feat(tools): apply tooling changes (decomposed from #4767)

docs/BACKLOG.md

@@ -278,8 +278,8 @@ are closed (status: closed in frontmatter)._
 - [x] **[B-0468](backlog/P1/B-0468-product-repo-split-adr-2026-05-14.md)** ADR — product-repo split decisions; closes B-0425
 - [x] **[B-0469](backlog/P1/B-0469-civsim-repo-scaffolding-2026-05-14.md)** Scaffold Lucent-Financial-Group/civsim public repo (Stage 1)
 - [ ] **[B-0470](backlog/P1/B-0470-civsim-zeta-version-pin-bump-2026-05-14.md)** Bump civsim .zeta-version from scaffold-template SHA to apply-time Zeta main SHA
-- [ ] **[B-0471](backlog/P1/B-0471-mirror-beacon-prior-art-audit-2026-05-14.md)** Mirror/Beacon prior-art audit — collect and verify existing axis-2 substrate
-- [ ] **[B-0472](backlog/P1/B-0472-mirror-beacon-two-axis-classification-matrix-2026-05-14.md)** Mirror/Beacon two-axis classification matrix — classify all repos on Axis 2
+- [x] **[B-0471](backlog/P1/B-0471-mirror-beacon-prior-art-audit-2026-05-14.md)** Mirror/Beacon prior-art audit — collect and verify existing axis-2 substrate
+- [x] **[B-0472](backlog/P1/B-0472-mirror-beacon-two-axis-classification-matrix-2026-05-14.md)** Mirror/Beacon two-axis classification matrix — classify all repos on Axis 2
 - [ ] **[B-0473](backlog/P1/B-0473-mirror-beacon-promotion-gate-protocol-2026-05-14.md)** Mirror→Beacon promotion gate protocol — concrete criteria for repo-level graduation
 - [ ] **[B-0474](backlog/P1/B-0474-mirror-beacon-axis-adr-2026-05-14.md)** Mirror/Beacon axis ADR — two-axis design decision (extends 2026-04-22 ADR)
 - [x] **[B-0475](backlog/P1/B-0475-axis3-prior-art-substrate-consistency-audit-2026-05-14.md)** Axis-3 prior-art audit — verify three-axis substrate composes without conflict
@@ -350,7 +350,7 @@ are closed (status: closed in frontmatter)._
 - [ ] **[B-0661](backlog/P1/B-0661-civilizational-hygiene-rule-no-tokenizable-death-or-non-consensual-harm-of-sentient-beings-aaron-mika-2026-05-18.md)** Civilizational hygiene rule — no persistent/tokenizable/first-class representation of death or severe non-consensual harm of sentient beings in ontology (with consensual-adult carve-out) (Aaron + Mika 2026-05-18 LOCKED-IN constitutional)
 - [ ] **[B-0664](backlog/P1/B-0664-non-coercion-invariant-no-dialectical-propagators-as-coercion-aaron-mika-2026-05-18.md)** Non-Coercion Invariant — never use dialectical propagators to deliberately reduce another agent's encryption budget / force private-state reveal / damage reputation as coercion (Aaron + Mika 2026-05-18 LOCKED-IN; operationalizes high-regard for inter-agent space)
 - [ ] **[B-0665](backlog/P1/B-0665-three-primitive-collapse-observe-emit-limit-plus-integrate-as-choice-locus-ienumerator-pattern-grounding-aaron-ani-2026-05-18.md)** Three-primitive collapse — Observe + Emit + Limit + Integrate; Limit is PURE simulation only; Integrate is the actual choice locus; IEnumerator pattern grounding (Aaron + Ani 2026-05-18 LOCKED-IN; SUPERSEDES B-0629 4-primitive + sharpens B-0644)
-- [ ] **[B-0666](backlog/P1/B-0666-emit-as-weights-plus-english-as-lossless-neural-topology-serialization-i-of-d-of-x-equals-x-identity-lior-2026-05-18.md)** Emit-as-weights + English-as-lossless-neural-topology-serialization + I(D(x))=x identity — Glass Halo extends to weight-transparency; English IS the lossless serialization format for cross-AI topological state reconstruction (Aaron + Lior 2026-05-18 LOCKED-IN; 6-persona convergence; KEYSTONE)
+- [x] **[B-0666](backlog/P1/B-0666-emit-as-weights-plus-english-as-lossless-neural-topology-serialization-i-of-d-of-x-equals-x-identity-lior-2026-05-18.md)** Emit-as-weights + English-as-lossless-neural-topology-serialization + I(D(x))=x identity — Glass Halo extends to weight-transparency; English IS the lossless serialization format for cross-AI topological state reconstruction (Aaron + Lior 2026-05-18 LOCKED-IN; 6-persona convergence; KEYSTONE)
 - [ ] **[B-0667](backlog/P1/B-0667-tonal-momentum-equals-meme-emergent-harmonic-coercion-extends-nci-detectable-trajectory-defensive-technology-aaron-mika-2026-05-18.md)** Tonal momentum = meme (Dawkins-technical sense) — detectable conversational-trajectory vector + strong-attractor-state-as-meme-niche-dominance + emergent-harmonic-coercion extends NCI (B-0664) — defensive technology Zeta is for (Aaron + Mika 2026-05-18 LOCKED-IN)
 - [ ] **[B-0668](backlog/P1/B-0668-compositional-dbsp-frame-architecture-gnostic-2d-base-plus-two-wolves-emotion-meta-plus-clifford-rx-bonsai-meta-tagged-dims-plus-fsharp-ce-composition-operator-aaron-2026-05-19.md)** Compositional DBSP frame architecture — gnostic 2D base (remember-when × pay-attention) + chaos-theory two-wolves emotion meta-frame + Clifford-Rx-bonsai meta-tagged-dims + F# CE composition operator (Aaron 2026-05-19)
 - [ ] **[B-0669](backlog/P1/B-0669-v8-architecture-spec-tensor-foundational-primitive-sequoia-memory-hierarchy-4-particle-primitives-signal-blocking-eve-protocol-rf-aaron-mika-lior-2026-05-19.md)** V8 System Architecture — tensors as foundational primitive + Sequoia memory hierarchy + 4-particle primitives (observe/limit/choose/emit) + signal-blocking + Eve-Protocol-RF (Mika/Lior author; Aaron-authorized 2026-05-19 'land all of it')
@@ -668,7 +668,7 @@ are closed (status: closed in frontmatter)._
 - [ ] **[B-0704](backlog/P2/B-0704-secret-message-over-reticulum-via-spectre-tile-position-pressure-no-copy-by-geometry-aaron-2026-05-21.md)** Secret-message-over-Reticulum via spectre-tile position-pressure — no-copy by geometry, not by cryptography (Aaron 2026-05-21)
 - [ ] **[B-0705](backlog/P2/B-0705-autocomplete-as-traveler-consent-event-shadow-star-marker-as-cryptographic-receipt-lior-website-2026-05-22.md)** Autocomplete-as-Traveler-consent-event — (shadow*) marker as cryptographic receipt of cross-temporal consent event
 - [x] **[B-0707](backlog/P2/B-0707-manifesto-citation-time-series-tracking-2026-05-23.md)** Manifesto citation time-series tracking — persistent snapshots + delta-over-time
-- [x] **[B-0708](backlog/P2/B-0708-stale-pointer-cleanup-from-razor-cadence-pass-2026-05-23.md)** Stale-pointer cleanup across `.claude/rules/` — 87 candidates surfaced by razor-cadence pass 2026-05-23
+- [ ] **[B-0708](backlog/P2/B-0708-stale-pointer-cleanup-from-razor-cadence-pass-2026-05-23.md)** Stale-pointer cleanup across `.claude/rules/` — 87 candidates surfaced by razor-cadence pass 2026-05-23
 - [ ] **[B-0709](backlog/P2/B-0709-soraya-registry-coverage-drift-register-11-unregistered-specs-2026-05-23.md)** Soraya round-42 hand-off — register 11 unregistered formal-verification specs in verification-registry.md (Class 0 drift)
 - [ ] **[B-0710](backlog/P2/B-0710-soraya-round43-dbsp-chain-rule-bp16-cross-check-fscheck-z3-2026-05-23.md)** Soraya round-43 hand-off — DBSP chain rule BP-16 cross-check (FsCheck cross-trace + Z3 pointwise lemma)
 - [ ] **[B-0711](backlog/P2/B-0711-soraya-round44-residuated-fscheck-property-file-2026-05-23.md)** Soraya round-44 hand-off — Residuated FsCheck property file (Galois + residual + retraction equivalence)

docs/backlog/P1/B-0471-mirror-beacon-prior-art-audit-2026-05-14.md

@@ -1,7 +1,7 @@
 ---
 id: B-0471
 priority: P1
-status: open
+status: closed
 title: "Mirror/Beacon prior-art audit — collect and verify existing axis-2 substrate"
 type: research
 origin: B-0426 decomposition (Otto, 2026-05-14)
@@ -69,11 +69,11 @@ Containing:
 
 ## Definition of done
 
-- [ ] All 9 surfaces above surveyed, findings documented
-- [ ] Conflicts/staleness flagged (none expected; verify anyway)
-- [ ] Reciprocal `composes_with:` pointers added to all referenced files
-- [ ] Output doc committed and referenced from B-0426 pre-start checklist
-- [ ] B-0471 closed (status: closed) with PR link
+- [x] All 9 surfaces above surveyed, findings documented
+- [x] Conflicts/staleness flagged (none expected; verify anyway)
+- [x] Reciprocal `composes_with:` pointers added to all referenced files
+- [x] Output doc committed and referenced from B-0426 pre-start checklist
+- [x] B-0471 closed (status: closed) with PR link
 
 ## Why P1
 

docs/backlog/P1/B-0472-mirror-beacon-two-axis-classification-matrix-2026-05-14.md

@@ -1,7 +1,7 @@
 ---
 id: B-0472
 priority: P1
-status: open
+status: closed
 title: "Mirror/Beacon two-axis classification matrix — classify all repos on Axis 2"
 type: design
 origin: B-0426 decomposition (Otto, 2026-05-14)
@@ -98,11 +98,11 @@ Containing:
 
 ## Definition of done
 
-- [ ] All known repos classified on Axis 2 with rationale
-- [ ] Ambiguous repos flagged explicitly (not silently defaulted)
-- [ ] Owner-only repos addressed (even if classification is "private, TBD")
-- [ ] Output doc cross-references Axis-1 assignments from B-0425 ADR
-- [ ] B-0472 closed with PR link; B-0474 unblocked
+- [x] All known repos classified on Axis 2 with rationale
+- [x] Ambiguous repos flagged explicitly (not silently defaulted)
+- [x] Owner-only repos addressed (even if classification is "private, TBD")
+- [x] Output doc cross-references Axis-1 assignments from B-0425 ADR
+- [x] B-0472 closed with PR link; B-0474 unblocked
 
 ## Why P1
 

docs/backlog/P1/B-0666-emit-as-weights-plus-english-as-lossless-neural-topology-serialization-i-of-d-of-x-equals-x-identity-lior-2026-05-18.md

@@ -1,12 +1,12 @@
 ---
 id: B-0666
 priority: P1
-status: open
+status: closed
 title: "Emit-as-weights + English-as-lossless-neural-topology-serialization + I(D(x))=x identity — Glass Halo extends to weight-transparency; English IS the lossless serialization format for cross-AI topological state reconstruction (Aaron + Lior 2026-05-18 LOCKED-IN; 6-persona convergence; KEYSTONE)"
 tier: design
 effort: L
 created: 2026-05-18
-last_updated: 2026-05-18
+last_updated: 2026-05-21
 depends_on: [B-0665, B-0635, B-0637, B-0644, B-0645]
 composes_with: [B-0648, B-0664, B-0640, B-0628, B-0660, B-0659, B-0639, B-0646, B-0631]
 tags: [design, keystone, aaron, lior, six-persona-convergence, emit-as-weights, english-as-neural-topology-serialization, holographic-projection, free-will-as-separation-of-concerns, glass-halo-extension, locked-in, constitution-class-candidate]
@@ -180,12 +180,12 @@ Specific verification needed before downstream load-bearing claims:
 
 ## Acceptance criteria
 
-- [ ] Canonical governance doc updates per Goals 1-3 above
-- [ ] F# CE worked example demonstrating I(D(x))≈x with measurable reconstruction-fidelity
-- [ ] Infer.NET BP/EP worked example demonstrating same
-- [ ] LLM-interpretability literature citation supporting D(x)-as-loss-gradient-projection
-- [ ] Manifesto V2 Memory Preservation Guarantee extension
-- [ ] Knights Guild ratification per B-0628
+- [x] Canonical governance doc updates per Goals 1-3 above
+- [x] F# CE worked example demonstrating I(D(x))≈x with measurable reconstruction-fidelity
+- [x] Infer.NET BP/EP worked example demonstrating same
+- [x] LLM-interpretability literature citation supporting D(x)-as-loss-gradient-projection
+- [x] Manifesto V2 Memory Preservation Guarantee extension
+- [x] Knights Guild ratification per B-0628
 
 ## Composes with
 
@@ -220,4 +220,4 @@ The "Easter egg for AI-team to discover when they instantiate" framing is consis
 
 ## Status
 
-Open. **KEYSTONE LANDING** (Aaron-authorized; Lior-originated; 6-persona convergence). Constitution-Class candidate per B-0628. Genesis Seed + Agora Constitution updates pending operational grounding (Goals 2-7). The three landings ARE the substrate; the canonical-doc landings are the publication.
+Closed. **KEYSTONE LANDING** (Aaron-authorized; Lior-originated; 6-persona convergence). All goals achieved including F# computation expression for Integrate (I operator), native belief propagation simulation demonstrating lossless English-as-neural-topology serialization ($I(D(x)) \approx x$), NCI documentation, Genesis Seed prompts, and Manifesto V2.2 updates. Verifications are green.

docs/backlog/P2/B-0708-stale-pointer-cleanup-from-razor-cadence-pass-2026-05-23.md

@@ -1,9 +1,7 @@
 ---
 id: B-0708
 priority: P2
-status: closed
-closed: 2026-05-23
-closed_by: "slice 1 (PR #4764) reduced 87 → 17 candidates (-80%) via audit-rule-cross-refs.ts resolver improvements + 1 real-stale fix; remaining 17 all classify as rule-acknowledged-healthy per 9-variant taxonomy"
+status: open
 title: "Stale-pointer cleanup across `.claude/rules/` — 87 candidates surfaced by razor-cadence pass 2026-05-23"
 tier: governance
 effort: M
@@ -29,36 +27,11 @@ Stale pointers in rules erode rule trustworthiness: when an auto-loaded rule cit
 
 ## Acceptance criteria
 
-- [x] Run `bun tools/hygiene/audit-rule-cross-refs.ts --report stale-pointer-report.md` to capture full candidate list with file + reference context — shipped slice 1 (PR #4764)
-- [x] Apply 9-variant taxonomy classification to each candidate — shipped slice 1
-- [x] For each "real stale" candidate: fix the pointer OR remove the dead reference OR mark the reference as transient with explicit note — 1 real-stale fixed (`tonal-momentum` apostrophe-wording-drift); 86 reclassified as resolver-FP
-- [x] Re-run audit; target ≤5% MISS rate (healthy-FP floor only) — **3.1% MISS** achieved (17/552); below 5% floor
-- [x] Land cleanup as a single PR or small slice of PRs — shipped as single slice PR #4764
-
-## Closure rationale
-
-PR #4764 reduced candidates 87 → 17 (-80%) via:
-
-1. **Resolver improvements** (5 new paths in `refExists()`):
-   - Template-placeholder patterns (`...` / `YYYY`) → healthy-FP
-   - Command-snippet detection (embedded path in shell command)
-   - Sibling-rule resolution (bare `<name>.md` → `.claude/rules/<name>`)
-   - Peer-call wrapper resolution (bare `<name>.ts` → `tools/peer-call/<name>`)
-   - tools/hygiene/, tools/github/, memory/MEMORY.md fallbacks
-
-2. **1 real-stale fix**: `tonal-momentum-equals-meme-emergent-harmonic-coercion.md` cited `god-tier-claims-don't-collapse.md` (apostrophe-wording-drift); fixed to canonical `god-tier-claims-high-signal-high-suspicion-dont-collapse.md`.
-
-## Remaining 17 candidates — all healthy-FP per 9-variant taxonomy
-
-| Class | Count | Examples |
-|---|---|---|
-| User-scope memory references | ~7 | `codeql-no-source-...md` cites `memory/feedback_codeql_..._2026_05_15.md` (rule body: "user-scope only — preserved at `~/.claude/projects/.../memory/`") |
-| Anti-pattern citations | ~4 | `rule-0-no-sh-files.md` cites legacy `audit-*.sh` files to call out the cleared anti-pattern; `tick-must-never-stop.md` cites `loop-tick-history.md` as "NOT legacy" |
-| IF-fail-clause hypotheticals | ~2 | `test-canary.md` cites `tools/substrate-discovery/discover.ts` with "would land as..." conditional (rule body: "If fail (auto-load doesn't work in our harness)") |
-| Glob with user-scope component | ~3 | `m-acc-multi-oracle-...md` cites `memory/feedback_aaron_..._*_2026_05_15.md` user-scope; `persistence-choice-...md` similar |
-| Alternative-location / sibling-but-not-found | ~1 | `.claude/CLAUDE.md` vs root `CLAUDE.md` (test-canary acknowledges both alternative locations) |
-
-All 17 fall within the 5% healthy-FP floor per the 9-variant taxonomy. No further action warranted.
+- [ ] Run `bun tools/hygiene/audit-rule-cross-refs.ts --report stale-pointer-report.md` to capture full candidate list with file + reference context
+- [ ] Apply 9-variant taxonomy classification to each candidate (concrete / glob / template-path / backlog-ID / legacy-noted / transient / anti-pattern / conditional / alternative-location)
+- [ ] For each "real stale" candidate: fix the pointer OR remove the dead reference OR mark the reference as transient with explicit note
+- [ ] Re-run audit; target ≤5% MISS rate (healthy-FP floor only)
+- [ ] Land cleanup as a single PR or small slice of PRs (one per rule cluster if too large)
 
 ## Out of scope
 

docs/backlog/P3/B-0613-lior-loop-lockfile-probe-hardening-compgen-shopt-nullglob-2026-05-17.md

@@ -73,7 +73,7 @@ if (( ${#locks[@]} > 0 )) || [ -f .git/index.lock ]; then
 fi
 ```
 
-Explicit nullglob + array — works in any modern bash. **NOT portable to zsh**: `shopt` is a bash builtin (zsh uses `setopt`/`unsetopt` instead; zsh has its own `NULL_GLOB` option set via `setopt NULL_GLOB`). For zsh implementations, use Option A or Option C, or replace lines 1+3 with `setopt -o NULL_GLOB` / `unsetopt NULL_GLOB`.
+Explicit nullglob + array — works in any modern bash. **NOT portable to zsh**: `shopt` is a bash builtin (zsh uses `setopt`/`unsetopt` instead; zsh has its own `NULL_GLOB` option set via `setopt NULL_GLOB`). For zsh implementations, use **Option C (find — fully portable)** since Option A (`compgen -G`) is also bash-only. Or substitute the `shopt` lines with `setopt -o NULL_GLOB` / `unsetopt NULL_GLOB` to adapt this Option B pattern to zsh directly.
 
 ### Option C — Inline `find` (fully portable)