOCOUNT:tests:tests/test_weights.py-->16<!--/AUTOCOUNT--> tests) | 2.5 |
| pi_star/protocol+registry | 124 | 280 (<!--AUTOCOUNT:tests:tests/test_pi_star_protocol_and_registry.py-->21<!--/AUTOCOUNT--> tests) | 2.3 |
| qa/progress.py | 85 | 226 (<!--AUTOCOUNT:tests:tests/test_qa_progress.py-->31<!--/AUTOCOUNT--> tests) | 2.7 |
| qa/prompts.py | 153 | 207 (<!--AUTOCOUNT:tests:tests/test_qa_prompts.py-->20<!--/AUTOCOUNT--> tests) | 1.35 |
| concepts/extract.py | 288 | 278 (<!--AUTOCOUNT:tests:tests/test_concepts_extract.py-->28<!--/AUTOCOUNT--> tests) | 0.97 |
| textbooks_manifest.py | 236 | 463 (<!--AUTOCOUNT:tests:tests/test_textbooks_manifest.py-->43<!--/AUTOCOUNT--> tests) | 1.96 |
| substrate/prometheus.py | 893 | 955 (<!--AUTOCOUNT:tests:tests/test_prometheus.py-->42<!--/AUTOCOUNT--> tests) | 1.07 |
| substrate/prometheus_audit.py | 239 | 595 (<!--AUTOCOUNT:tests:tests/test_prometheus_audit.py-->25<!--/AUTOCOUNT--> tests) | 2.49 |

Pattern: small contract-defining modules (weights, prompts,
warrant_chain) get 1.4-3.6× test LOC because they're foundation;
larger modules (warrant_resolver, aliases) settle around
0.5-1.0× because they're more code-with-tests-per-feature than
contract-with-tests-per-rule.

The ratio is a code-review heuristic: a new substrate-paper-spec'd
primitive without ≥1× test/code ratio is suspect on landing.

### Cross-reference

This appendix is the **per-discipline INDEX** — start here when
auditing "where are the tests for X?". The complementary
**per-pattern CHECKLIST** for new calculator-style code lives at
`docs/calculator-test-patterns.md`: KAT regression, hand-formula,
monotonicity, closure, parametrized invalid-input, CLI subprocess,
doc parity, module-export shape — with a 9-item checklist for new
modules and an explicit "doesn't apply to verifier-style code"
caveat. Codified 2026-05-10 from the three-module pattern bench
(t3_bound_calculator + phi_alignment_probe + anchor_prg).

When adding a new substrate-paper-spec'd primitive: walk the
checklist in `calculator-test-patterns.md` to design the test
file, then add a row here under the matching discipline.