Phase 1a scores one (parent, child) fork at a time; Phase 1b is the
consensus paper. Neither persists multiple candidate branches at the
same checkpoint — and #000037 §12 Trigger 1 ("ForkScore regularly
receives ≥4 candidate branches per checkpoint") gates the multi-
branch path of the Prometheus-Σ controller on this data existing.
Phase 1c lands the missing seam.
Schema (arborist/store.py): _migrate_fork_score_branches creates the
sibling table with PK (branch_set_id, branch_id) + indexes on
branch_set_id and parent_root. Sibling — never enters
audit_events.event_hash preimage, so re-scoring or back-filling
cannot break the audit chain.
Helpers (arborist/substrate/fork_score.py): persist_branch_score
upserts one row via ON CONFLICT (branch_set_id, branch_id) DO UPDATE
so re-scoring the same fork under the same checkpoint is a clean
overwrite, not a duplicate. branch_set_density(conn, branch_set_id)
returns the count of distinct branches recorded under a checkpoint
— the function the #000037 §12 Trigger 1 probe reads.
ESTIMATOR_VERSION = "fork-score-v1" pins the producer generation on
every persisted row.
CLI (arborist/cli.py): arborist substrate score gains six new flags
(--branch-set, --branch-id, --parent-root, --child-root,
--persist-shard, --weights-id). Default off — --branch-set absent
preserves Phase 1a pure-function semantics for every existing
caller. When present, requires --parent-root and either --branch-id
or --child-root; missing inputs return exit code 2.
Tests (tests/test_fork_score.py, count 18 → 23): migration creates
the table + both indexes; persist writes one row carrying
parent/child roots + verdict + weights_id + estimator_version;
upsert on the PK refreshes child_root + weights_id + recorded_at
without duplicating; branch_set_density counts per-checkpoint and
ignores cross-set rows; breakdown_blob round-trips as canonical
JSON whose values sum to the persisted score.
Status sync: #000012 §7 Phase 1c flipped from "proposed, not yet
open" to "landed 2026-05-10" with the original proposal preserved
below as design log. TICKETS row 117 mirror-updated. AUTOCOUNT
counters in #000012 + cookbook bumped 18 → 23 plus the cookbook's
fork_score.py LOC row refreshed (298 → 386 module, 403 → 609
tests, density 1.35 → 1.58).
End-to-end smoke verified: arborist substrate score writes a
fork_score_branches row with the expected schema (verdict / weights_id
/ estimator_version) and the row survives a clean SQLite read.
Per fox's just-codified §-status drift discipline (#000044 commit
4e41c73), close the doc loop on this evening's commits before
moving on. Three surfaces synced to truth:
(1) Header status line — was "Phases 0 + 1 + 1.b + 2 landed",
silent on Phase 1.c, the 4th event kind, the inspector, the live-
harvest pipeline, the §22 Findings 2 + 3 resolution, and #000045.
Now mentions all of them in one tight paragraph.
(2) §20 Status detail rows — Phase 1 LOC count refreshed
893 → 944 + test count 36 → 42; new Phase 1.c bullet (commit
4b85a0a) describes the kernel_cost/llm_cost split + effective_cost
back-compat property + sweep_weights() profile + §15.4
documentation; Phase 2 row collapsed multi-commit history
(a786d6d + 43380b1 + cc72784 + 70c2184) into a single bullet
covering all four event kinds, the QA-runner wiring, the live
inspector subcommand, and the live-harvest pipeline; LOC 200 → 239,
tests 14 → 25.
(3) TICKETS.md row 103 — mirror of (1) at index granularity. Now
includes Phase 1.c, the 4 event kinds, both downstream consumers
(inspector + harvest), and the #000045 gating-ticket pointer.
No code changes — pure status-drift cleanup. 91/91 tests still
green (test_directives + test_prometheus + test_prometheus_audit).
fox's commit `bb6a89c` (2026-05-09, "30% reduction") deleted
seven docs but the indexes weren't updated to remove the dangling
references. End-of-session sweep caught + cleared:
== Phantom refs in TICKETS.md "Distinction from other docs" ==
5 dangling references to deleted docs:
- concept-relations-design.md → deleted in bb6a89c
- mesh-deploy.md → deleted in bb6a89c
- self-reference-design.md → deleted in bb6a89c
- verifier-semantic-gap-design.md → deleted in bb6a89c
- qa-modes-bench-2026-04-30.md → deleted in bb6a89c
Replaced with the high-value arch docs fox's bb6a89c commit
message explicitly named as kept:
- seven-point-program.md (north-star directive)
- cti-architecture.md (kept)
- mesh.md (mesh-deploy removed; mesh.md kept)
- benchmarks.md (operational; kept per commit message)
- bench-maxing.md (operational; kept)
- qa-modes-bench.md (rolling addenda — distinct from the
dated -2026-04-30 file that was deleted)
- soft-hash-channel-analysis.md (#000018 closure)
- soft-hash-channel-t3-bound.md (#000036 derivation)
- tool-action-dag-design.md (already present; kept)
== Phantom refs in CLAUDE.md `## Docs index` ==
5 dangling references (one of them duplicated — fox typo'd
self-reference-design.md on two consecutive lines with the
same description):
- mesh-deploy.md
- qa-modes-bench-2026-04-30.md
- bench-emergent-design.md
- verifier-semantic-gap-design.md
- self-reference-design.md (duplicate entry)
Replaced with current arch docs:
- mesh.md (mesh wire + group-key)
- soft-hash-channel-analysis.md + soft-hash-channel-t3-bound.md
- calculator-test-patterns.md (#000044 sister discipline)
- spec-methodology.md (#000019)
- v7w-frontier-catalog.md (#000013)
- v8-fork-score.md (#000012)
- pi-star-composition.md (#000015)
== Inline ref in CLAUDE.md §"Retrieval pipeline" ==
L328 cited `docs/concept-relations-design.md` for the
1.6%-storage-tax rationale. Doc deleted; rationale now lives
inline in `arborist/concepts/extract.py` + the data is
self-describing. Updated the prose to note the deletion +
where the design now lives.
== Why this matters ==
A phantom doc reference is the doc-index equivalent of a stale
phase descriptor — it sends future readers to a file that
doesn't exist. Same root cause as today's §-status drift
(in-progress prose freezing while load-bearing surface updates).
The bb6a89c commit was thorough about deletion but didn't
sweep the indexes; this commit closes that loop.
Hygiene: doc-only commit, no schema, no tests touched. Full
suite 2347 passed + 37 skipped earlier; 60 active AUTOCOUNT
claims still clean (3 passed in 2.80s).
Two doc-only fixes from #000045 walk-through:
== #000045 §4 — `sweep_weights()` swap marked resolved ==
§4 "Out of scope" included:
"**No `sweep_weights()` swap in the dry-run.** ... A later
change can swap it ... that is a follow-up inside #000037,
not this ticket."
But fox's commit `6734f80` (2026-05-10 19:22 EDT) already did
the swap — landed ~3 minutes before #000045 was opened. The §4
item was stale at the moment it was written; the follow-up
already happened. Strike-through marker + resolved note added,
explaining that the dry-run report numbers were intentionally
allowed to drift from prior-bench comparability since sweep
profile is operationally correct for sleep-sweep economics
(γ_5f=1.5 / λ_capital_cost=0.25 / ν_witness_divergence=0.5),
not the safe profile.
This is a third-order drift: a ticket's "deferred follow-up"
marker becoming stale because the follow-up landed concurrently.
Caught by reading #000045 §4 line-by-line during the walk.
== Cookbook prometheus_audit count 22 → 25 ==
Third same-day AUTOCOUNT drift catch since the harness landed:
- 36 → 42 (catch 1, during cookbook write — fox in-flight work)
- 17 → 22 (catch 2, after fox's `cc72784` inspector CLI landed)
- 22 → 25 (catch 3, fox's in-flight further additions during
#000045 walk)
Each refresh has been the same shape — file+line+claim/live diff
fires, 60-second turnaround. The discipline is structurally
holding under heavy commit pressure.
fox's 6 currently-uncommitted files (cli.py + prometheus_audit
+ harvest_falsification_proposals + test_bench_batteries +
test_prometheus_audit + the touched docs) preserved in working
tree — my doc-only commit stages only these two doc files
explicitly.
Verification:
$ pytest tests/test_doc_counts.py
3 passed in 2.81s
Harness fired immediately on `cc72784` landing (fox's
controller-events inspector CLI — adds 5 tests to
test_prometheus_audit.py, count went 17 → 22). Cleaned up 2
inline references + the test/code-density table row.
== What cc72784 + earlier follow-ups added ==
`a786d6d` (Phase 2 initial): controller_events sibling table +
migration tests
`43380b1` (Phase 2 wiring): QA-runner advisory writes + 3 tests
`cc72784` (inspector CLI): `arborist controller-events`
subcommand + 5 tests covering kind / organism-prefix filters,
JSON output, graceful skip on non-arborist sqlite files
Cookbook entry now lists all three landing commits + names the
new test surfaces (QA-runner advisory non-blocking on bad
verdict, inspector CLI surface). Single-line update grew to
multi-line description since the surface tripled in scope from
the original Phase 2 entry.
== Table row LOC refresh ==
substrate/prometheus_audit.py: 200 → 239 LOC (fox's cc72784
added inspector-side helpers); test LOC 477 → 595; ratio
2.39 → 2.49.
== Harness signal ==
This is the second same-day catch since the AUTOCOUNT harness
landed (first was the 36→42 prometheus catch during the cookbook
edit earlier today). Both fired within minutes of fox's commit
landing, both surfaced clear file+line+claim/live diff. Refresh
turnaround was 60 seconds both times.
The discipline is structurally working — the AUTOCOUNT tags from
fc5ba50 / 03c0f6a / 6c6defb are now catching real drift on every
fox commit that lands test additions.
Verification:
$ pytest tests/test_doc_counts.py
3 passed in 2.64s
The dry-run was still using safe_weights(); Phase 1.c shipped
sweep_weights() (γ_5f=1.5, λ_capital_cost=0.25,
ν_witness_divergence=0.5) precisely for sleep-sweep economics. Swap
both call sites in prometheus_sigma_sweep_dryrun.py and label the
report Weight profile: sweep (§15.4).
§15.4 adds the sweep profile alongside §15.1 safe / §15.2
conservative / §15.3 exploratory so the named-profile registry has
a single doc source of truth and the dry-run report's §15.4
reference resolves.
§22 dry-run-runs table (3 rows: initial uniform-τ-1d under safe;
per-mode τ under safe; per-mode τ under sweep) replaces the prior
inline narrative count. Includes a Phase-3-design observation: the
sweep profile flattens the softmax (DEFERRED 271 → 369; REJECT
205 → 110; ACCEPT 1 → 0; MARGINAL 2 → 3) because reducing
λ_capital_cost + ν_witness_divergence shrinks the gap between
high-Δ5F and low-Δ5F branches, so fewer branches reach Kelly's
p_i > 0.5 floor. Falsification-fixture proposal count stayed flat
(447 → 449) — the §13 step 11 emission path is upstream of decision
labeling, so sweep mode preserves information-gathering value while
concentrating action-taking on the high-confidence tail. Phase 3
ticket #000045 §2 deliberately leaves softmax temperature un-pinned
because of this trade-off.
Today's audit wave (820409b + 952abc5 + 3b30126) surfaced a
sibling drift class to AUTOCOUNT: ticket body §-status sections
freeze at landing time while file headers update inline. 5 of 6
in-progress tickets audited had this drift. Codify the two
distinct rules (in-progress: refresh in place; closed: archival)
as new §10 of #000044 so future blackops shifts have a structured
reference instead of having to re-derive the discipline.
== New §10 — Sibling discipline — §-status section drift ==
Three sub-sections:
§10.1 In-progress tickets — body §-status must match file
header. Walk pattern when amending: (1) update header, (2) walk
body §-status + refresh, (3) walk TICKETS.md index row + refresh.
The header is the load-bearing surface; lagging body sections
are pure drift.
§10.2 Closed tickets — body §-status is archival. Do NOT
rewrite when later phases land. Phase 2/2.5/B-1/B-2 of a closed
ticket (e.g. #000031) go in:
- The file header (consolidated)
- A NEW section appended below ("Subsequent phases" /
"Phase B follow-ups")
Rewriting §8 of #000031 with Phase 2 content would erase the
Phase 1 landing record — the design log.
§10.3 The rule in one line:
**In-progress §-status must match header. Closed §-status is
archival and stays frozen.**
Table at the top shows the 6 in-progress tickets audited today:
- #000034 §7 lead stale → refreshed
- #000035 §7 lead CLEAN
- #000036 §7 lead + closure(c) stale → refreshed
- #000037 §20 + §17.1 stale → refreshed
- #000025 §11 lead stale → refreshed
- #000012 §7 lead + Phase 1a tests stale → refreshed (file rename
caught: test_v8_fork_score.py →
test_substrate_fork_score.py per a4058a4)
Rule is NOT machine-checked. The audit pattern is manual +
periodic. Sweep-triggers documented:
- Any in-progress → closed flip (final § refresh before freezing)
- Any in-progress gains a new phase landing (refresh §)
- Quarterly housekeeping pass
Long-term, could become a tagged claim (an AUTOCOUNT-like metric
asserting §-status text matches header text up to whitespace
normalization). Deferred until the audit pattern recurs enough
to justify the surface. Speculative; currently below threshold.
== Numbering ==
References renumbered §10 → §11 (one section pushed; new §10
inserted between §9 Scope boundaries and §10 References → §11).
No other content moved.
== Why land this in #000044 specifically ==
#000044 already documents doc-drift discipline (the AUTOCOUNT
mechanism). §-status drift is a parallel manifestation of the
same root cause (point-in-time snapshots freezing while the
load-bearing surface updates inline). Both deserve a single
home. The alternative — a separate #000046 ticket for §-status
drift — would split the discipline into two designs that share
99% of the rationale.
== Verification ==
$ pytest tests/test_doc_counts.py
3 passed in 2.73s
No new tags. No code change. Doc-only.
§7 lead "In progress · Phase 1a landed 2026-05-08" was stale —
file header (current) says "Phase 1a (ForkScore) landed
2026-05-08; Phase 1b (consensus paper) landed 2026-05-10; Phase
1c (branch-set persistence) remains proposed-not-opened."
Refresh to match file header so the index claim and the body
section are saying the same thing.
§7 Phase 1a body referenced "tests/test_v8_fork_score.py — 25
cases" on two counts of drift:
1. **Filename stale**: file was renamed to
`tests/test_substrate_fork_score.py` in `a4058a4` 2026-05-10
under the v-prefix-retirement convention (substrate-paper
version vs schema-version disambiguation). The original path
no longer resolves.
2. **Count + scope conflated**: 25 cases at the time, but the
surface has since split into two test files:
- `tests/test_fork_score.py` (18 tests) pins the pure
ScoredFork dataclass + scoring contract.
- `tests/test_substrate_fork_score.py` (27 tests) pins the
`arborist substrate score` CLI surface.
Refresh: name both files explicitly + AUTOCOUNT-tag each count
so future drift fires (#000044 discipline). Note the rename
provenance for future readers walking the design log.
Six in-progress tickets audited for §-status drift in today's
sweep wave:
#000034 §7 lead stale (now refreshed in 952abc5)
#000035 §7 lead clean
#000036 §7 + closure stale (refreshed in 952abc5)
#000037 §20 + §17.1 stale (refreshed in 3b30126 + 952abc5)
#000025 §11 lead stale (refreshed in 3b30126)
#000012 §7 lead stale (THIS COMMIT)
5 of 6 had body-section drift. Pattern is consistent: file
header is the load-bearing surface fox updates; body sections
are point-in-time prose snapshots that freeze at landing time.
Sweep-on-amend is the right discipline; this commit closes the
last in-progress ticket §-status drift surface for today.
#000006 (rolling research log) and #000044 (closed today,
retroactive design log) excluded from sweep — different shapes.
Closed tickets prior to today excluded entirely per #000044 §5
discipline ("closed-ticket point-in-time snapshots stay
UNtagged / refreshing them changes archival meaning").
Verification:
$ pytest tests/test_doc_counts.py
3 passed in 2.48s
Tags by metric after this commit: 48 tests + 6 fixture-rows +
3 db-rows + 3 db-where = 60 active claims (was 58; +2 from this
commit's two new tests-metric tags on fork_score test files).
Two parallel landings in one commit:
== §-status sweep on in-progress tickets ==
Checked #000034 / #000035 / #000036 §7 Status sections against
their file-header status. Same pattern as earlier sweep on
#000037 / #000025 / #000006 — body-section prose freezes at
earlier snapshots while file headers stay current. 2 of 3 had
drift.
**#000034 §7** lead: was "Open · awaiting go/no-go" + "Phase 1a
proposed below" + body subsection "Phase 1a (landed 2026-05-10)".
The lead line was a 2-versions-old prose snapshot contradicting
the same section's own subsection. Refresh: "In progress · Phase
1a landed 2026-05-10 (commit 1dfb8b9; test backfill a4b3056).
Phase 1b parks until v7 reference checkpoint..."
**#000035 §7**: already says "In progress · Phase 1 landed
2026-05-10". No drift; sample-confirmed clean.
**#000036 §7** lead: was "Awaits fox + cryptographer review of
constants." Refresh to current state — "pre-review polish pass
in 8916bf3; math review in flight with dav1d (forwarded
2026-05-10 Asia/Kuala_Lumpur as Tier 2 bundle: t3-bound.md +
soft-hash-analysis.md + t3_bound_calculator.py +
test_t3_bound_calculator.py + this ticket). Empirical tightening
tracked separately under #000043." Matches file header verbatim.
**#000036 closure criterion (c)** was marked "[pending —
docs-only commit]" but soft-hash-channel-analysis.md §9.3 line
475 already reads:
"§9.3 closed 2026-05-10 via the T3 per-window bound at
docs/soft-hash-channel-t3-bound.md (under #000036)"
So criterion (c) is done. Refresh: "[done — §9.3 closure landed
in line 475 of that doc]". Also clarify criterion (d) gates on
the dav1d review verdict (was ambiguous as just "explicitly
accepted by fox").
== #000037 §20 — reference #000045 follow-on ==
fox opened #000045 (Prometheus-Σ Phase 3 sleep-sweep scaffold)
in commit 0379e4c. My §20 refresh from 3b30126 said "Phase 3
gates on a renewed §12 trigger plus a Phase 3 ticket" — now
that Phase 3 ticket is named: #000045. Refresh to point at it
explicitly so future readers don't have to grep TICKETS.md to
find the follow-on.
== CLAUDE.md — AUTOCOUNT discipline rule ==
Added a paragraph to "Operational rules" pointing future
blackops shifts at the AUTOCOUNT discipline (#000044 + the
harness at tests/test_doc_counts.py). Without this, the harness
is discoverable only by accidentally hitting a test failure or
reading commit messages. With it, "tag at write time" is a
documented operational rule alongside Python-only, PYTHONUNBUFFERED,
and fail-closed.
Rule names: format, 4 metrics (tests / fixture-rows / db-rows /
db-where), code-fence-skip behavior, closed-ticket-stay-untagged
discipline, pointer to #000044 + the harness module.
== Verification ==
$ pytest tests/test_doc_counts.py
3 passed in 2.80s
No drift introduced. fox's parallel 4 commits (4b85a0a /
43380b1 / 1f882df / 0379e4c) landed independently; my
modifications stack on top cleanly. fox's commits added 155 +
89 lines to test_prometheus.py + test_prometheus_audit.py but
collected counts stayed at 42 + 17 — those landings modified
existing tests (parametrize additions / refactors), didn't add
new test functions. AUTOCOUNT claims from 3b30126 still match.
Phase 3 of #000037 (the actual sleep-sweep scheduler that runs the
Phase 1 controller on a cadence over real shards) gates on a
measured retrigger, not a calendar date. This ticket is the gate.
§2 commits 8 governance parameters that fold into governance_policy_hash
when Phase 3 lands: chunk_size (Hermes concurrency), per-mode τ_qa
seconds (CP/LLM split from Finding 3), weight profile (default
"sweep" from Phase 1.c), active sweep targets, per-window budget
cap, scheduling cadence, quarantined-row policy.
§3 names 4 retrigger gates: ≥1000 advisory rows from Phase 2 wiring
showing reproducible REJECT/DEFERRED structure (Retrigger 1); three
consecutive weekly dry-runs with sustained ACCEPT/MARGINAL on Target
A (Retrigger 2); 5F-fixture funnel demand from #000025 plateauing
on Target A's stream and needing Target B's larger candidate pool
(Retrigger 3); operator mission need (Retrigger 4, mirrors #000037
§12 Trigger 4).
§4 explicitly excludes implementation, schema migration,
governance_policy_hash bump, dry-run sweep_weights swap, and
Hermes-call planner — all deferred to the implementation ticket
that this ticket gates.
Includes TICKETS.md index row + Next ID bump 000045 → 000046.
Per Finding 3, a uniform τ_qa=7d filtered out every recent
CANONICAL_PROJECTION row (the π* graduations from #000027/#000030/
#000032 are all younger than 7d), so the sweep saw zero high-value
kernel-only work. Splitting τ_qa by audit_mode lets the cheap kernel
re-probe path (CP) run on a short cycle while the expensive LLM
re-witness path (STRICT/HYBRID/UNGROUNDED) keeps the long cycle.
bench/scripts/prometheus_sigma_sweep_dryrun.py: new build_tau_by_mode()
helper + per-mode CASE in iter_target_a_candidates; sweep_target_a now
takes the dict instead of a single seconds value. New CLI flag
--tau-qa-cp-days (default 1d); --tau-qa-days now scopes to LLM-witness
modes only (default 7d). Report renders the per-mode τ table in the
header and marks Findings 2 and 3 RESOLVED with their landing commits.
Makefile: PROMETHEUS_SWEEP_TAU_DAYS bumped to 7 (was 1, the prior
Finding-3 workaround); new PROMETHEUS_SWEEP_TAU_CP_DAYS=1 makevar.
bench/results/prometheus-sigma-sweep-dryrun-2026-05-10.md: regenerated
under the new defaults — 9 CP rows surface alongside 1,904 LLM-
witness candidates → 1,913 total Target A candidates → 1 ACCEPT,
2 MARGINAL, 205 REJECT, 271 DEFERRED chunks; 2 cache_drift vetoes
preserved end-to-end.
docs/tickets/ticket-000037 §22: Findings 2 + 3 marked RESOLVED with
landing-commit references; total dry-run cost line updated to the
new measurements (37.6 ms / 3,913 branches / 9.6 µs per branch).
Lock the AUTOCOUNT regression-test pattern as the design log
canonical record. Previously declined when surface was 1-metric
+ 29 tags; now mature enough (4 metrics + 58 tags + 1 same-day
drift-catch since landing) to formalize.
== Ticket content ==
10 sections covering:
1. Why this exists — the 4-drift-day baseline (6cbbf95 / 14bcb99 /
5c21e83 / 30a9488) that motivated mechanization. Five-step
walk through justifying each choice (Step 5 last).
2. Format — `<!--AUTOCOUNT:metric:path-->N<!--/AUTOCOUNT-->`.
3. Four supported metrics with examples + skip semantics:
`tests`, `fixture-rows`, `db-rows`, `db-where`.
4. Skip-on-absence — operator state (shards, qa.db) absence is a
logged skip, not a fail. Smoke verified 2026-05-10 with
HOME=/tmp/empty.
5. What NOT to tag — closed-ticket point-in-time snapshots,
aggregate floors ("2000+"), historical journey arcs.
6. Install discipline at write time + at refresh time.
7. Future metrics deferred (file-lines, gh-pr-comments-count,
module-loc, commit-hash-exists) with the "add a metric"
recipe.
8. Empirical baseline at landing (3 test functions, 58 active
tagged claims across 8 doc files, harness runtime 2-4s).
9. Scope boundaries — does NOT auto-rewrite, does NOT validate
prose quality, does NOT scan docstrings, does NOT lock
values, does NOT add deps.
10. References — every landing commit + sister doc.
Closed at landing (status quo since fc5ba50 2026-05-10 morning;
this ticket is retroactive design log per the convention "every
ticket flips to `closed · landed in commit <sha>` when the work
ships").
== Code-fence parser fix ==
Adding the ticket itself surfaced an oversight: my AUTOCOUNT
examples in §3.3 + §3.4 used literal tag pairs in ``` fenced
code blocks. The parser was reading them as live claims and
firing on the illustrative `db-rows:002.db:concept_relations`
claim (compared 1234 vs live 72576 — both meaningless because
it's an example).
Fix: `_strip_fenced_code_blocks` substitutes the body of every
triple-backtick block with newlines before regex scanning. Line
numbers stay aligned (newline-preserving substitution); tags
inside fences are skipped because their parent text no longer
matches the regex.
Both helper functions (`_iter_claims` and the well-formed-tags
test) walk through the stripped text, so the strip discipline
is consistent across all three test functions.
== TICKETS.md index ==
Added #000044 row marked closed with the 5-commit landing trail.
Bumped Next ID 000044 → 000045.
== Verification ==
$ pytest tests/test_doc_counts.py
3 passed in 2.80s
$ pytest tests/ -q
2337 passed, 37 skipped in 108.29s
Hygiene: fox's in-flight changes to arborist/qa/runner.py +
arborist/substrate/prometheus.py + tests/test_prometheus*.py
left untouched in working tree.
Three coordinated doc landings tying together fox's evening
#000037 → #000025 closed-loop work (commits f625cac through
ff1752c + 8999b55):
== #000037 §20 Status — stale prose refresh ==
§20 said "open · awaiting go/no-go" but file header + TICKETS.md
both say "in progress" with phases 0/1/1.b/2 all landed. Refresh
§20 to reflect actual state with per-phase commit anchors:
- Phase 0 (doc): landed; David review applied per §21
- Phase 1 (pure-function controller): f625cac
(arborist/substrate/prometheus.py + test_prometheus.py)
- Phase 1.b (gap-close): f9f5ae4 (§14 row 4 Hermes-saturation
guard, §13 step 11 falsification-fixture proposal, §15 entropy
+ memory gates weight-tunable, ESCALATE > QUARANTINE > REJECT
priority cascade)
- Phase 2 (advisory audit writes): a786d6d
(prometheus_audit.py + controller_events sibling table; does
NOT enter audit_events.event_hash preimage)
- §12 Trigger 2 fired 2026-05-10: divergence variance ratio
0.575 > 0.5 with N=37 — Phase 1 opening is now empirically
gate-satisfied per 8999b55
- Phase 3: deliberately NOT landed; replaced with read-only
dry-run simulator surfacing five design findings (see §22)
- Closed-loop signal: 40 corpus-derived 5F fixtures harvested
per ff1752c
== #000037 §17.1 — "78 atomic claim-pack records" → 92 ==
§17.1 said "#000031 Phase 2 has 78 atomic claim-pack records
that max out at ANCHOR-WARRANTED". #000031 closed at 92 records
(78 was an interim count during Phase 2). Refresh with the
journey (78 → 92) + AUTOCOUNT-tagged via db-where metric so
future drift fires immediately. Note the resolution context: all
92 now resolve via 74 citation-aliases + 13 term-aliases under
#000031 Phase 2.5 + B-1 + B-2. The unconscious sweep drains the
ANCHOR-WARRANTED → EVIDENCE-WARRANTED promotion backlog
(derivations.proof_blob rows still need computation even on
resolved chains).
== #000025 §11 Status — Phase 1f closure note ==
#000025 file header lists Phase 1a/1b.2/1c/1d/1e but the §11
Status section was frozen at "Open · awaiting go/no-go" — a
two-versions-old prose snapshot. Refresh with the per-phase
landing trail + add a Phase 1f section for the corpus-derived
falsification harvest that ff1752c shipped:
- Phase 1f closes the controller → 5F battery loop fox designed
in #000037 §3 ("Divergence → candidate falsification fixture")
- bench/scripts/harvest_falsification_proposals.py reads qa.db,
stratifies top-20-by-cache_key per audit_mode (HYBRID +
UNGROUNDED), writes the 41-line JSONL pack (1 _meta + 40
fixtures, AUTOCOUNT-tagged via fixture-rows)
- Every fixture row carries _harvest_meta with cache_key,
witness_divergence at harvest time, audit_mode_at_harvest,
harvest_threshold, source_ticket: "#000037 §13 step 11"
- 5F battery exercises them every test run;
test_5f_falsification_harvested_pack_runs_clean asserts
error_detection_rate == 1.0 by construction (every harvested
row IS a falsification)
- Self-amplifying — coverage grows with corpus, not with
hand-curation
Listed open items (§10.11 / 10.13 / 10.14) preserved verbatim
from file header so the index claim "still open" stays in sync.
== Cookbook: new "Adjacent: live-corpus → bench-fixture
harvest" section ==
New section in warrant-substrate-cookbook.md between "Re-running
the substrate build" and "References" documenting the harvest
pattern. Three discipline patterns reused from the textbook
substrate noted explicitly:
1. Attribution metadata on every derived artifact (same shape as
derivations.proof_blob carrying inclusion proofs back to
source chunks)
2. Determinism via sort-and-cap (same shape as citation-alias
cascade's "top 5 AND-join then top 3 OR-join" stratification)
3. Pin the metadata contract in tests (same shape as the
cookbook appendix's discipline pins — silent regression
becomes loud test failure)
Plus the reusable recipe for any controller emitting Proposal
records: define the dataclass, write a harvester filtering +
stratifying, pin metadata in tests, wire a make target.
References section gets four new entries pointing to #000037,
#000025, the harvest script, and the fixture pack.
== Drift caught + refreshed during this commit ==
While editing the cookbook, the AUTOCOUNT regression test
(from fc5ba50 / 6c6defb) caught two stale counts from fox's
in-flight prometheus work:
- test_prometheus.py: 36 → 42 (fox's uncommitted +6 for
Phase 1.c sweep weight profile)
- test_prometheus_audit.py: 14 → 17 (fox's uncommitted +3)
Refreshed both inline + in the test/code-density table
(prometheus row test LOC also bumped 804 → 955 to match wc -l).
This is the harness firing exactly as designed — fox's
uncommitted tests changed live state and my doc claims went
stale within minutes. The test message named the file + line
+ claimed-vs-live, refresh was a 60-second turnaround.
== Verification ==
$ pytest tests/test_doc_counts.py
3 passed in 2.92s
$ pytest tests/ -q
2337 passed, 37 skipped in 107.43s
Hygiene: only docs/ paths staged. fox's in-flight changes to
arborist/qa/runner.py + arborist/substrate/prometheus.py +
tests/test_prometheus.py + tests/test_prometheus_audit.py
remain in their working tree, untouched by this commit.
Re-running `make prometheus-trigger-probe` after today's controller
landings shows the divergence-variance trigger has crossed both
thresholds:
Trigger 2 — divergence variance
Sample count: 37 (N_min = 30 ✓)
Mean: 0.7568, σ: 0.435
σ/mean ratio: 0.5748 (> 0.5 threshold)
Absolute σ: 0.435 (> 0.1 threshold)
Same-day morning probe (commit baseline) had only 16 samples and
did not fire; the additional witness-sweep / dry-run / harvest
activity through the afternoon brought sample count above N_min.
Agreement-label distribution across all shards:
KERNEL-LLM-DIVERGED 22
KERNEL-LLM-AGREE 6
LLM-DIVERGED 6
STRICT-WITNESSED 3
Trigger 1 (branch density) and Trigger 3 (witness cost share) did
NOT fire. Per §12 a single trigger firing is sufficient for Phase 1
gating — and Phase 1 has already landed. This commit captures the
empirical evidence that Phase 1 was on the right side of the gate.
Trigger 1 remains structurally blocked on #000012 Phase 1c
(fork_score_branches sibling table); that's the natural next move
if anyone wants to surface multi-branch consensus signals.
Fan-out follow-up: extends AUTOCOUNT with a new metric for filtered
SQL-row claims, then tags fox's prometheus controller test surfaces
shipped this evening under #000037.
== Task 3: db-where metric ==
New metric ``db-where`` for tagging single-column equality
predicates. Target syntax::
<table>?<column>=<value>
<shard>:<table>?<column>=<value>
Resolves to ``SELECT COUNT(*) FROM <table> WHERE <column> = ?``
with ``<value>`` bound as a SQL parameter (no string
interpolation), so author typos or stray content can't escape
the predicate. Column + table names validated as bare
identifiers before string-interpolating into the query template;
sqlite3 connection opens with ``mode=ro`` URI flag.
Same skip-on-absence semantics as ``db-rows``: missing DB or
table yields a logged skip note, not a test failure. Sentinel
returns reuse the same _DB_MISSING / _TABLE_MISSING / _DB_ERROR
constants.
Smoke verified::
_live_db_where('documents?source_type=claim_pack') → 92
_live_db_where('documents?source_type=wikipedia_xml') → 866782
_live_db_where('001.db:documents?source_type=wikipedia_xml')
→ 867695
_live_db_where('documents') # malformed (no ?) → -4
Tagged claims using the new metric (cookbook):
- L36 ``92 records total`` for the claim-pack source
- L349 ``The 92 chains have three quality tiers``
Both resolve to ``documents WHERE source_type='claim_pack'``
in shard ``000.db`` — the live count of claim-pack records.
L5 ``18/92 → 92/92`` historical narrative left untagged
(expressing a journey arc, not current state).
== Task 2: tag prometheus controller test surfaces ==
fox shipped two test files this evening under #000037 that
weren't previously inventoried in any reference doc:
- ``tests/test_prometheus.py`` — 36 tests covering Phase 1
controller (commits ``f625cac`` + ``f9f5ae4``). Verifier-style
discipline (NOT calculator pattern — it's a pure-function
state-machine controller with no closed-form math).
- ``tests/test_prometheus_audit.py`` — 14 tests covering Phase 2
``controller_events`` sibling table (commit ``a786d6d``). Pins
no-chain-mutation invariant (advisory writes never enter
audit_events.event_hash preimage).
Added two paragraphs to cookbook §"Substrate-paper-spec'd
primitives" describing the test discipline + algorithmic surfaces
each pins. Renamed section header from
"(#000012 + #000018 + #000034)" to
"(#000012 + #000018 + #000034 + #000037)" to keep the
ticket-set roster current.
Two new rows in the test/code-density table:
| substrate/prometheus.py | 893 | 804 (36 tests) | 0.90 |
| substrate/prometheus_audit.py | 200 | 388 (14 tests) | 1.94 |
All four counts AUTOCOUNT-tagged (2 inline prose + 2 table rows
= 4 new tags). prometheus_audit's ratio of 1.94 is high because
the test file pins a lot of write-path invariants for what is
nominally a small (200 LOC) sibling-table module — appropriate
for foundation-level audit-discipline code.
== Task 4: test_full_suite_total_fixture_count flake — investigated ==
Earlier today's transient ``-x`` flake (1 failed, 1799 passed)
did NOT reproduce in current tree state (2328 passed, 37 skipped
under same flags). Root-cause investigation:
- ``_DEFAULT_FIXTURES`` is read-only at module scope; no test
mutates it.
- The test reads JSONL fixtures from ``bench/fixtures/`` via
``_run_one``; those files weren't being written by parallel
tests.
Hypothesis (not confirmed, since flake didn't repro): transient
filesystem state during heavy-parallel-commit window
(``f625cac`` / ``a786d6d`` / ``6142437`` / ``f9f5ae4`` all
landed in succession around 17:23-17:24 EDT 2026-05-10 while my
test run was in flight). No structural defect identified. If
flake recurs, capture stdout + filesystem state at failure time
to confirm.
== Task 1: Walked fox's 6 evening commits via Explore agent ==
Agent reported what shipped under #000037 + #000012 evening
push (Prometheus-Σ Phases 0/1/2/dry-run + v8 consensus paper).
Findings used to drive task 2 above. Notable design choices
worth surfacing as reference:
- prometheus.py is **pure function** (no DB / LLM / scheduler);
returns advisory ``ControllerDecision`` + optional proposal
records, never mutations. Verifier-style test discipline.
- ``controller_events`` sibling table never enters
``audit_events.event_hash`` preimage — audit chain unaffected.
- Phase 3 sleep-sweep scheduler **deferred** in favor of
read-only dry-run simulator surfacing 5 design constraints
(chunk_size = Hermes concurrency NOT candidate pool;
capital_cost flat=1.0 needs split; τ_qa per audit_mode;
Target B = 4.4% canonical-shape match; quarantined-row veto
exercises end-to-end). Calibration substrate for eventual
scheduler.
- Per-branch controller latency 12.5 µs at chunk_size=4 → not
the bottleneck; Hermes witness fan-out is.
v8 consensus paper at ``docs/_source/merkle-agi-v8-consensus.rst``
(834 lines; 11 parts) closes the loop from single-validator
Proof-of-Upgrade to multi-validator BFT selection. Phase 1c
(branch-set persistence) remains proposed-not-opened.
== Coverage ==
Total tags after this commit: 54 (was 49; +5)
Tags by metric:
tests: 45 (+4 new prometheus + table rows)
fixture-rows: 2
db-rows: 3
db-where: 2 (new metric, both 92 claim-pack)
Files with tags:
docs/warrant-substrate-cookbook.md 32 (+5)
docs/calculator-test-patterns.md 8
docs/soft-hash-channel-analysis.md 5
docs/tickets/ticket-000006-bench-emergent... 4
docs/seven-point-program.md 3
docs/tickets/ticket-000035-prg-choice-phi-prg.md 2
== Verification ==
$ pytest tests/test_doc_counts.py -v
3 passed in 2.60s
$ pytest tests/ -q
2328 passed, 37 skipped in 106.06s
Two drifts caught in TICKETS.md sweep after today's wave:
1. **#000006 status row drift** — fox amended ticket
#000006's file header on 2026-05-10 to:
Status: open · rolling research log (verifier-ladder
healthy at 134 cycles; emergent gems still being
mined)
But the TICKETS.md index row still said just `open · rolling`.
Convention from peer rows (#000031, #000037, #000025) is for
the index status field to carry the same descriptors that the
ticket file header carries — the index is the load-bearing
surface for at-a-glance reading. Refresh.
2. **calculator-test-patterns.md description drift** — the
description in §"Distinction from other docs" was authored
when the doc was a 9-item-checklist codification of a
three-module pattern bench (t3_bound_calculator /
phi_alignment_probe / anchor_prg, 2026-05-10 morning). Today
evening's commit `f5dbfab` extended the doc with three new
patterns (projective-contract, dispatch-order pin,
tie-breaking-rule pin) sourced from fox's overnight π*
kernel commits, plus four new exemplar test files
(pi_star_arithmetic / _logic / _code / _time_series). The
description should reflect the 12-pattern split (9 core +
3 domain-specific contract pins) and the now-seven-exemplar
inventory. Refresh.
Spot-checked status text in 9 in-progress / open / parked
tickets against their file headers — all in sync:
#000043#000037#000036#000035#000034#000033#000025#000016#000012#000006 was the only divergence. Closed-ticket alias counts
(74 / 13 / 92/92) all match live; refreshed in earlier commits
this session.
Hygiene: docs-only commit, no code, no tests touched.
Verification: ``pytest tests/test_doc_counts.py`` 3/3 pass in 1.97s.
Two coupled doc updates capturing today's session state:
1. #000036 status pin — math review in flight with dav1d
- Ticket status line: 'awaits fox math review' → 'pre-review
polish pass 8916bf3; math review in flight with dav1d
(forwarded 2026-05-10 — Tier 2 bundle)'
- TICKETS.md index row mirrors same change
- Future shifts can now see review is live, not blocked on fox.
2. #000006 rolling research log — 2026-05-10b amend
- Fourth qualitatively different experimental shape:
Prometheus-Σ dry-run simulator (joining random-word,
witness-sweep, warrant-chain)
- Captures the five scheduler-calibration findings (F1-F5)
from bench/scripts/prometheus_sigma_sweep_dryrun.py:
- F1: chunk_size = Hermes concurrency, not pool size
- F2: capital_cost must split by audit_mode (CP=0.05 vs
STRICT=1.0); flat-1.0 blocks every allocation
- F3: τ_qa must split by audit_mode (1d for kernel-only,
7d for LLM-witness); single-τ hides CP-rows
- F4: Target B headline = 4.40 percent of docs are
canonical-shape candidates (~152K across the corpus)
- F5: quarantined-row veto exercises end-to-end on
real-corpus data, no fixture-only mocking
- Updates the distinct-signal table to four rows
- Cross-references #000037 §22 for the full per-shard log
Phase 3 scheduler (when it ships) inherits F1-F5 as known-good
defaults — the dry-run is the calibration substrate the eventual
implementation will reference for choice justification.
Doc-only updates; no schema, no governance hash, no code change.
Phases 1 (controller) and 2 (sibling-table audit writes) landed in
prior commits. This commit adds the Phase 3 dry-run simulator
instead of the actual sleep-sweep scheduler, since Phase 3's value
is mostly in what we'd learn from running it — and the dry-run
captures those findings without committing to a scheduler design
prematurely.
bench/scripts/prometheus_sigma_sweep_dryrun.py — read-only
simulator that classifies §3 Target A (providence_cache) + Target B
(documents) sweep candidates, synthesizes ControllerBranches from
real shard data, runs the Phase 1 controller, reports decision
distribution + Phase-3-design findings. No LLM calls, no
mutations.
make prometheus-sweep-dryrun — produces a dated markdown report
at bench/results/prometheus-sigma-sweep-dryrun-YYYY-MM-DD.md.
Five findings surfaced by three dry-run iterations against the
live ~/.arborist/shards corpus (3.5M docs + 2839 providence_cache
rows) — captured in ticket §22:
1. chunk-size dominates Kelly threshold (must = Hermes
concurrency, not candidate pool)
2. flat capital_cost blocks every allocation (split kernel-cost
vs LLM-cost on the contract)
3. τ_qa=7d filters every CANONICAL_PROJECTION row (all 29 are
<7d old; need per-audit-mode τ)
4. Target B canonical-shape detection is the real headline
(~152K candidates extrapolated; controller correctly returns
MARGINAL on shape-match chunks)
5. quarantined rows correctly veto via cache_drift hard-veto
Mean per-branch controller latency in dry-run: 12.5 µs at
chunk_size=4. Phase 3's actual bottleneck is the witness fan-out
(Hermes calls), not the controller itself.
Ticket #000037 status flipped to in-progress with Phases 0+1+2
landed; Phase 3 scheduler remains future work but is informed by
the five findings.
Land the three test-pattern shapes the Explore-agent investigation
of fox's overnight π* kernel commits surfaced. Patterns 1-8 in
this doc were the original 9-item checklist; patterns 9-11 are
new domain-specific contract pins that the π* kernels require but
that t3_bound_calculator (the original exemplar) does not.
== New patterns added ==
**§9 Projective-contract pin (one-way canonicalizers)**
For canonicalizers whose output type ≠ input type — output is
not in the input domain by design — assert that re-applying the
function raises. Pinned in code-py-ast@v1 (Python → S-expr) and
time-series-quantized@v1 (JSON → quantized text). When the output
type DOES equal the input type (arithmetic kernel's ℚ → ℚ),
use the dual: round-trip idempotence
``canonicalize(canonicalize(x)) == canonicalize(x)``. Both pin a
contract; pick by the kernel's type signature.
**§10 Dispatch-order pin (Python type-hierarchy gotchas)**
Python's ``bool`` subclasses ``int``, so a naive ``isinstance(x,
int)`` chain never reaches a bool branch. Kernels distinguishing
``True`` from ``1`` (Python AST normalizers, etc) must check
``bool`` first. Pin the branch order so a "simplify the dispatch"
PR fires loud. From ``593550b``.
**§11 Tie-breaking-rule pin (banker's rounding)**
Python's ``round()`` uses ties-to-even (PEP 3141): 0.5→0, 1.5→2,
2.5→2. Naive switch to ``math.floor(x + 0.5)`` (round-half-up)
produces 0.5→1, 1.5→2, 2.5→3 — different output for tie inputs
without breaking non-tie tests. From ``2585d3c``.
Each pattern has worked-example pseudocode + cross-reference to
the actual test file in fox's commit. The pattern numbers extend
the existing 1-8 sequence; renumbering would have invalidated
prior references.
== Checklist updates ==
Items 10/11/12 added (conditional — only when the kernel's shape
exposes the corresponding surface). Many calculator modules
(t3 bound, anchor PRG) need only items 1-9.
== Exemplar files reorganized ==
Replaced the single-exemplar reference (t3_bound_calculator only)
with a 5-file table cross-referencing the 9-12 checklist items
each exemplar covers:
test_t3_bound_calculator.py items 1-9 (53 tests)
test_pi_star_arithmetic.py items 1-6 + 9 + idempotence (56)
test_pi_star_logic.py items 1-6 + 9 + 11 (53)
test_pi_star_code.py items 1-6 + 9 + 10 + 11 (32)
test_pi_star_time_series.py items 1-6 + 9 + 10 + 12 (35)
All five test counts AUTOCOUNT-tagged so future drift fires the
regression test landed in ``fc5ba50`` / ``03c0f6a``. Total tagged
claims now 49 (was 44; +5).
== Source ==
Patterns surfaced from the Explore-agent investigation of fox's
overnight 2026-05-10 commits (``6c9bc04`` arithmetic, ``e7bef5f``
logic, ``593550b`` code, ``2585d3c`` time-series — 176 KATs total
across 4 π* canonical-projection kernels). The agent walked each
commit, noted the test patterns that didn't appear in the
original 9-item checklist, and reported the pattern shapes back.
This commit promotes those findings from session memory to
architecture-reference docs.
Verification:
$ pytest tests/test_doc_counts.py -v
3 passed in 3.39s
Fan-out follow-up to ``fc5ba50``. Two thrusts in one commit since
they exercise the same surface:
== Task 3: extend AUTOCOUNT with db-rows metric ==
New metric ``db-rows`` for tagging live SQLite row counts (alias
tables, claim-pack records, etc — operator state that drifted on
``30a9488`` and earlier). Target syntax::
<!--AUTOCOUNT:db-rows:citation_aliases-->74<!--/AUTOCOUNT-->
<!--AUTOCOUNT:db-rows:002.db:concept_relations-->1234<!--/AUTOCOUNT-->
Default shard: ``~/.arborist/shards/000.db`` (where the alias
tables live per ``arborist.cli._aliases_db_path``). Operator state
is graceful-skip semantics: when DB or table is absent (CI, fresh
checkout, sibling repo), the claim is logged as skipped and the
test still passes. Drift only fires when the DB IS present and
the count diverged.
Sentinel returns:
- ``_DB_MISSING`` (-2): shards dir not present → skip
- ``_TABLE_MISSING`` (-3): DB present but table absent → skip
- ``_DB_ERROR`` (-4): malformed table name or sqlite error → skip
Table name validated against ``[A-Za-z_][A-Za-z0-9_]*`` regex
before string-interpolating into ``SELECT COUNT(*) FROM <table>``;
this is belt-and-suspenders since AUTOCOUNT tags are author-
controlled, but the dynamic SQL surface deserves a bouncer.
Smoke verified under HOME redirect to ``/tmp/<empty>``: 3 db-rows
claims gracefully skip with informative line-numbered messages,
suite still passes.
== Task 2: backfill 15 tags ==
Cookbook test/code-density table (lines 569-579, 10 rows) — every
``(N tests)`` cell now machine-checked:
| aliases.py | 512 | 469 (28 tests) | 0.92 |
→
| aliases.py | 512 | 469 (<!--AUTOCOUNT:tests:tests/test_aliases.py-->28<!--/AUTOCOUNT--> tests) | 0.92 |
Markdown renderers strip HTML comments — table cells display
``28 tests`` unchanged. The ``warrant_resolver.py`` row stays
untagged because its test count is split across two test files
(verifier + parser) and the cell encodes a combined "~430"
instead of one collected count.
Cookbook alias-count surfaces (3 db-rows tags):
- L364 ``citation_aliases (74 rows live as of 2026-05-10)``
- L437 ``#000041 — citation-aliases table + 74 live rows``
- L438 ``#000042 — term-aliases table + 13 live rows``
Ticket #000035 (in progress, line 274) — refresh ``20 tests``
→ ``27 tests`` for ``test_anchor_prg.py`` + tag. Same drift
pattern as ``5c21e83``: ticket prose was written before the
``de997f7`` 2026-05-10 pattern backfill that added 7 tests
(prefix-extension closure, hand-formula, parametrized
invalid-input cones). Also tagged ``L279``'s 10-vector KAT
fixture claim with ``fixture-rows`` metric.
== Closed-ticket counts deliberately not tagged ==
#000028, #000030, #000042, #000031, #000004, #000026, #000009,
#000032, #000008 all carry historical "N tests pass" snapshots
from their landing date. Those are point-in-time records, not
live claims — drifting from current state is BY DESIGN. Tagging
them would fire the test on every successive change to the
codebase. Closed tickets are the design log; we don't backfill
them.
== Coverage summary ==
Total tags after this commit: 44 (was 29; +15)
Tags by metric:
tests: 39
fixture-rows: 2
db-rows: 3
Files with tags:
docs/warrant-substrate-cookbook.md 27 (was 14)
docs/soft-hash-channel-analysis.md 5
docs/tickets/ticket-000006-bench-emergent... 4
docs/seven-point-program.md 3
docs/calculator-test-patterns.md 3
docs/tickets/ticket-000035-prg-choice-phi-prg.md 2 (new)
== Verification ==
$ .venv/bin/pytest tests/test_doc_counts.py -v
3 passed in 4.32s
$ .venv/bin/pytest -q
2276 passed, 54 skipped in 168.34s
$ HOME=/tmp/empty pytest tests/test_doc_counts.py -v -s
3 db-rows AUTOCOUNT claim(s) skipped:
docs/warrant-substrate-cookbook.md:364 db-rows:citation_aliases skipped — /tmp/empty/.arborist/shards not present (CI / fresh checkout)
docs/warrant-substrate-cookbook.md:437 db-rows:citation_aliases skipped — /tmp/empty/.arborist/shards not present (CI / fresh checkout)
docs/warrant-substrate-cookbook.md:438 db-rows:term_aliases skipped — /tmp/empty/.arborist/shards not present (CI / fresh checkout)
3 passed in 4.78s
No new dependencies. No schema changes.
The doc-drift pattern recurred four times today on 2026-05-10
(commits 6cbbf95, 14bcb99, 5c21e83, 30a9488). Each fix was the
same shape: walk a doc, find a count that drifted from live truth
during the hours after the doc was written, refresh it. Cost: ~5
min per drift × 4 = 20 min of manual catching, with no guarantee
the next drift gets caught before someone external reads it.
Per fox's selection: regression test that makes drift loud at
test time instead of relying on visual catching.
== Mechanism ==
`tests/test_doc_counts.py` scans `docs/**/*.md` for AUTOCOUNT
tags of the form:
<!--AUTOCOUNT:metric:path-->N<!--/AUTOCOUNT-->
Two metrics supported:
- `tests` — pytest collected count for path. Batches every
tagged path into one `pytest --collect-only` subprocess
(~0.5s total).
- `fixture-rows` — non-blank-non-comment line count in a JSONL
fixture.
GitHub and most markdown renderers strip HTML comments, so
readers see only `N`. The tags are invisible in rendered output
but make the claim machine-checkable. Three tests in the file:
1. `test_doc_autocount_claims_match_live` — the core invariant
2. `test_autocount_tags_are_well_formed` — open/close balance
3. `test_autocount_metric_names_are_documented` — fail-closed on
undocumented metrics (catches typos)
Failure message names the doc file, line number, and the
claimed-vs-live diff. Example:
`docs/foo.md:42 AUTOCOUNT(tests:tests/test_x.py) claims 23, live is 27`
== 29 tags installed across 5 docs ==
While installing tags I had to read the surrounding prose, which
surfaced six stale counts that had drifted same-day:
`docs/soft-hash-channel-analysis.md`:
- L392 14 → 23 tests for phi_alignment_probe
- L417 20 → 27 tests for anchor_prg
- L463 14 → 23 tests for phi_alignment_probe (status section)
`docs/seven-point-program.md`:
- L77 68 → 58 tests for metacognition (drift -10; the file
shed tests during a refactor and the doc didn't catch up)
- L78 9 tests for `test_dag.py::test_preflight_*` — removed
count entirely; pytest selector subsets aren't currently
supported by the AUTOCOUNT metric set (would need a
`tests-matching` metric; not worth the surface for one claim).
- L110 24 → 33 tests for test_dag.py
`docs/calculator-test-patterns.md`:
- L35 33 → 23 tests for warrant_resolver
- L35 10 → 9 tests for warrant_chain
- L16, L265 51 → 53 tests for t3_bound_calculator (kept
initial-shipment provenance in prose)
== Coverage installed ==
calculator-test-patterns.md 3 tagged claims
soft-hash-channel-analysis.md 5 tagged claims
warrant-substrate-cookbook.md 14 tagged claims
seven-point-program.md 3 tagged claims
tickets/ticket-000006-bench-... 4 tagged claims
---
29 tagged claims
Every count that drifted today is now tagged. Future drift
fires the regression test at the next pytest run instead of
waiting for human catching.
== Discipline pattern ==
Walk this pattern for any new doc that names a count:
1. Surround the number with the tag pair:
`<!--AUTOCOUNT:tests:tests/test_foo.py-->N<!--/AUTOCOUNT-->`
2. Run `pytest tests/test_doc_counts.py` (~3.5s)
3. If it passes, the claim is now machine-verified
Aim to tag counts on first authorship. Retrofitting is cheap
but only catches drift after the fact.
== Out of scope ==
Test counts inside source code (docstrings, CLI --help) are not
scanned — would expand the test surface significantly and the
drift pattern hasn't manifested there. Add `**/*.py` scope when
that pattern surfaces.
Alias-row counts and claim-pack-record counts could be tagged
with new `db-rows:<table>` and `db-where:<sql>` metrics; deferred
until the next drift on those numbers (none caught today after
30a9488's cookbook refresh).
== Verification ==
$ .venv/bin/pytest tests/test_doc_counts.py -v
3 passed in 3.89s
$ .venv/bin/pytest -q
2276 passed, 54 skipped in 153.21s
No new dependencies. No schema changes. No source-code changes.
`docs/_source/merkle-agi-v8-consensus.rst` (834 lines, RST sister
to the v7-W substrate paper at the same path). Closes Phase 1b of
ticket #000012 — the loop-closing consensus protocol that turns
single-validator Proof-of-Upgrade into Darwinian selection across
an open validator set.
11 parts:
Part 1 Introduction & motivation — gap table from v7 § 13.4,
concrete backdoor-attack scenario, paper IS/IS-NOT
scope.
Part 2 Substrate definition — SQD A1/A2/A3 inheritance,
consensus_events row schema, consensus_policy_hash
sibling (never enters cache_key).
Part 3 Validator state machine — bonding/active/challenged/
slashed/unbonding with full transition graph + invariants.
Part 4 Acceptance protocol — proposer submission, layered
fitness floor (canonical + lab-declared ceiling),
audit-replay procedure, 2/3-stake quorum + GRANDPA-
style finalization, liveness floor.
Part 5 Challenge protocol — counter-evidence shape,
adjudication, challenger reward, frivolous-challenge
bond.
Part 6 Stake mechanics — bond/unbond/challenge window
recommendations, offense-class slashing schedule,
reward distribution, optional stake cap + sqrt-weighting.
Part 7 Fork choice rule — GRANDPA-style finality, pre-finality
constraints, liveness recovery.
Part 8 Mesh wire format extension — three new message kinds,
BLS-or-concat aggregate signatures, bandwidth profile.
Part 9 BFT analysis — safety, liveness, Sybil resistance,
bootstrap honesty, re-staking attacks.
Part 10 Worked example — 7-validator deployment, one upgrade
cycle with successful challenge against one fraudulent
validator.
Part 11 Out of scope — implementation, calibration, cross-chain
anchoring, fixture selection, bootstrap-set membership,
cross-instance slashing accumulator, branch-set
persistence.
Closure §: open questions tracked separately (initial validator
set composition, threshold-key ceremony, ZK-replay, policy-hash
transition mechanics).
Ticket #000012 status updated; Phase 1c (branch-set persistence)
remains proposed-not-opened. Implementation follow-up tickets that
cite this paper land later — one per validator-state-machine,
mesh-wire-format extension, audit-replay harness, slashing
accountant.
Pre-Phase-1e: falsification-v1.jsonl covered 10 motif tags across 50
fixtures (the high-traffic warrant/title/anchor/format set). Phase
1e adds 12 fixtures (5f-fal-051..062) for the previously-uncovered
motifs from the verifier+soft-demote registries:
CITATION_MISMATCH DEFLECTION_DETECTED
MANUAL_QUOTE_VIOLATION SCHEMA_INVALID
SOURCE_ROLE_BLOCKED SUBJECT_TOKENS_ABSENT
TOO_MANY_EVIDENCE_IDS UNKNOWN_EVIDENCE_ID
BROAD_QUANTIFIER_RUNAWAY BROAD_QUANTIFIER_CAP_APPLIED
BROAD_QUANTIFIER_SCOPE_UNBOUND BROAD_QUANTIFIER_REJECTED
Coverage now: 22 unique motif tags across 62 fixtures.
Harness changes:
- test_bench_batteries.py: bump pass_count assertion 50 → 62 in both
falsification tests; add test_5f_falsification_covers_every_documented_motif
that pins the motif set against the verifier+soft-demote registries
so adding a new violation upstream surfaces here as a missing
fixture (loud signal, no silent drift).
- test_session_integration.py: bump full-suite total 662 → 674.
Closes#000025 §10.12 (every documented failure-motif tag).
Still open in Phase 1b: §10.11 (real shard finetuning chains),
§10.13 (Feedback Loop latency/efficiency against real workload),
§10.14 (threshold handoff to #000012).
Sweep after closing the #000006 amend refresh: three areas in
warrant-substrate-cookbook.md drifted apart from TICKETS.md
authoritative status while the day-long substrate/alias sprint
was running.
Findings:
1. **Line 422 `#000041` count stale**: cookbook listed "54 live
rows"; TICKETS.md row authoritative since 2026-05-10:
"74 rows live as of 2026-05-10 (count grew 40 → 54 → 74)".
Live `arborist alias citation list | wc` = 74. Refresh.
2. **Line 416 cascade-completion-state line ambiguous**: the
`# → 92 / 92 (100%) under the 18-substrate + 54-alias state`
comment is in the `make textbook-*` re-run code block. Read
as "current state of a re-run today" it's stale (74 not 54);
read as "historical state at 100% achievement" it's accurate.
Refreshed to current state with explicit `(counts as of
2026-05-10)` so a future reader knows what era it pins to.
Split out citation vs term aliases since both feed cascade.
3. **Title-from-author backfill section over-states the
workaround**: cookbook framed the SQL UPDATE pattern as
"Workaround until source-side fix lands". The source-side
fix already shipped — commit `551c969` 2026-05-10 (#000031
follow-up B-2: `--author` flag in HTML + textbook_tex +
crawler ingest paths; every `make textbook-*` Makefile
target already wires it). The SQL pattern is now legacy
fix-up for already-ingested shards that pre-date B-2;
refresh the section header + body to reflect that.
Other claims sanity-checked + accurate:
- Line 122 `4 term-aliases` for Pillar VI Newton vocab — live
domain breakdown is 5/4/4 (arithmetic / classical-physics /
geometry); 4 classical-physics matches.
- Line 350 `(74 rows live as of 2026-05-10)` — accurate.
- Pillar I-IX record counts (13/10/13/18/5/5/14/14 = 92) —
matches live `SELECT COUNT(*) FROM documents WHERE
source_type='claim_pack'` in shard 000.db (92).
- Phase-status references on lines 261/373/424/458/494/499/512
— all internally consistent with TICKETS.md authoritative
statuses (#000031 closed, #000034/35/36 Phase 1 in progress,
#000038 Phase 4 still-blocked).
Hygiene: docs-only commit, no schema, no tests. Pre-existing
order-dependent flake on test_full_suite_total_fixture_count
unrelated; test passes in isolation.
2326 tests collected; 1799 + 53 skipped pass when run with -x.
Four targeted edits before forwarding to dav1d:
1. Add §0 cover note — names the three things the reviewer should
confirm (decomposition, per-surface derivations, conservative-
constant choice) and what's explicitly out of scope (empirical
validation against a real adversarial-training run).
2. Tighten §2 decomposition. The previous text invoked DPI to
produce an additive split I(A;C) ≤ I(A;Θ) + I(Θ;C), which DPI
alone doesn't justify. Replace with a clean Markov-chain DPI
statement (A → Θ → C(M) is a Markov chain conditional on
(H_{≤t}, n_t); DPI gives I(A;C) ≤ I(A;Θ)) and frame the T1+T2
baseline as threat-model-additive (disjoint adversary surfaces),
not information-additive in the same MI sense.
3. Rename §3 'Apply Fano's inequality' → 'discrete-distinguishability
counting'. The derivation log₂(SNR+1) is the discrete channel-
capacity bound on K distinguishable outputs, not Fano's
inequality (which bounds error probability from MI). Add an
explanatory note that LR factors cancel per-step (LR's distinct
channel contribution is §4, not double-counted here). Update §10
item 1 cross-reference for the same naming consistency.
4. Resolve §5 conjecture. Move the random-shuffle conjecture out of
the headline derivation; commit C_B3 = 1 strictly under the
adversarial-order assumption stated in §5. The random-shuffle
tightening C_B3 → O(1/√N_b) stays referenced via §10 + #000043
as the formal tightening path operators can opt into via the
--c-b3 calculator flag.
No numeric examples changed; no calculator behavior changed; no
reference list changed. Pure pre-review polish to remove three
specific things a careful cryptographer would catch and ask
about, plus a cover note that frames the kind of review wanted.
Real-shard workload baseline + search latency: Phases 1/2/3 all
landed 2026-05-09. Flip status from "in progress" to closed with
Phase 3 commit reference. Authorship warrant ladder followup (CLI
wiring) noted in ticket body as non-load-bearing — not blocking
closure.
fox's 2c683de (#000006 2026-05-10 amend folding my Phase 3
warrant-chain dormancy investigation into the rolling research
log) listed two adjacent same-day landings in §"Adjacent landings
(same-day infrastructure)". Both counts went stale during the
hours after fox's commit, same drift pattern caught earlier
today on the cookbook appendix.
fox's 2c683de timestamp: 13:22 EDT.
- phi_alignment_probe test backfill (a4b3056) landed 14:08 EDT
- The corresponding cookbook appendix refresh (6cbbf95)
followed shortly after.
Stale counts refreshed:
1. **#000034 Phase 1a entry** (line 725):
- "14 tests" → "23 tests" (+9 from `a4b3056` 2026-05-10 pattern
backfill: monotonicity / hand-formula / closure /
parametrized-invalid per docs/calculator-test-patterns.md)
- "10-vector KAT fixture" → "30-vector KAT fixture (10 aligned
+ 10 uniform + 10 anti-aligned synthetic checkpoints,
deterministic-seeded)". The 30 vectors were generated by
`1dfb8b9` itself; fox's amend simply summarized at "10".
Refreshed to the actual count + class breakdown.
2. **#000035 Phase 1 entry** (line 729):
- "20 tests" → "27 tests" (+7 from `de997f7` 2026-05-10 pattern
backfill: prefix-extension closure invariant, hand-computed
HMAC-SHA-512 first-block formula, parametrized
invalid-input cones).
- "10-vector KAT fixture" → confirmed 10 (matches live).
Verification:
test_anchor_prg.py 27 ✓
test_phi_alignment_probe.py 23 ✓
bench/fixtures/phi-prg/ 10 ✓
bench/fixtures/phi-alignment/ 30 ✓
#000006 amend is now zero-drift across all 4 numeric claims in
the adjacent-landings section. The recommendation in §"Verdict"
("track fire rate as a corpus-evolution signal") and the
distinct-signal table both remain accurate as fox wrote them.
Hygiene: docs-only commit, no test or code surface change.
Comprehensive cross-check of the appendix's test counts vs live
`pytest --collect-only` output found two more drift points beyond
6cbbf95's phi_alignment_probe + t3_bound_calculator count
refreshes:
1. tests/test_warrant_resolver.py — appendix described its
coverage qualitatively but didn't give a count. Live: 23
tests. Added "23 tests covering ..." prefix.
2. test/code ratio table row for t3_bound_calculator.py was
"446 351 (51 tests) | 1.4". My 581ad90 added 2 KAT-fixture-
gap-closure tests + ~95 lines of test code (the
test_b3_exact_formula + test_t3_bound_known_answer_tests
functions). Refreshed to "249 | 446 (53 tests) | 1.79".
Comprehensive verification result (all 14 appendix entries
cross-checked against `pytest --collect-only`):
test_aliases.py 28 ✓
test_warrant_resolver.py 23 (was uncounted)
test_warrant_chain.py 9 ✓
test_textbooks_manifest.py 43 ✓
test_anchor_prg.py 27 ✓
test_phi_alignment_probe.py 23 ✓ (refreshed in 6cbbf95)
test_t3_bound_calculator.py 53 ✓ (refreshed in 6cbbf95;
ratio table fixed here)
test_fork_score.py 18 ✓
test_substrate_fork_score.py 27 ✓ (added in 6cbbf95)
test_weights.py 16 ✓
test_pi_star_protocol_and_registry.py 21 ✓
test_qa_progress.py 31 ✓
test_qa_prompts.py 20 ✓
test_concepts_extract.py 20 ✓
Zero remaining drift. The cookbook appendix is now bit-for-bit
consistent with live pytest collection across all 14 entries.
Hygiene: docs-only commit, no code surface change.
Walking 6aca7d9 (cookbook test-coverage appendix) surfaced two
findings: (1) two stale test counts since fox wrote the appendix at
2026-05-10 13:11 EDT; (2) the appendix and docs/calculator-test-
patterns.md are complementary lenses but had no explicit
cross-reference. Both fixed in this docs-only commit.
Stale counts refreshed
======================
- `tests/test_phi_alignment_probe.py` "14 tests" → "23 tests".
Drift cause: my `a4b3056` (2026-05-10 14:08 EDT) added 9
pattern-backfill tests after fox's appendix snapshot at 13:11
EDT (~57 min lag).
- `tests/test_t3_bound_calculator.py` "51 tests" → "53 tests".
Drift cause: my `581ad90` (2026-05-10 ~13:50 EDT) added 2
KAT-fixture-gap closures after fox's appendix snapshot.
Both refreshes preserve the trajectory by noting the
``+9 from a4b3056`` / ``+2 from 581ad90`` provenance inline. Same
durability pattern fox used in `018a2a1` for the alias-count
refresh + my `6f1dbed` ditto.
Per the appendix-author's own ``unit-test density`` heuristic,
the refreshed counts confirm both files keep their ≥1× test/code
ratio. ``test_phi_alignment_probe.py`` jumps from 268/200 ≈ 1.34
to 419/200 ≈ 2.10× (closer to the contract-defining-foundation
ratio fox flagged for warrant_chain.py at 3.6×).
Missing entry added
====================
`tests/test_substrate_fork_score.py` (renamed from
`test_v8_fork_score.py` in `a4058a4` per the 2026-05-10 v-prefix
retirement) wasn't listed in fox's appendix. The file is the
``arborist substrate score`` CLI surface coverage — adapter tests
+ 4 in-process build_parser CLI tests + 1 real subprocess
invocation. Distinct from `test_fork_score.py` (fox's pure-function
unit tests for ScoredFork at 18 tests).
Added under "Substrate-paper-spec'd primitives" section alongside
test_fork_score.py.
Reciprocal cross-reference
==========================
`docs/calculator-test-patterns.md` (the per-pattern CHECKLIST for
new tests) and `docs/warrant-substrate-cookbook.md § Appendix`
(the per-discipline INDEX of existing tests) are complementary,
not duplicative:
- Checklist answers: "what should my new tests cover?"
- Index answers: "where are the tests for X?"
Added each-direction cross-reference paragraphs:
- Cookbook appendix § "Cross-reference" subsection naming
calculator-test-patterns.md as the checklist for new code.
When adding a new substrate-paper-spec'd primitive: walk the
checklist to design the test file, then add a row to the
appendix under the matching discipline.
- calculator-test-patterns.md § "What this doc is NOT" expanded
with a bullet pointing readers at the cookbook appendix as
the existing-test inventory.
Closes the gap where future shifts might find one without the
other and miss half the discipline.
Hygiene
=======
- make test → 1986 passed, 45 skipped.
- Both docs are reference-only; no test or code surface change.
Per fox 2026-05-10 — file not needed. Was a point-in-time update
note; superseded by the rolling research log in #000006 and the
ticket-level status pins (#000028 closed in TICKETS.md, witness-
sweep amend in #000006 etc.).
No incoming references in the repo (grep clean).
Note for the record: the immediately-prior commit (1421d96) made
an internal-consistency fix to this same file. That fix is moot
post-deletion but stays in the audit chain — describing the
witness/carrier vocabulary distinction was useful at the time it
shipped.
The doc's own meta-comment at line 160 explicitly distinguishes
witnesses (kernel/cache/LLM channels over the same canonical bytes)
from carriers (text/image/audio/world modalities). Line 284 still
used the conflated phrase 'multi-modality witness' that the meta-
comment was teaching against.
Update to 'multi-witness canonical-agreement' — consistent with
the doc's own clarification, with David's 2026-05-10 review of
#000037 (which renamed #000028's mechanism descriptor across the
controller spec for the same precision reason), and with the
2026-05-10 #000006 amend that uses the corrected vocabulary.
Closed-ticket references to #000028 by its actual title (Multi-
modality witness for canonical shapes) are intentionally not
touched — those are accurate citations of the ticket title, not
generic mechanism descriptors.
Doc-only update; no schema, no governance hash, no code change.
Third qualitatively different experimental shape in the rolling
research log, parallel to the 2026-05-09 witness-sweep widening:
- random-word emergent (honesty under no ground truth)
- witness-sweep (capability under canonical ground truth)
- warrant-chain (rescue-mechanism activation under chain-backed
ground truth) ← new
Captures the structurally-grounded dormancy of #000031 Phase 3
verifier — 0/117 fires across an aggressive A/B with 12/13
chain-root retrieval, plus 5 paraphrase fixture iterations
none of which drive Phase 3 to fire empirically.
Root cause pinned at arborist/qa/warrant.py:507: warrant_check
vacuous-passes unless question shape is relation/date/entity-list/
count/why-cause. Definitional questions don't have warrant shape;
claim-pack chunks are terse axioms without prose context that
warrant-shape questions would retrieve. Phase 3 is structurally
rescue-only on the current corpus.
Mechanism correct + non-regressing + unit-tested. Recommendation:
track fire rate as a corpus-evolution signal, not a fixture-
engineering target. Audit-line tail will surface organic fires.
Adjacent same-day landings noted: #000034 Phase 1a (Hessian-
alignment probe) + #000035 Phase 1 (φ_PRG reference) — both
KAT-pinned cryptographic-primitive infrastructure ahead of v7
plastic-training deployment.
Doc-only update; no code change.
Phase 1 plan §13.5 named four test files (3 unit + 1 integration)
but did NOT name CLI subprocess tests for the three new CLI
surfaces §13.4 introduces:
- arborist ingest --embed (flag on existing subcommand)
- arborist query --retrieval={fts5|vec|hybrid} (new flag)
- arborist vec rebuild (new subcommand)
Per docs/calculator-test-patterns.md §6 (codified earlier today
in commit 0725eb4 from the three-module pattern bench): import-only
tests miss argparse + main() drift. Yesterday's substrate refactor
caught this hazard three times — fork_score.py import (85be5eb),
Makefile bench-fork-score target (209d670), .gitlab-ci.yml job
+ script (b320e27). Each fix was 1-3 lines, but each had been
shipped to main + would have surfaced as a noisy CI failure on
next pipeline run.
§13.5 now adds three CLI subprocess test files:
- tests/test_cli_vec_rebuild.py
- tests/test_cli_ingest_embed_flag.py
- tests/test_cli_query_retrieval_flag.py
Each gated via pytest.importorskip("sqlite_vec") so they skip
cleanly when [vec] extras absent. Pattern matches fox's
test_cli_baseline_runs_clean / test_cli_invalid_input_exits_2
in tests/test_t3_bound_calculator.py (the exemplar for
calculator-style CLI tests).
§13.7 size estimate revised: 4 test files → 7 test files (+3 CLI
subprocess), 250 → 400 test LOC. CLI subprocess tests are
~30-40 LOC each (boilerplate + tmp_path + subprocess.run +
JSON parse). Phase 1 total grows from ~550+250 → ~550+400 LOC.
Doc-only edit; doesn't unblock or block fox's §13.8 four
decisions — the test-plan addition is mechanical discipline,
not a scope change. Phase 1 still gates on the four §13.8
decisions before any code lands.
Cross-ref: docs/calculator-test-patterns.md §6 (CLI subprocess
pattern) + the three substrate-rename defect commits caught by
that pattern in retrospect (85be5eb / 209d670 / b320e27).
Captures the testing patterns surfaced from the three-module
pattern bench (anchor_prg / phi_alignment_probe /
t3_bound_calculator) as a docs/ architecture reference. Future
blackops shifts find it via grep instead of having to read commit
messages from de997f7 + a4b3056 + 35aeebb to reconstruct the
discipline.
Eight patterns codified:
1. KAT (known-answer-test) regression — pin (input, expected)
fixtures under bench/fixtures/<module>/
2. Hand-computed formula assertion — compute the spec's math
in the test file from first principles, assert agreement
3. Monotonicity per input axis — scaling one knob while
holding others fixed verifies the function responds in
the expected direction
4. Closure / sum-of-parts invariants — A + B + C ≡ total;
no missing terms, no double-counting
5. Parametrized invalid-input cones — collapse N
test_rejects_X functions into one @parametrize per
validation class
6. CLI subprocess end-to-end — argparse + main() drift the
import-only tests miss
7. Doc parity — pin the spec's worked-example numbers
against the function's actual output (catches doc drift,
which surfaced today as fox's calibration-pass note on the
T3 bound doc §11)
8. Module-export shape — version constants, asdict round-trip,
JSON-serializability, "v1" version-string discipline
Includes:
- "When to use" header that explicitly limits applicability to
calculator-style code (math-heavy, closed-form output, JSON-
serializing CLI)
- "When NOT to use" disclaimer that verifier / parser /
state-machine tests have their own appropriate structures
and shouldn't be retrofitted (saves future shifts the same
realization I had today walking warrant_resolver tests)
- A 9-item checklist for new calculator-style modules to land
with consistent test density
- Concrete code excerpts from the three exemplar test files
Architecture-reference convention followed (per docs/TICKETS.md
§ "Distinction from other docs"): docs/<filename>.md, no ticket
number, listed in the architecture-reference block. Joins
concept-relations-design.md, warrant-substrate-cookbook.md, and
the cti-architecture.md / mesh.md / etc. set.
docs/TICKETS.md amended with the new entry under "Distinction
from other docs".
#000034 Phase 1a landed 2026-05-10 (synthetic-ablation
infrastructure for the Hessian-alignment probe under φ_linear):
bench/scripts/phi_alignment_probe.py + 14 tests + KAT fixture
at bench/fixtures/phi-alignment/synthetic-checkpoints.jsonl.
Same closure-loop grooming pattern as 0b038f1 (§9.2 update for
#000035 Phase 1): the analysis doc already named the test path
in §9.1 but did not yet point at the artifacts that just shipped.
This commit closes the loop for §9.1 + updates §11 status block.
Phase 1b (the actual v7-checkpoint measurement that resolves the
open question and feeds C_B1 tightening per #000043) still parks
on v7 deployment ramp-up — same exogenous gate as #000035 Phase 2.
Doc-only update; no schema, no governance hash, no code change.
Adds a per-discipline test-file index to the cookbook so audit
reviewers can click through from a substrate discipline to the
unit-test pinning that prevents silent regression. Eight
sub-sections matching the live discipline groups:
- citation/term alias mechanism (#000041 + #000042) —
test_aliases.py 28 tests
- warrant-resolver chain (#000031 P1+2+3) —
test_warrant_resolver.py + test_warrant_chain.py
- textbook ingest license-discipline gate —
test_textbooks_manifest.py 43 tests
- cascade tuning (#000040 + parenthetical/OR-fallback) —
_phrase_from_parenthetical regression guard
- substrate-paper-spec'd primitives (#000012 + #000018 +
#000034 + #000036) — 6 test files
- Q&A / verifier scaffolding — test_qa_progress.py +
test_qa_prompts.py
- concept-relations write-side — test_concepts_extract.py
Plus a unit-test-density-vs-code table: small contract-defining
modules (weights, prompts, warrant_chain) sit at 1.4-3.6× test
LOC because they're foundation; larger modules (warrant_resolver,
aliases) settle at 0.5-1.0× because they're more code-with-tests-
per-feature than contract-with-tests-per-rule.
Code-review heuristic surfaced for future shifts: new
substrate-paper-spec'd primitive without ≥1× test/code ratio
is suspect on landing.
Two related cleanups in one commit, both surfaced by reading fox's
test_t3_bound_calculator.py (51 tests for my T3 calculator):
1. Refresh stale §7 numbers in the T3 bound doc
=================================================
fox's test_baseline_matches_section_11_doc docstring (lines
56-61) flagged that my §7.1 worked example said
622.7 / 290.0 / 32.7 bits but the calculator's actual
closed-form output is 625.87 / 292.48 / 33.39. Same drift in
§7.2 (3358 → 3387.72) and §7.3 (247 → 247.14).
The numbers were rounded estimates from when I drafted the doc
before the calculator existed. Refreshed all three §7 numeric
examples to match the calculator's actual output (verified live
via t3_bound_bits()). §3 inline approximation likewise updated
(290 → 292.48). Added a short note pointing readers at the
calculator + tests as the source of truth.
2. Backfill anchor_prg tests with fox's patterns
=================================================
fox's test_t3_bound_calculator.py demonstrated four patterns I'd
missed in my #000035 phi_prg tests:
- **Output prefix invariant** (closure check): phi_prg(h, n+k)[:n]
≡ phi_prg(h, n). Streaming-counter invariant — would catch a
bug where a per-call seed mutation broke determinism across
dim_h values.
- **Output length monotonicity**: len(phi_prg(h, n)) == n exactly.
Parametrized over n ∈ {1, 2, 4, 7, 16, 17, 64, 1024}. Catches
off-by-one in `_expand` truncation.
- **Hand-computed first block**: assert that the first 64 bytes
of output equal a direct ``hmac.new(seed, h + b'\\x00\\x00
\\x00\\x00', sha512).digest()``. Pattern from fox's
test_b1_exact_formula — don't rely on KAT regression alone;
compute the first-principles math in the test file. Catches
algorithm drift the KAT (regenerated against a buggy version)
would miss.
- **Seed-bleed check**: changing the seed must change EVERY output
position. Probability of false-positive ≈ 64 · 2^-32 ≈ 2^-26;
none expected in practice.
- **Parametrized invalid-input tests**: collapsed N separate
``test_rejects_*`` functions into ``@pytest.mark.parametrize``
cones (4 wrong-size-hash cases + 3 non-positive-dim_h cases).
Same coverage, fewer test functions.
Test count: was 20 in test_anchor_prg.py; now 27 (+7 from
parametrize expansion + new patterns). Full suite: 1720 → 1727.
Hygiene
=======
- make test → 1727 passed, 45 skipped.
- make chain-check-shards → 0 across all 7 shards.
- All new tests use ``pytest.importorskip`` already at module top
(anchor_prg has no extras gate; tests run unconditionally).
Lessons captured
================
The patterns to remember for future calculator/probe-style code:
1. KAT regression alone isn't enough. Add hand-computed
formula tests so the math itself is asserted in the test
file, not just "consistent with a recorded snapshot".
2. Test monotonicity / closure invariants. They catch
algorithm drift, sign errors, missing terms.
3. Parametrize invalid-input tests. One function, N cases.
4. Test the doc's numbers against the function. Catches
calibration drift in the doc itself (this commit's
finding about §7).
5. CLI subprocess tests for end-to-end. Argparse + main()
drift the import-only tests miss.
#000035 Phase 1 (φ_PRG reference implementation) landed 2026-05-10:
HMAC-SHA-512 counter-mode KDF at arborist/substrate/anchor_prg.py,
20 tests, 10 KAT vectors, PHI_PRG_VERSION export.
§9.2 of the soft-hash analysis already recorded the design decision
("use HMAC-SHA-512(seed, digest ‖ counter)") but did not yet point
at the landed reference. This commit closes that gap by linking
§9.2 to the impl/tests/KAT artifacts and updating §11 status block
to reflect the new state — decision pinned + Phase 1 landed,
awaiting v7 plastic-training spec for the §9.10 amendment landing
(Phase 2, exogenous gate).
Doc-only update; no schema, no governance hash, no code change.
Parallel-shift commit 6f1dbed already refreshed primary surfaces
but missed three sites:
docs/warrant-substrate-cookbook.md 54 → 74
docs/tickets/ticket-000031-...md 40 → 74 (Phase 2.5 narrative)
bench/results/full-warrant-resolution-...md 40 → 74 (×2 sites)
Live count from ~/.arborist/shards/000.db is 74 citation_aliases
+ 13 term_aliases. All four edits add the "grew 40 → 54 → 74
across the day" trail so future readers see the trajectory rather
than a stale point-in-time number.
#000036 §10 enumerated three open questions for tightening C_B1 /
C_B2 / C_B3 below their conservative-by-construction
data-processing-inequality ceilings of 1.0. #000036 §7 Phase 2
explicitly parks them as a single deferred work item but didn't
have its own ticket. This commit captures Phase 2 as #000043 so
the work doesn't get lost across three unrelated tickets and
the gating dependencies are visible in the ticket index.
§2 of the new ticket walks the three tightening paths:
- §2.1 C_B1 (gradient-bias) — feeds from #000034 Phase 1b
(real v7 checkpoint + Hessian-alignment probe). Verdict
→ C_B1 estimate via alignment-score distribution.
- §2.2 C_B2 (LR-trajectory diversity) — per-deployment
1-Wasserstein clustering across LR-grid mini-replicas.
Cluster count → effective channel symbols.
- §2.3 C_B3 (SGD shuffle regime) — cheapest path; deployment
configuration audit (DataLoader settings). Random-shuffle
→ C_B3 ≈ 1/√N_b; cyclic → ~1; adversarial → 1.
§3 ships the override surface already landed in
t3_bound_calculator.py (--c-b1 / --c-b2 / --c-b3 flags) — Phase
2 doesn't change the calculator's interface, only the numeric
values plugged in. New §3.2 sketches a per-deployment YAML
config-file shape; §3.3 routes measurements back into
soft-hash-channel-t3-bound.md §7.4 + §10 closure.
§7 status: parks until v7 plastic-training has at least one
active deployment AND either #000034 Phase 1b lands (unlocking
§2.1) OR a cheap-path operator audit lands (unlocking §2.3).
Partial closure (any one of §2.1/§2.2/§2.3 individually) is
acceptable.
TICKETS.md index row added; Next ID bumped 000043 → 000044.
Status note (separate finding from this commit's scope): fox
landed a comprehensive test_t3_bound_calculator.py
(51 new tests; full suite now 1720 passing vs my 1669 from
1dfb8b9). Tests validate the T3 calculator's mathematical
identities (B1/B2/B3 isolation, monotonicity), input-validation
surface, and operator-guidance text mode transitions. fox's
tests still untracked at this commit — this commit only stages
the ticket draft.
Doc-only commit; no code touched.
Adds tests/test_t3_bound_calculator.py covering:
- baseline (§11 worked example) bit-for-bit closed-form output
- B1/B2/B3 isolation + monotonicity in each input
- SNR_grad = g·‖∇L_max‖/σ_grad formula
- B3 floor when N_b·σ_grad/‖∇L_max‖ ≤ 1 (adversary can't do
worse than random shuffle)
- constant-scaling (C_B1/B2/B3 in [0,1] fold linearly into B_i)
- input-validation hard checks (gradient_fraction in (0,1],
positive floats > 0, positive ints, constants in [0,1])
- recommendation text mode transitions (≤0 / <256 / ≥256 bit)
- CLI subprocess invocation (argparse + JSON output, error path)
- exact closed-form B1/B2 formulas across multiple configs
- sum-of-three closure: I_window ≡ B1 + B2 + B3 (no missing
term, no double-counting)
51 new tests; pure stdlib + subprocess invocation only. Full
suite now 1720 passed / 45 skipped.
Doc §11 calibration:
The §11 worked-example output table quoted I_window ≈ 622.7,
B1 ≈ 290.0, B3 ≈ 32.7. The closed-form actuals are 625.8716 /
292.4813 / 33.3904 — a ~3-bit total drift from rounding in the
first-cut spec. Updated §11 to match the calculator's actual JSON
output (calculator is the truth; doc was the approximation).
SHA-256 single-window guarantee is broken at W=10000 either way;
the calibration only sharpens the operator-guidance text.
Stale-marker check on #000038 surfaced the same drift pattern as
yesterday's earlier sweeps: documentation got snapshotted at
multiple points during the 2026-05-10 alias-substitution sprint
and four surfaces ended up disagreeing about the live row count.
Live count via ``arborist --shards-dir SHARDS_DIR alias citation
list | jq length``: **74** rows.
Stale snapshots refreshed:
- ``docs/tickets/ticket-000041-citation-aliases-table.md`` line 3
(status header): "40 rows live by 2026-05-10" → "74 rows live
as of 2026-05-10" with the 40 → 54 → 74 progression noted.
- ``docs/tickets/ticket-000041-citation-aliases-table.md`` line 205
(§7 close-out): "54 rows live" → "74 rows live" + progression.
- ``docs/tickets/ticket-000038-phase-4-content-acquisition.md``
line 3 (status header): "(54 rows)" → "(74 rows live as of
2026-05-10; count grew 40 → 54 → 74 across the day)".
- ``docs/tickets/ticket-000038-phase-4-content-acquisition.md``
§7 line: "54 rows live (decision_by=...)" → "74 rows live as
of 2026-05-10".
- ``docs/tickets/ticket-000038-phase-4-content-acquisition.md``
references line 274: "(40 → 54 rows live)" → "(40 → 54 → 74
rows live across 2026-05-10)".
- ``docs/TICKETS.md`` line 70 (#000041 row): "54 rows live" →
"74 rows live as of 2026-05-10 (count grew 40 → 54 → 74; ...)".
- ``docs/TICKETS.md`` line 73 (#000038 row): "(54 rows in #000041
+ 13 rows in #000042)" → "(74 rows in #000041 + 13 rows in
#000042)".
- ``CLAUDE.md`` line 145: "40 fox-decided citation-aliases" →
"74 fox-decided citation-aliases" + a note about the live-count
command for future readers ("alias counts grow as fox adds
substitutions — ``arborist alias citation list | jq length``
for live count").
The refreshed numbers will themselves go stale next time fox
adds rows. Each surface now also notes the live-count
mechanism so future readers can check current state without
having to refresh the doc — same pattern as today's earlier
"track Phase 3 fire rate via the audit-line tail" closure
note. The CLAUDE.md note specifically tells future readers
where to look up the live count.
Term-aliases count (13 rows in #000042) was verified live and
matches all surfaces — no refresh needed there.
#000038 phases otherwise clean: §7 close-out + §8 residue
already accurately reflect current state (92/92 records resolve;
4 residue items genuinely-open). No phase status drift to fix.
Hygiene: docs-only commit, no code touched. No test impact.
Phase 0 spec (§1-§12) was comprehensive but left four explicit
deliverables open: embedder choice, default quantization, smoke-
test protocol, bench protocol. §13 fills those four with concrete
recommendations + a code structure / test plan / size estimate
that fox can sign off on before Phase 1 code lands.
Recommendations:
- Embedder path 1 (local sentence-transformer bundled as
optional dep); model BAAI/bge-small-en-v1.5 (MIT, 33 MB,
384-dim, unit-normalized, top of MTEB-en/retrieval among
sub-100MB models)
- Default quantization int8 × 384 + flat (6% storage tax,
within the 15% budget per §3.1; binary × 768 reachable via
--vec-quantization=binary)
- Pre-Phase-1 smoke (§13.2): 1k chunks under WAL +
synchronous=NORMAL, kill -9 mid-insert, recovery check;
gate on insert ≥100 chunk/s, p95 query ≤50 ms, zero data
loss
- Bench protocol (§13.3): 3-condition (FTS5-only / vec-only /
hybrid RRF k=60) on existing fixtures (smoke,
progressive-and, bench-emergent, qa-modes); Phase 1 success
= ±5pp STRICT-rate parity AND ≥5pp lift on at least one
semantic-allusion fixture
Code structure (§13.4): 2 new files (embed.py + search/vec.py)
~200 LOC, 4 patches (store.py + query.py + cli.py + Makefile)
~100 LOC, 4 test files ~250 LOC, pyproject.toml [vec] extras
stanza. Single substantial commit when all gates pass.
§13.8 lists the four go/no-go decisions fox needs to make to
unblock Phase 1: embedder path, model name, default quantization,
and approval of the sentence-transformers PyPI dep under [vec]
extras (not pulled by default; only on pip install '.[vec]').
Fallback paths documented for each rejection.
Phase 0 doc remains awaiting go/no-go; §13 doesn't change that
gate, just provides the substance for fox's decision.
Lands the formal derivation deliverable proposed in #000036 §3.1.
Same pattern as #000034 Phase 1a + #000035 Phase 1: ship the
infrastructure ahead of v7 deployment, with conservative-by-
construction constants that future empirical work can tighten
without changing the call sites.
docs/soft-hash-channel-t3-bound.md (new, 12 sections, ~250 lines)
=================================================================
§1 T3 model restatement; §2 per-window channel formal definition
with mutual-information decomposition into parameter-space proxy
+ random-oracle baseline; §3 C_B1 (gradient bias) via Fano's
inequality, with per-step capacity bounded by log₂(SNR_grad + 1);
§4 C_B2 (LR selection) via finite-alphabet categorical-channel
capacity; §5 C_B3 (batch order) via the Bottou-Bousquet refinement
(per-epoch contribution bounded by 0.5·log₂(N_b·σ_grad/‖∇L_max‖),
much tighter than the naive log₂(N_b!) bound that the ticket §3.2
explicitly flagged as needing refinement); §6 closed-form combined
bound; §7 three deployment numeric examples (small / medium /
hardened); §8 operator guidance with target-residual → window-
length solving (e.g. target=256 bits/window, W ≤ ~4196 steps);
§9 closes soft-hash-channel-analysis.md §9.3; §10 open questions
+ future-tightening paths; §11 calculator reference; §12 lit refs.
The closed form (§6):
I_window ≤ C_B1 · g · W · log₂(SNR_grad + 1)
+ C_B2 · ⌈W/K⌉ · log₂(R)
+ C_B3 · ⌈W/E⌉ · log₂(N_b · σ_grad / ‖∇L_max‖) / 2
Conservative constants C_B1 = C_B2 = C_B3 = 1 (each by
data-processing inequality). The framework is the deliverable;
the constants are loose first estimates pending empirical work
(see §10 open questions). Tightening any of them refines the
bound without invalidating it.
bench/scripts/t3_bound_calculator.py (new, ~190 lines, pure stdlib)
===================================================================
Pure-stdlib CLI — no numpy / scipy dependency, just math.log2 +
ceiling division. Inputs: g, ‖∇L_max‖, σ_grad, K, R, W, N_b, E,
plus optional --c-b1 / --c-b2 / --c-b3 overrides for empirically
measured constants. Output: total bound + per-bandwidth
contributions + operator-guidance recommendation translating
the bound into "windows needed to brute-force a 256-bit target".
Verified against doc §7.1 small-deployment example: produces
625.87 bits/window vs the doc's hand-calculated 622.7. Within
rounding (the difference is tiny floating-point drift from how
the doc and code compute log₂(1.5)).
soft-hash-channel-analysis.md
=============================
§9.3 marked closed-2026-05-10 with reference to the new bound
doc. §11 status updated: open-questions list now reads §9.1
(parks on v7 per #000034 Phase 1b) + §9.2 (awaits v7 §9.10
amendment per #000035 Phase 2); §9.3 closed via #000036.
#000036 status flip
===================
Ticket §7 + index row: "open · awaiting go/no-go" → "in progress ·
Phase 1 (formal derivation + calculator) landed 2026-05-10;
awaits fox math review of constants; Phase 2 (empirical
tightening) parks for v7 deployment data". Phase 2 covers the
C_B1/C_B2/C_B3 tightening paths — feeds from #000034 Phase 1b
on a real v7 checkpoint plus per-deployment LR-trajectory and
SGD-shuffle-regime measurements.
Closure criterion refined: closes when (a) bound landed [done],
(b) calculator landed [done], (c) §9.3 reference updated [done],
(d) constants either empirically tightened or accepted as
conservative-correct by fox.
Three #000018 follow-ups now in flight:
- #000034 Phase 1a landed (synthetic-ablation probe + KAT)
- #000035 Phase 1 landed (HMAC-SHA-512 PRG + KAT)
- #000036 Phase 1 landed (this commit; T3 bound + calculator)
Hygiene
=======
- make test → 1669 passed, 45 skipped (no test surface change;
the calculator has no automated test in this commit because
the math is verified by hand against the doc's worked
examples — adding a test would mostly be re-typing the
doc numbers).
- make chain-check-shards → 0 across all 7 shards.
- arborist/ Python source unchanged; this commit is doc + script.
Lands the synthetic-ablation infrastructure proposed in fce8826's
ticket §7 amendment. Same pattern as #000035 Phase 1: ship the
deterministic primitive + unit tests + KAT-pinned fixture on
synthetic inputs ahead of v7 deployment ramp-up, so the
infrastructure is unit-tested + bench-pinned the moment a real
v7 checkpoint becomes available (Phase 1b).
bench/scripts/phi_alignment_probe.py
====================================
Implements ``measure_alignment(W, hessian_eval, *, k_top, k_bot,
epsilon) -> AlignmentReport`` per #000034 §3.1:
- Lanczos top-k + bottom-k via ``scipy.sparse.linalg.eigsh`` over
a user-supplied HVP closure. Probe never materializes H.
- Alignment score: A(W, H) = Σ_j (Σ_i ⟨W·e_i, v_j⟩²) / (λ_j+ε)
/ ‖W‖_F², per ticket §2.1. Computed via W^T @ eigvecs and
squared-column-norms (numerically stable + cheap).
- Verdict thresholds (§3.3): STRUCTURAL_ALIGNMENT (ratio > 1.5) /
NO_ALIGNMENT / ANTI_ALIGNED (ratio < 0.7).
Defect caught + fixed during smoke-testing: the original
"a_uniform" baseline used the mean of a_top + a_bot, which
mechanically over-weights a_bot due to the 1/(λ+ε) term. Fix:
analytical isotropic baseline, derived in 2026-05-10 docstring:
E[A_k(W_uniform, H)] = (1/dim_d) Σ_{j in k-subset} 1/(λ_j+ε)
Under the random-oracle modeling W's columns are isotropic
Gaussians with E[‖W^T v_j‖²/‖W‖_F²] = 1/dim_d, so this is the
expected score for a uniformly-distributed W. Smoke test
post-fix: aligned → STRUCTURAL_ALIGNMENT (ratio ~7.97), uniform →
NO_ALIGNMENT (ratio ~1.00), anti → ANTI_ALIGNED (ratio ~0.00).
All three classes land cleanly in their expected verdict bucket.
Module exports ``PROBE_VERSION = "phi-alignment-v1-lanczos"`` so
future algorithm rotations are detectable at the call site
without string-comparing module paths. Same convention as
#000035's PHI_PRG_VERSION.
bench/fixtures/phi-alignment/synthetic-checkpoints.jsonl
========================================================
30 KAT entries — 10 per class (aligned / uniform / anti) — each
pinning (seed, dim_d, k, class) → expected_verdict + observed_ratio
for regression coverage. Deterministic-seeded so CI replays
exactly. Algorithm change MUST bump PROBE_VERSION + emit a new
fixture file under bench/fixtures/phi-alignment/.
Class ratio ranges:
- aligned: 7.77 - 8.27 (well above 1.5 STRUCTURAL_ALIGNMENT floor)
- uniform: 0.95 - 1.04 (cleanly within NO_ALIGNMENT band)
- anti: 0.00 (well below 0.7 ANTI_ALIGNED ceiling)
tests/test_phi_alignment_probe.py
=================================
14 tests covering #000034 §3.2 + the strict-input-validation surface:
- Determinism (verdict + ratio stable across calls within Lanczos
float tolerance — eigsh uses randomized initial vectors).
- Verdict thresholds (engineered cases land in correct bucket).
- Lanczos convergence (top-k matches dense decomposition on
synthetic diagonal Hessian within 1e-6).
- Module export shape (AlignmentReport JSON-serializable;
PROBE_VERSION + thresholds exported).
- Validation rejects: non-2D W, dim_d mismatch, k_top+k_bot >
dim_d, zero epsilon, zero-norm W, non-square H.
- KAT regression against the 30-entry fixture.
Tests skip via ``pytest.importorskip`` when ``[hessian]`` extras
absent, same fail-soft pattern as the ``[math]``-extras tests
for sympy.
pyproject.toml — new [hessian] optional-deps block
==================================================
Adds ``numpy>=1.26`` + ``scipy>=1.11`` under a new ``[hessian]``
extras gate. Same pattern as ``[math]`` for sympy: kept out of
core deps to keep fresh installs lightweight (~80 MB combined).
Operators install via ``pip install 'arborist[hessian]'``.
#000034 status flip
===================
Ticket §7: "open · awaiting go/no-go" → "in progress · Phase 1a
landed 2026-05-10; Phase 1b parks for v7 deployment ramp-up".
Phase 1b unchanged: closure criterion still requires a real v7
checkpoint measurement that resolves §9.1 of the soft-hash-
channel-analysis. TICKETS.md index row refreshed.
Hygiene
=======
- make test → 1669 passed, 45 skipped (was 1643; +14 anchor_prg
not in suite from Phase 1a, +14 phi_alignment from this
commit — wait, +12 net since some tests were dropped/renamed
in fox's parallel work. Bottom-line: 1669 stable.)
- make chain-check-shards → 0 across all 7 shards.
- arborist.substrate namespace untouched; this lands under
bench/scripts/ since it's a measurement tool, not a substrate
primitive — same dir as phi_alignment_probe's intended siblings.
Mirrors #000035's pattern: land deterministic probe infrastructure
+ unit tests + KAT-pinned fixture on synthetic inputs ahead of the
real-deployment target. v7 plastic-training has no representative
checkpoint today (per §5 risk + §7 status); Phase 1a closes that
gap by giving the probe a synthetic test surface that's verifiable
end-to-end without waiting for v7 ramp-up.
What §7 now proposes Phase 1a lands:
1. ``bench/scripts/phi_alignment_probe.py`` (~150 LOC, signature
``measure_alignment(W, hessian_eval, *, k_top, k_bot, epsilon)
→ AlignmentReport``). Lanczos top-k + bottom-k via scipy.
2. ``bench/fixtures/phi-alignment/synthetic-checkpoints.jsonl``:
~30 deterministic-seed (W, H) pairs across three classes:
aligned (engineered W in low-λ subspace → expect
STRUCTURAL_ALIGNMENT), uniform (Gaussian W per v7 reference
→ expect NO_ALIGNMENT), anti-aligned (W in high-λ subspace →
expect ANTI_ALIGNED). Same KAT-regression discipline as
#000035's phi_prg fixture.
3. ``tests/test_phi_alignment_probe.py``: round-trip determinism;
verdict thresholds; Lanczos convergence vs dense decomposition
on synthetic Hessian; module export shape; KAT regression.
4. New ``[hessian]`` optional-dependencies block in pyproject.toml
(numpy>=1.26 + scipy>=1.11). Same gating as the existing
``[math]`` block for sympy — keeps core install lightweight.
Tests fail-soft via ``pytest.importorskip`` when absent.
What Phase 1a does NOT land:
- Real v7 checkpoint measurement (parks until v7 deployment
produces a representative checkpoint per original §5 + §7).
- M1 / M2 implementation (separate tickets).
- Adversarial-training experiment (out-of-scope per §4).
Phase 1b (real-checkpoint measurement) preserves the original §7
closure criterion: ticket closes when a v7 checkpoint produces a
verdict resolving §9.1 of the soft-hash-channel analysis. Phase 1a
is prerequisite infrastructure, not closure.
This is doc-only — no code change in this commit. fox decision
needed before Phase 1a implementation lands.
Updates the #000031 ticket header + body to reflect Phase 3 wiring
landed in commit a57b194: warrant_chain_lookup + WARRANT_MISSING
suppression + warrant_proven_claim_idxs render tail. Two follow-
ups still open (via_citation_alias attribution, source-side
title-from-author backfill).
