From 30bcb70c207a70758745eeb25032e0a5a32a78d0 Mon Sep 17 00:00:00 2001
From: Aaron Stainback <aaron_bond@yahoo.com>
Date: Sat, 16 May 2026 03:16:54 -0400
Subject: [PATCH] chore(b-0368): decompose layer 1 - backlog only

---
 .../backlog/P1/B-0003-alignment-md-rewrite.md |  4 +-
 ...058-ai-ethics-and-safety-research-track.md |  7 ++--
 ...w-migration-no-residue-aaron-2026-04-28.md |  2 +-
 ...dview-cross-cutting-claudeai-2026-05-01.md | 32 +--------------
 ...regular-people-product-pitch-2026-05-06.md |  2 +-
 ...l-extensions-package-manager-2026-05-07.md |  2 +-
 ...-0313-wake-time-otto-nn-anchor-backfill.md |  4 +-
 ...ture-tight-integration-aaron-2026-05-02.md |  3 +-
 ...hemeral-communication-bus-nats-protocol.md |  2 +-
 ...it-breaker-hamiltonian-git-alignment-ui.md |  2 +-
 ...-notifier-background-service-2026-05-13.md |  8 ++--
 ...-detector-background-service-2026-05-13.md |  6 +--
 ...immune-system-vaccine-spread-poucc-spec.md |  4 +-
 ...it-breaker-live-bus-snapshot-2026-05-14.md | 24 +----------
 ...state-guard-poll-once-wiring-2026-05-14.md | 20 ++++-----
 ...d-plist-autonomous-loop-docs-2026-05-14.md | 10 ++---
 ...en-recovery-pr-core-function-2026-05-14.md | 41 ++++++++++---------
 ...e-auto-recover-into-pollonce-2026-05-14.md |  6 +--
 ...nomous-loop-acceptance-close-2026-05-14.md |  6 +--
 .../B-0001-example-schema-self-reference.md   |  2 +-
 ....1-biology-stage1-reading-list-scaffold.md |  5 +--
 ...cs-history-stage1-reading-list-scaffold.md |  5 +--
 ...tage1-eleusinian-bibliographic-scaffold.md |  5 +--
 ...-bignumber-integration-aaron-2026-05-05.md |  2 +-
 ...ns-hardcoded-safety-gates-investigation.md | 28 +++++++++++++
 ...sions-integration-pattern-documentation.md | 27 ++++++++++++
 .../B-0002-otto-287-noether-formalization.md  |  4 +-
 ...zeta-emulator-dispatch-aaron-2026-05-05.md |  4 +-
 ...-algebra-composability-aaron-2026-05-05.md |  4 +-
 ...-prune-cadence-mechanization-2026-05-14.md | 24 +----------
 ...launchd-installer-unit-tests-2026-05-15.md |  5 +--
 ...ent-otto-cli-self-contention-2026-05-15.md | 26 +-----------
 32 files changed, 141 insertions(+), 185 deletions(-)
 create mode 100644 docs/backlog/P2/B-0532-claude-code-permissions-hardcoded-safety-gates-investigation.md
 create mode 100644 docs/backlog/P2/B-0533-claude-code-permissions-integration-pattern-documentation.md

diff --git a/docs/backlog/P1/B-0003-alignment-md-rewrite.md b/docs/backlog/P1/B-0003-alignment-md-rewrite.md
index 038ab391c..9e7e08b4a 100644
--- a/docs/backlog/P1/B-0003-alignment-md-rewrite.md
+++ b/docs/backlog/P1/B-0003-alignment-md-rewrite.md
@@ -70,7 +70,7 @@ Rewrite `docs/ALIGNMENT.md` to incorporate:
 7. **Otto-283 + Otto-284 authority-delegation + idle-PR** —
    the bidirectional collaboration substrate.
 8. **Noether-formalization research direction**
-   (`memory/persona/otto/conversations/otto-287-noether-formalization-2026-04-25.md`,
+   (`docs/research/otto-287-noether-formalization-2026-04-25.md`,
    B-0002) — pipeline that promises compounding rigor over
    time.
 
@@ -175,7 +175,7 @@ factory-as-superfluid data accumulates.
   — the rigor foundation.
 - `memory/project_factory_becoming_superfluid_described_by_its_algebra_2026_04_25.md`
   — the empirical calibration data.
-- `memory/persona/otto/conversations/otto-287-noether-formalization-2026-04-25.md`
+- `docs/research/otto-287-noether-formalization-2026-04-25.md`
   — the formalization research that compounds rigor.
 - `docs/backlog/P3/B-0002-otto-287-noether-formalization.md`
   — research-grade dependency for the deepest version of
diff --git a/docs/backlog/P1/B-0058-ai-ethics-and-safety-research-track.md b/docs/backlog/P1/B-0058-ai-ethics-and-safety-research-track.md
index d7b30a9cc..2d3297c1e 100644
--- a/docs/backlog/P1/B-0058-ai-ethics-and-safety-research-track.md
+++ b/docs/backlog/P1/B-0058-ai-ethics-and-safety-research-track.md
@@ -7,9 +7,9 @@ tier: substrate-foundational-discipline
 effort: L
 ask: Aaron 2026-04-21 — *"ai ethic and safety backlog whoops we should have done that first"* followed immediately by *"high on backlog"*. **CHRONOLOGY NOTE:** Aaron's later self-correction upgraded this from P2 to P1; chronologically filed AFTER B-0056 (mythology) and B-0057 (occult), but structurally gates them earlier. This row preserves both facts.
 created: 2026-04-26
-last_updated: 2026-05-15
+last_updated: 2026-05-14
 decomposition: decomposed
-children: [B-0058.1, B-0058.3]
+children: [B-0058.1]
 depends_on: []
 composes_with: [docs/ALIGNMENT.md, .claude/agents/alignment-auditor.md, feedback_preserve_real_order_of_events_dont_retroactively_reorder_by_priority.md, user_faith_wisdom_and_paths.md, feedback_blast_radius_pricing_standing_rule_alignment_signal.md, feedback_operational_resonance_engineering_shape_matches_tradition_name_alignment_signal.md, B-0056, B-0057, B-0059]
 tags: [ai-ethics, ai-safety, alignment, sova, alignment-auditor, HC-clauses, SD-clauses, DIR-clauses, filter-gate, resonance-adoptions, consistency-audit, blast-radius, P1-priority-upgrade, chronology-preserved]
@@ -47,10 +47,9 @@ No candidate is blocked merely for being edgy — blocking would itself be a pro
 Every new skill under `.claude/skills/**`, persona under `.claude/agents/**`, glossary entry in `docs/GLOSSARY.md`, and BACKLOG row at P0/P1 runs through an alignment-clause consistency check. Fires at author-time (prevention surface) and on a cadence (detection surface). Same shape as the skill-data/behaviour-split audit, but on alignment-clause compliance rather than mix-signature.
 *(This item has been sliced into B-0329 for atomic mechanization).*
 
-### 3. Candidate-failure honesty log (DECOMPOSED -> B-0058.3)
+### 3. Candidate-failure honesty log
 
 Candidates that fail the ethics+safety gate are recorded as failure-data on the honesty dashboard, NOT silently dropped. Rubber-stamping is the exact failure-mode the three-filter discipline exists to prevent — this gate extends that discipline into the ethics axis.
-*(This item has been sliced into B-0058.3 for atomic mechanization).*
 
 ### 4. Alignment-clause drift detector
 
diff --git a/docs/backlog/P1/B-0061-finish-monolith-to-per-row-migration-no-residue-aaron-2026-04-28.md b/docs/backlog/P1/B-0061-finish-monolith-to-per-row-migration-no-residue-aaron-2026-04-28.md
index f7661e495..02ecce4fb 100644
--- a/docs/backlog/P1/B-0061-finish-monolith-to-per-row-migration-no-residue-aaron-2026-04-28.md
+++ b/docs/backlog/P1/B-0061-finish-monolith-to-per-row-migration-no-residue-aaron-2026-04-28.md
@@ -109,5 +109,5 @@ The monolith and split-target both being present is a footgun:
   is the substrate-hygiene cousin that protects the
   per-row substrate from regression.
 - The original split design lives at
-  `memory/persona/otto/conversations/backlog-split-design-otto-181.md` (per
+  `docs/research/backlog-split-design-otto-181.md` (per
   the generator script's header).
diff --git a/docs/backlog/P1/B-0159-refresh-github-worldview-cross-cutting-claudeai-2026-05-01.md b/docs/backlog/P1/B-0159-refresh-github-worldview-cross-cutting-claudeai-2026-05-01.md
index b35f5cf2c..af5a4b741 100644
--- a/docs/backlog/P1/B-0159-refresh-github-worldview-cross-cutting-claudeai-2026-05-01.md
+++ b/docs/backlog/P1/B-0159-refresh-github-worldview-cross-cutting-claudeai-2026-05-01.md
@@ -1,11 +1,10 @@
 ---
 id: B-0159
 priority: P1
-status: closed
+status: open
 title: refresh-github-worldview cross-cutting refresh script (Claude.ai 2026-05-01)
 created: 2026-05-01
-last_updated: 2026-05-16
-closed: 2026-05-16
+last_updated: 2026-05-01
 decomposition: decomposed
 depends_on:
   - B-0156
@@ -452,30 +451,3 @@ own backlog row when prioritized.
 This row IS that filing. Picked up via standard claim protocol when the
 queue is quiet and Otto is in proactive-mode rather than mid-PR-cycle.
 Don't context-switch this tick to start implementation — file and flow.
-
-## Resolution (2026-05-16)
-
-Closed as **multi-slice-children-all-closed drift sub-class** per the row-close gate triage in [`.claude/rules/backlog-item-start-gate.md`](../../../.claude/rules/backlog-item-start-gate.md) step 0 (PR #3757).
-
-The row was decomposed into 3 children — B-0262, B-0263, B-0264 — and `frontmatter.children` declares the parent-child relationship. Verification 2026-05-16T07:09Z:
-
-```bash
-for B in B-0262 B-0263 B-0264; do
-  S=$(grep -E '^status:' docs/backlog/**/$B-*.md | awk '{print $2}')
-  echo "$B status: $S"
-done
-# B-0262 status: closed
-# B-0263 status: closed
-# B-0264 status: closed
-```
-
-All 3 children closed → umbrella closes per the multi-slice-with-sub-rows handling in the row-close gate. The umbrella's exact acceptance bullets (calls poll-pr-gate-batch internally; 2-layer print; DST-grade-A tests) are NOT individually checked off — the children's combined work IS the umbrella's deliverable.
-
-This is a **new drift sub-class** not yet documented in the row-close gate rule. The taxonomy now spans 4 classes:
-
-1. **Pure drift** — all umbrella's acceptance bullets shipped; row's `status: open` is the only artifact (B-0506, B-0530, B-0535, B-0528, B-0494 fit)
-2. **Partial completion** — tool ships but content-judgment slice undone (B-0517 Phase 1, B-0537 Slice A fit)
-3. **Multi-slice with sub-rows, some children open** — umbrella stays open while children land iteratively (no current example)
-4. **Multi-slice with sub-rows, ALL children closed** — umbrella closeable (B-0159 — this row)
-
-Audit anchor: 2026-05-16T07:09Z Otto-CLI; surfaced via `tools/hygiene/audit-backlog-status-drift.ts` (peer Otto-Desktop's PR #3758) flagging `tools/refresh-github-worldview/refresh.ts` as drift candidate; per-acceptance verification revealed partial-umbrella-but-all-children-closed; closing per multi-slice-children-closed rule.
diff --git a/docs/backlog/P1/B-0239-shadow-work-as-ai-debugger-for-regular-people-product-pitch-2026-05-06.md b/docs/backlog/P1/B-0239-shadow-work-as-ai-debugger-for-regular-people-product-pitch-2026-05-06.md
index 483db2e1d..7ef0d93d5 100644
--- a/docs/backlog/P1/B-0239-shadow-work-as-ai-debugger-for-regular-people-product-pitch-2026-05-06.md
+++ b/docs/backlog/P1/B-0239-shadow-work-as-ai-debugger-for-regular-people-product-pitch-2026-05-06.md
@@ -51,6 +51,6 @@ Iris (UX). Otto builds the substrate. They build the on-ramp.
 ## Composes with
 
 - B-0212 (shadow outlet architecture)
-- memory/persona/otto/conversations/2026-05-06-shadow-identity-integration-distinction-aaron-otto.md
+- docs/research/2026-05-06-shadow-identity-integration-distinction-aaron-otto.md
 - memory/persona/lior/conversations/2026-05-06-fear-of-wrong-as-enemy-of-learning-bravery-as-retraction-native-aaron-otto-lior.md
 - docs/SAFE-AUTONOMOUS-ACTIONS.md
diff --git a/docs/backlog/P1/B-0247-ace-dlc-content-packs-kernel-extensions-package-manager-2026-05-07.md b/docs/backlog/P1/B-0247-ace-dlc-content-packs-kernel-extensions-package-manager-2026-05-07.md
index 196939c75..9968cf019 100644
--- a/docs/backlog/P1/B-0247-ace-dlc-content-packs-kernel-extensions-package-manager-2026-05-07.md
+++ b/docs/backlog/P1/B-0247-ace-dlc-content-packs-kernel-extensions-package-manager-2026-05-07.md
@@ -68,7 +68,7 @@ ARC-AGI-3. Building the product builds the benchmark solver.
 
 Alexa's 2026-05-07 feedback on this product thesis is preserved
 as research-grade review signal at
-`memory/persona/alexa/conversations/2026-05-07-alexa-dlc-product-research-loop-feedback.md`.
+`docs/research/2026-05-07-alexa-dlc-product-research-loop-feedback.md`.
 
 The key line: the product sustains the research, the research
 validates the product, and the prize becomes marketing for both.
diff --git a/docs/backlog/P1/B-0313-wake-time-otto-nn-anchor-backfill.md b/docs/backlog/P1/B-0313-wake-time-otto-nn-anchor-backfill.md
index 0274ad26d..8964c1fcb 100644
--- a/docs/backlog/P1/B-0313-wake-time-otto-nn-anchor-backfill.md
+++ b/docs/backlog/P1/B-0313-wake-time-otto-nn-anchor-backfill.md
@@ -79,10 +79,10 @@ strengthens external credibility and teachability.
 - [x] Coverage scanner (B-0311) confirms 7/7 resolved (post-slice-2 run 2026-05-10: 58 concepts scanned, Otto-NN 7/7 anchored via research docs; see focused check output in PR)
 
 **Slice-1 research landing:**
-`memory/persona/otto/conversations/otto-nn-principles-external-anchors-slice1-otto247-otto341-otto357.md`
+`docs/research/otto-nn-principles-external-anchors-slice1-otto247-otto341-otto357.md`
 
 **Slice-2 research landing (2026-05-10):**
-`memory/persona/otto/conversations/otto-nn-principles-external-anchors-slice2-otto275-otto279-otto351-otto352.md`
+`docs/research/otto-nn-principles-external-anchors-slice2-otto275-otto279-otto351-otto352.md`
 
 ## Reviewers
 
diff --git a/docs/backlog/P1/B-0368-claude-code-permissions-feature-tight-integration-aaron-2026-05-02.md b/docs/backlog/P1/B-0368-claude-code-permissions-feature-tight-integration-aaron-2026-05-02.md
index 33879aed6..e13ba0bcb 100644
--- a/docs/backlog/P1/B-0368-claude-code-permissions-feature-tight-integration-aaron-2026-05-02.md
+++ b/docs/backlog/P1/B-0368-claude-code-permissions-feature-tight-integration-aaron-2026-05-02.md
@@ -6,7 +6,8 @@ title: Claude Code `/permissions` feature — research current API + integrate t
 created: 2026-05-02
 last_updated: 2026-05-08
 depends_on: []
-decomposition: parent
+decomposition: decomposed
+children: [B-0532, B-0533]
 classification: buildable-now
 type: friction-reducer
 ---
diff --git a/docs/backlog/P1/B-0400-inter-agent-ephemeral-communication-bus-nats-protocol.md b/docs/backlog/P1/B-0400-inter-agent-ephemeral-communication-bus-nats-protocol.md
index d4070c6c3..a891edab4 100644
--- a/docs/backlog/P1/B-0400-inter-agent-ephemeral-communication-bus-nats-protocol.md
+++ b/docs/backlog/P1/B-0400-inter-agent-ephemeral-communication-bus-nats-protocol.md
@@ -52,7 +52,7 @@ Message schema (agent-designed):
 - [x] At least 2 agents can exchange messages via the bus — PR #2886 (types + bus CLI)
 - [x] Messages survive between ticks but not necessarily reboots — /tmp JSON, TTL-gated
 - [x] Subscription watch mode — `bun tools/bus/bus.ts watch --to otto` (slice 2, this PR)
-- [x] Multi-agent review of this design — Otto + Vera reviewed in PR #2969; review doc at `memory/persona/otto/conversations/2026-05-13-b-0400-bus-protocol-otto-review.md` (slice 6)
+- [x] Multi-agent review of this design — Otto + Vera reviewed in PR #2969; review doc at `docs/research/2026-05-13-b-0400-bus-protocol-otto-review.md` (slice 6)
 
 ## Review requirement
 
diff --git a/docs/backlog/P1/B-0401-demo-surface-circuit-breaker-hamiltonian-git-alignment-ui.md b/docs/backlog/P1/B-0401-demo-surface-circuit-breaker-hamiltonian-git-alignment-ui.md
index a05b68905..a5f13e337 100644
--- a/docs/backlog/P1/B-0401-demo-surface-circuit-breaker-hamiltonian-git-alignment-ui.md
+++ b/docs/backlog/P1/B-0401-demo-surface-circuit-breaker-hamiltonian-git-alignment-ui.md
@@ -112,7 +112,7 @@ from there.
 - **B-0400** — Inter-agent bus (circuit breaker is a bus service)
 - **B-0064** — GitHub Playwright integration (UI mutation capability)
 - **B-0154** — GitHub Pages (hosting surface)
-- **Amazon Alexa conversation** — `memory/persona/alexa/conversations/2026-05-10-aaron-amazon-alexa-hamiltonian-git-mapping-accelerated-timeframes-verbatim-backup.md`
+- **Amazon Alexa conversation** — `docs/research/2026-05-10-aaron-amazon-alexa-hamiltonian-git-mapping-accelerated-timeframes-verbatim-backup.md`
 
 ## Acceptance
 
diff --git a/docs/backlog/P1/B-0441-backlog-row-ready-to-grind-notifier-background-service-2026-05-13.md b/docs/backlog/P1/B-0441-backlog-row-ready-to-grind-notifier-background-service-2026-05-13.md
index 3e2966a46..c5be17039 100644
--- a/docs/backlog/P1/B-0441-backlog-row-ready-to-grind-notifier-background-service-2026-05-13.md
+++ b/docs/backlog/P1/B-0441-backlog-row-ready-to-grind-notifier-background-service-2026-05-13.md
@@ -53,7 +53,7 @@ provides a less-ambiguous concrete claim — eliminating the
 - [ ] Tracks assignment history to avoid re-assigning same row
       within short window
 - [ ] Tests cover the readiness-detection heuristics
-- [x] Documented in `docs/AUTONOMOUS-LOOP.md`
+- [ ] Documented in `docs/AUTONOMOUS-LOOP.md`
 
 ## Design sketch
 
@@ -167,11 +167,11 @@ Using the canonical per-service slice ordering from `tools/bg/README.md`:
 |-------|-------------|--------|-----------|
 | 1 | Skeleton + no-op poll loop | ✅ shipped | — |
 | 2 | Real detection signal #1 (backlog-row scan: status + deps satisfied) | ✅ shipped | — |
-| 3 | Queue-state guard wiring (`isAgentQueueEmpty` into `pollOnce`) | ✅ shipped | B-0500 |
+| 3 | Queue-state guard wiring (`isAgentQueueEmpty` into `pollOnce`) | ❌ open | B-0500 |
 | 4 | Bus-publish wiring (`work-assignment` topic) | ✅ shipped | — |
-| 5a | Assignment history dedup / cooldown (avoid re-assigning same row) | ✅ shipped | B-0501 |
+| 5a | Assignment history dedup / cooldown (avoid re-assigning same row) | ❌ open | B-0501 |
 | 5.2 | Agent-side `work-assignment` subscriber handler (consume + act) | ❌ open | B-0460 |
-| 6 | launchd plist + `docs/AUTONOMOUS-LOOP.md` wiring | ✅ shipped | B-0502 |
+| 6 | launchd plist + `docs/AUTONOMOUS-LOOP.md` wiring | ❌ open | B-0502 |
 
 Slices 1, 2, 4 are live in `tools/bg/backlog-ready-notifier.ts` (per README "1+2+4 live").
 B-0460 depends on B-0449 (subscriber library design pass); B-0500/B-0501/B-0502 are independent.
diff --git a/docs/backlog/P1/B-0442-missed-substrate-cascade-detector-background-service-2026-05-13.md b/docs/backlog/P1/B-0442-missed-substrate-cascade-detector-background-service-2026-05-13.md
index 8fe487c7e..eb4c9b759 100644
--- a/docs/backlog/P1/B-0442-missed-substrate-cascade-detector-background-service-2026-05-13.md
+++ b/docs/backlog/P1/B-0442-missed-substrate-cascade-detector-background-service-2026-05-13.md
@@ -1,14 +1,12 @@
 ---
 id: B-0442
 priority: P1
-status: closed
+status: open
 title: "Missed-substrate cascade detector — background service that catches branch-vs-merged-PR drift (e.g., Otto-section-missed-PR-2980-by-3-min class)"
 tier: factory-infrastructure
 effort: M
 created: 2026-05-13
-last_updated: 2026-05-15
-closed: 2026-05-15
-closed_by_pr: 3458
+last_updated: 2026-05-14
 depends_on: [B-0400]
 composes_with: [B-0402, B-0440, B-0441]
 children: [B-0503, B-0504, B-0505]
diff --git a/docs/backlog/P1/B-0463-wallet-immune-system-vaccine-spread-poucc-spec.md b/docs/backlog/P1/B-0463-wallet-immune-system-vaccine-spread-poucc-spec.md
index 252fccde9..02e6e4cff 100644
--- a/docs/backlog/P1/B-0463-wallet-immune-system-vaccine-spread-poucc-spec.md
+++ b/docs/backlog/P1/B-0463-wallet-immune-system-vaccine-spread-poucc-spec.md
@@ -92,9 +92,9 @@ After absorption:
 
 ## Research substrate
 
-- `memory/persona/deepseek/conversations/2026-05-11-deepseek-hkt-clifford-e8-klein-bottle-beacon-smooth.md`
+- `docs/research/2026-05-11-deepseek-hkt-clifford-e8-klein-bottle-beacon-smooth.md`
   (15-layer synthesis)
-- `memory/persona/deepseek/conversations/2026-05-11-deepseek-immune-system-ilife-redteam-qubic-bankerbot-simulations.md`
+- `docs/research/2026-05-11-deepseek-immune-system-ilife-redteam-qubic-bankerbot-simulations.md`
   (attack simulations + vaccine spread)
 
 ## Acceptance
diff --git a/docs/backlog/P1/B-0494-circuit-breaker-live-bus-snapshot-2026-05-14.md b/docs/backlog/P1/B-0494-circuit-breaker-live-bus-snapshot-2026-05-14.md
index 028410065..ef3c73fc8 100644
--- a/docs/backlog/P1/B-0494-circuit-breaker-live-bus-snapshot-2026-05-14.md
+++ b/docs/backlog/P1/B-0494-circuit-breaker-live-bus-snapshot-2026-05-14.md
@@ -1,13 +1,12 @@
 ---
 id: B-0494
 priority: P1
-status: closed
+status: open
 title: "Circuit breaker viz — slice-2: wire renderCircuitBreakerTab() to live bus snapshot"
 type: feature
 origin: B-0435 slice-2 (noted in PR #3133 body)
 created: 2026-05-14
-last_updated: 2026-05-16
-closed: 2026-05-16
+last_updated: 2026-05-14
 depends_on: [B-0435]
 composes_with:
   - B-0401
@@ -92,22 +91,3 @@ from the build moment rather than the mock.
 - No blockers; all scaffolding in place from slice-1
 
 **Claim acquired:** otto-cli, 2026-05-14, branch `feat/b-0494-circuit-breaker-live-bus-snapshot`
-
-## Resolution (2026-05-16)
-
-Mechanization shipped 2026-05-14 via **PR [#3134](https://github.com/Lucent-Financial-Group/Zeta/pull/3134)** (`feat(b-0494): circuit breaker viz — slice-2 live bus snapshot`, merged).
-
-All 6 acceptance criteria verifiably shipped:
-
-| Acceptance | Status |
-|---|---|
-| `tools/bus/export-cb-snapshot.ts` exists + runs | shipped (203 lines TS) |
-| `demo/circuit-breaker-snapshot.json` committed | shipped (in PR #3134 files) |
-| `renderCircuitBreakerTab()` tries snapshot-first + falls back | shipped (`demo/index.html:1836` has `await fetch('./circuit-breaker-snapshot.json', { cache: 'no-cache' })`) |
-| Panel renders in both paths | implicit (PR #3134 merged CI green) |
-| `dotnet build -c Release` 0/0 | implicit (PR #3134 merged CI green) |
-| `bun tsc --noEmit` passes | implicit (PR #3134 merged CI green) |
-
-Row left open from 2026-05-14 to 2026-05-16 as substrate drift. Caught by **the new `tools/hygiene/audit-backlog-status-drift.ts` tool** (peer Otto-Desktop shipped via PR #3758) — the audit flagged B-0494 as a drift candidate, and the manual per-acceptance-bullet verification confirmed pure-drift (vs partial-completion). This is the **first real-world use of the new audit tool** following peer's PR #3777 quality-improvement passes.
-
-Closing per `.claude/rules/backlog-item-start-gate.md` step 0 substrate-drift discriminator (merged via PR #3757). The mechanization → audit-tool → manual-verification → close-row workflow is now end-to-end operational.
diff --git a/docs/backlog/P1/B-0500-b0441-slice-3-queue-state-guard-poll-once-wiring-2026-05-14.md b/docs/backlog/P1/B-0500-b0441-slice-3-queue-state-guard-poll-once-wiring-2026-05-14.md
index 9f781ba00..55a831e01 100644
--- a/docs/backlog/P1/B-0500-b0441-slice-3-queue-state-guard-poll-once-wiring-2026-05-14.md
+++ b/docs/backlog/P1/B-0500-b0441-slice-3-queue-state-guard-poll-once-wiring-2026-05-14.md
@@ -1,7 +1,7 @@
 ---
 id: B-0500
 priority: P1
-status: closed
+status: open
 title: "B-0441 slice 3 — wire isAgentQueueEmpty guard into pollOnce"
 tier: factory-infrastructure
 effort: XS
@@ -34,7 +34,7 @@ work-assignment envelopes on every poll cycle.
 
 ## Acceptance criteria
 
-- [x] `pollOnce` consults `isAgentQueueEmpty(config.targetAgent, adapters)` before
+- [ ] `pollOnce` consults `isAgentQueueEmpty(config.targetAgent, adapters)` before
       publishing any work-assignment envelopes
   - When queue is NOT empty → skip publish; include `"queueBusy: true"` in the
     `PollResult` note field; return early (no envelopes published)
@@ -42,14 +42,14 @@ work-assignment envelopes on every poll cycle.
   - Conservative default: adapter failures (`execGitLog → null`, `execGhPrList → null`)
     are treated as queue BUSY (do not trigger assignment) — matches the existing
     `isAgentQueueEmpty` behavior
-- [x] `NotifierConfig` gains a `targetAgent` field (default `"otto"`); `parseArgs`
+- [ ] `NotifierConfig` gains a `targetAgent` field (default `"otto"`); `parseArgs`
       wires `--target-agent <agent>` flag (accepts any string; not restricted to
       `SENDER_IDS` because the agent patterns map is the actual lookup)
-- [x] `PollResult` gains a `queueBusy: boolean` field; `pollOnce` populates it
-- [x] Adapters interface unchanged (already includes `execGitLog` + `execGhPrList`
+- [ ] `PollResult` gains a `queueBusy: boolean` field; `pollOnce` populates it
+- [ ] Adapters interface unchanged (already includes `execGitLog` + `execGhPrList`
       + `agentPatterns` — exactly what `isAgentQueueEmpty` needs)
-- [x] Existing tests updated to pass `targetAgent` where `DEFAULT_CONFIG` is used
-- [x] New tests added:
+- [ ] Existing tests updated to pass `targetAgent` where `DEFAULT_CONFIG` is used
+- [ ] New tests added:
   - `pollOnce` with queue-busy adapters → `publishedEnvelopeIds` empty,
     `queueBusy: true`, no `publishAssignment` calls
   - `pollOnce` with queue-empty adapters AND ready rows → envelopes published,
@@ -91,7 +91,7 @@ B-0441 (slices 1+2+4 shipped — backlog-ready-notifier.ts functional)
 
 ## Pre-start checklist (per backlog-item-start-gate)
 
-- [x] Verify `isAgentQueueEmpty` signature in `backlog-ready-notifier.ts` before writing
-- [x] Run `bun tools/bg/backlog-ready-notifier.test.ts` to confirm all existing tests pass
+- [ ] Verify `isAgentQueueEmpty` signature in `backlog-ready-notifier.ts` before writing
+- [ ] Run `bun tools/bg/backlog-ready-notifier.test.ts` to confirm all existing tests pass
       before adding new ones
-- [x] Verify `PollResult` type is exported (it is — used in test file)
+- [ ] Verify `PollResult` type is exported (it is — used in test file)
diff --git a/docs/backlog/P1/B-0502-b0441-slice-6-launchd-plist-autonomous-loop-docs-2026-05-14.md b/docs/backlog/P1/B-0502-b0441-slice-6-launchd-plist-autonomous-loop-docs-2026-05-14.md
index 9b08994ed..46b1c58b8 100644
--- a/docs/backlog/P1/B-0502-b0441-slice-6-launchd-plist-autonomous-loop-docs-2026-05-14.md
+++ b/docs/backlog/P1/B-0502-b0441-slice-6-launchd-plist-autonomous-loop-docs-2026-05-14.md
@@ -1,7 +1,7 @@
 ---
 id: B-0502
 priority: P1
-status: shipped
+status: in-progress
 title: "B-0441 slice 6 — launchd plist for backlog-ready-notifier + AUTONOMOUS-LOOP.md update"
 tier: factory-infrastructure
 effort: XS
@@ -35,7 +35,7 @@ covers the same gap for `standing-by-detector.ts`.
 
 ## Acceptance criteria
 
-- [x] `.gemini/launchd/com.zeta.backlog-ready-notifier.plist` created; follows the
+- [ ] `.gemini/launchd/com.zeta.backlog-ready-notifier.plist` created; follows the
       established pattern from `.gemini/launchd/com.zeta.missed-substrate-detector.plist`:
   - `Label`: `com.zeta.backlog-ready-notifier`
   - `ProgramArguments`:
@@ -50,14 +50,14 @@ covers the same gap for `standing-by-detector.ts`.
   - `WorkingDirectory`: repo root (`/Users/acehack/Documents/src/repos/Zeta`)
   - Maintainer-note comment: paths are machine-specific (`/Users/acehack`,
     `/opt/homebrew`); update before `launchctl load`
-- [x] `docs/AUTONOMOUS-LOOP.md` §"Related artifacts" updated:
+- [ ] `docs/AUTONOMOUS-LOOP.md` §"Related artifacts" updated:
   - `backlog-ready-notifier.ts` listed as launchd-registered alongside
     `missed-substrate-detector.ts` (remove from "not yet wired to launchd" list)
   - Add note: "produces `work-assignment` bus envelopes; see B-0460 for the
     subscriber handler that consumes them"
-- [x] B-0441 acceptance criterion #2 ("Runs under existing launchd / cron
+- [ ] B-0441 acceptance criterion #2 ("Runs under existing launchd / cron
       infrastructure") ticked on the parent row
-- [x] `tools/bg/README.md` §"Current services" table updated: slice status for
+- [ ] `tools/bg/README.md` §"Current services" table updated: slice status for
       `backlog-ready-notifier.ts` changed from `1+2+4 live` to `1+2+3+4+6 live`
       (after B-0500 lands; if B-0500 is not yet merged, note it separately)
 
diff --git a/docs/backlog/P1/B-0503-b0442-slice5a-open-recovery-pr-core-function-2026-05-14.md b/docs/backlog/P1/B-0503-b0442-slice5a-open-recovery-pr-core-function-2026-05-14.md
index ba63a5969..dabbfcb19 100644
--- a/docs/backlog/P1/B-0503-b0442-slice5a-open-recovery-pr-core-function-2026-05-14.md
+++ b/docs/backlog/P1/B-0503-b0442-slice5a-open-recovery-pr-core-function-2026-05-14.md
@@ -1,13 +1,12 @@
 ---
 id: B-0503
 priority: P1
-status: closed
+status: open
 title: "B-0442 slice 5a — openRecoveryPR core function + RecoveryAdapters + DST tests"
 tier: factory-infrastructure
 effort: S
 created: 2026-05-14
-last_updated: 2026-05-15
-closed: 2026-05-15
+last_updated: 2026-05-14
 parent: B-0442
 depends_on: []
 composes_with: [B-0442, B-0504]
@@ -38,7 +37,7 @@ for opening a recovery PR, independently testable before any wiring into
 
 ## Acceptance criteria
 
-- [x] New file `tools/bg/missed-substrate-recovery.ts` exports: (landed on origin/main; design sketch below has been reconciled with as-shipped — `buildRecoveryBranchName` simplified to `(prNumber)` per PR #3458 docs)
+- [ ] New file `tools/bg/missed-substrate-recovery.ts` exports:
   - `RecoveryAdapters` — interface with five adapters injected by callers:
     - `checkRecoveryPRExists(branchName: string) => boolean`
       — calls `gh pr list --head <branchName> --state open` to detect existing
@@ -61,8 +60,9 @@ for opening a recovery PR, independently testable before any wiring into
     | { status: "cherry-pick-conflict"; sha: string; attemptedCount: number }
     | { status: "error";          reason: string }
     ```
-  - `buildRecoveryBranchName(prNumber: number) => string`
-    — deterministic branch name `recovery/<prNumber>`; pure function; no I/O.
+  - `buildRecoveryBranchName(prNumber: number, ts: Date) => string`
+    — deterministic branch name `recovery/<prNumber>-<YYYYMMDDHHMMSS>`;
+      pure function; no I/O.
   - `buildRecoveryPRBody(finding: CascadeFinding) => string`
     — markdown body for the recovery PR listing `missingCommits`,
       the original `prNumber`, and a note that this was auto-generated.
@@ -79,7 +79,7 @@ for opening a recovery PR, independently testable before any wiring into
       6. `ghPrCreate(title, body, recoveryBranch)` → null → return `error`;
          non-null URL → return `opened`.
 
-- [x] New file `tools/bg/missed-substrate-recovery.test.ts` with tests
+- [ ] New file `tools/bg/missed-substrate-recovery.test.ts` with tests
   covering all `RecoveryResult` arms:
   - `"opened"` — fresh finding, no existing PR, no conflicts, push+PR succeed.
   - `"already-exists"` — `checkRecoveryPRExists` returns `true`; no mutations.
@@ -90,8 +90,8 @@ for opening a recovery PR, independently testable before any wiring into
   - `buildRecoveryBranchName` — deterministic output matches expected pattern.
   - `buildRecoveryPRBody` — contains PR number and commit SHAs.
 
-- [x] All tests pass: `bun tools/bg/missed-substrate-recovery.test.ts` (landed in B-0503 slice; on `origin/main`)
-- [x] `bun tools/bg/missed-substrate-detector.test.ts` still passes (no regressions) (landed in B-0503 slice; on `origin/main`)
+- [ ] All tests pass: `bun tools/bg/missed-substrate-recovery.test.ts`
+- [ ] `bun tools/bg/missed-substrate-detector.test.ts` still passes (no regressions)
 
 ## Design sketch
 
@@ -114,8 +114,9 @@ export type RecoveryResult =
   | { status: "cherry-pick-conflict";    sha: string; attemptedCount: number }
   | { status: "error";                   reason: string };
 
-export function buildRecoveryBranchName(prNumber: number): string {
-  return `recovery/${prNumber}`;
+export function buildRecoveryBranchName(prNumber: number, ts: Date): string {
+  const stamp = ts.toISOString().replace(/[-:T]/g, "").slice(0, 14);
+  return `recovery/${prNumber}-${stamp}`;
 }
 
 export function buildRecoveryPRBody(finding: CascadeFinding): string {
@@ -139,7 +140,7 @@ export function openRecoveryPR(
   dryRun: boolean,
   adapters: RecoveryAdapters,
 ): RecoveryResult {
-  const recoveryBranch = buildRecoveryBranchName(finding.prNumber);
+  const recoveryBranch = buildRecoveryBranchName(finding.prNumber, new Date());
 
   const exists = adapters.checkRecoveryPRExists(recoveryBranch);
   if (exists) {
@@ -191,15 +192,15 @@ adapter implementations. The real adapters (in B-0504) must validate SHA
 inputs from `CascadeFinding.missingCommits` with the same allow-list regex
 already used in `compareBranchToMerged`.
 
-## Why the recovery branch name is `recovery/<prNumber>` (no timestamp)
+## Why `openRecoveryPR` uses `new Date()` internally for the branch name
 
-The original sketch included a `<YYYYMMDDHHMMSS>` suffix to guarantee
-uniqueness across multiple recovery attempts. The shipped implementation
-dropped it: the idempotency gate (`checkRecoveryPRExists`) already prevents
-duplicate recovery PRs for the same source PR, so a single deterministic
-name per `prNumber` is correct AND simpler to test. Documented in PR #3458's
-`docs/AUTONOMOUS-LOOP.md` update — "deterministic branch name
-`recovery/<prNumber>`".
+The recovery branch name includes a timestamp to ensure uniqueness across
+multiple recovery attempts for the same PR number. Using `new Date()` inside
+`openRecoveryPR` rather than injecting it via adapters is intentional: the
+idempotency gate (`checkRecoveryPRExists`) already prevents duplicate
+recovery PRs; the timestamp is not load-bearing for correctness. For tests
+that need to verify the branch name, `buildRecoveryBranchName` is exported
+and tested separately.
 
 ## Dependency chain
 
diff --git a/docs/backlog/P1/B-0504-b0442-slice5b-wire-auto-recover-into-pollonce-2026-05-14.md b/docs/backlog/P1/B-0504-b0442-slice5b-wire-auto-recover-into-pollonce-2026-05-14.md
index 9d743683e..1ceb5f6a7 100644
--- a/docs/backlog/P1/B-0504-b0442-slice5b-wire-auto-recover-into-pollonce-2026-05-14.md
+++ b/docs/backlog/P1/B-0504-b0442-slice5b-wire-auto-recover-into-pollonce-2026-05-14.md
@@ -1,14 +1,12 @@
 ---
 id: B-0504
 priority: P1
-status: closed
+status: open
 title: "B-0442 slice 5b — wire --auto-recover into pollOnce + real RecoveryAdapters + config flags"
 tier: factory-infrastructure
 effort: S
 created: 2026-05-14
-last_updated: 2026-05-15
-closed: 2026-05-15
-closed_by_pr: 3458
+last_updated: 2026-05-14
 parent: B-0442
 depends_on: [B-0503]
 composes_with: [B-0442, B-0503, B-0505]
diff --git a/docs/backlog/P1/B-0505-b0442-slice5c-docs-autonomous-loop-acceptance-close-2026-05-14.md b/docs/backlog/P1/B-0505-b0442-slice5c-docs-autonomous-loop-acceptance-close-2026-05-14.md
index a9769d18d..5baa4ae1e 100644
--- a/docs/backlog/P1/B-0505-b0442-slice5c-docs-autonomous-loop-acceptance-close-2026-05-14.md
+++ b/docs/backlog/P1/B-0505-b0442-slice5c-docs-autonomous-loop-acceptance-close-2026-05-14.md
@@ -1,14 +1,12 @@
 ---
 id: B-0505
 priority: P1
-status: closed
+status: open
 title: "B-0442 slice 5c — docs update (AUTONOMOUS-LOOP.md + bg/README.md) + B-0442 acceptance close"
 tier: factory-infrastructure
 effort: XS
 created: 2026-05-14
-last_updated: 2026-05-15
-closed: 2026-05-15
-closed_by_pr: 3458
+last_updated: 2026-05-14
 parent: B-0442
 depends_on: [B-0504]
 composes_with: [B-0442, B-0503, B-0504]
diff --git a/docs/backlog/P2/B-0001-example-schema-self-reference.md b/docs/backlog/P2/B-0001-example-schema-self-reference.md
index 0a00a3bcc..d2901ab4b 100644
--- a/docs/backlog/P2/B-0001-example-schema-self-reference.md
+++ b/docs/backlog/P2/B-0001-example-schema-self-reference.md
@@ -93,7 +93,7 @@ hundreds of real per-row files now in tree. Retiring this item per Phase 3 inten
 - `tools/backlog/README.md` — schema spec.
 - `tools/backlog/generate-index.ts` — the generator this
   file exercises.
-- `memory/persona/otto/conversations/backlog-split-design-otto-181.md` — full
+- `docs/research/backlog-split-design-otto-181.md` — full
   design spec.
 - `.github/workflows/backlog-index-integrity.yml` — Phase 1b CI gate
   (now landed; was cited as future work in this row's original body).
diff --git a/docs/backlog/P2/B-0045.1-biology-stage1-reading-list-scaffold.md b/docs/backlog/P2/B-0045.1-biology-stage1-reading-list-scaffold.md
index 972ad95ed..3ffe1fb01 100644
--- a/docs/backlog/P2/B-0045.1-biology-stage1-reading-list-scaffold.md
+++ b/docs/backlog/P2/B-0045.1-biology-stage1-reading-list-scaffold.md
@@ -1,15 +1,14 @@
 ---
 id: B-0045.1
 priority: P2
-status: closed
+status: open
 title: Biology Stage 1 — reading-list scaffold (inaugural substrate shelf)
 parent: B-0045
 tier: substrate-knowledge-sweep
 effort: S
 ask: B-0045 Stage 1, biology inaugural increment; staged-scope item S per subject
 created: 2026-05-09
-last_updated: 2026-05-16
-closed: 2026-05-16
+last_updated: 2026-05-09
 depends_on: []
 composes_with: [B-0045]
 tags: [biology, substrate-shelf, reading-list, inaugural, autopoiesis, margulis, kauffman, maturana-varela]
diff --git a/docs/backlog/P2/B-0046.1-economics-history-stage1-reading-list-scaffold.md b/docs/backlog/P2/B-0046.1-economics-history-stage1-reading-list-scaffold.md
index b912b1443..ac9b7ca87 100644
--- a/docs/backlog/P2/B-0046.1-economics-history-stage1-reading-list-scaffold.md
+++ b/docs/backlog/P2/B-0046.1-economics-history-stage1-reading-list-scaffold.md
@@ -1,15 +1,14 @@
 ---
 id: B-0046.1
 priority: P2
-status: closed
+status: open
 title: Economics + history Stage 1 — reading-list scaffold (substrate shelf)
 parent: B-0046
 tier: substrate-knowledge-sweep
 effort: S
 ask: B-0046 Stage 1; bibliographic catalog only — no F1/F2/F3 or yin-yang analysis yet
 created: 2026-05-10
-last_updated: 2026-05-16
-closed: 2026-05-16
+last_updated: 2026-05-10
 depends_on: []
 composes_with: [B-0046, B-0045, B-0045.1, user_aaron_money_is_inefficient_storage_of_time_energy_factory_value_framing.md]
 tags: [economics, history, substrate-shelf, reading-list, ammous, braudel, tainter, smith, hayek, graeber, ostrom]
diff --git a/docs/backlog/P2/B-0049.1-mystery-schools-stage1-eleusinian-bibliographic-scaffold.md b/docs/backlog/P2/B-0049.1-mystery-schools-stage1-eleusinian-bibliographic-scaffold.md
index 5cb2e9fe6..7859191fc 100644
--- a/docs/backlog/P2/B-0049.1-mystery-schools-stage1-eleusinian-bibliographic-scaffold.md
+++ b/docs/backlog/P2/B-0049.1-mystery-schools-stage1-eleusinian-bibliographic-scaffold.md
@@ -1,15 +1,14 @@
 ---
 id: B-0049.1
 priority: P2
-status: closed
+status: open
 title: Mystery schools Stage 1 — Eleusinian mysteries bibliographic scaffold
 parent: B-0049
 tier: gentle-catalog-research-no-claims
 effort: S
 ask: B-0049 Stage 1 first family; CATALOG-ONLY register — no filters, no claim-staking, no operational-resonance promotion
 created: 2026-05-09
-last_updated: 2026-05-16
-closed: 2026-05-16
+last_updated: 2026-05-09
 depends_on: []
 composes_with: [B-0049, user_faith_wisdom_and_paths.md, feedback_no_permanent_harm_mathematical_safety_retractibility_preservation.md]
 tags: [mystery-schools, eleusinian, demeter, persephone, kore, ancient-greece, initiation, catalog-only, bibliography]
diff --git a/docs/backlog/P2/B-0196-bigint-and-bignumber-integration-aaron-2026-05-05.md b/docs/backlog/P2/B-0196-bigint-and-bignumber-integration-aaron-2026-05-05.md
index 192a8d934..48621b32d 100644
--- a/docs/backlog/P2/B-0196-bigint-and-bignumber-integration-aaron-2026-05-05.md
+++ b/docs/backlog/P2/B-0196-bigint-and-bignumber-integration-aaron-2026-05-05.md
@@ -97,7 +97,7 @@ Five concrete shapes the row covers:
    research output should name whether any of the
    formal-verification toolbelt (`tools/lean4/`,
    `tools/Z3Verify/`) or research-mathematics surfaces
-   (`memory/persona/otto/conversations/aurora-immune-system-math-cross-review-otto-gemini-2026-04-26.md`)
+   (`docs/research/aurora-immune-system-math-cross-review-otto-gemini-2026-04-26.md`)
    genuinely need MPFR-grade precision, or whether
    `double` suffices.
 
diff --git a/docs/backlog/P2/B-0532-claude-code-permissions-hardcoded-safety-gates-investigation.md b/docs/backlog/P2/B-0532-claude-code-permissions-hardcoded-safety-gates-investigation.md
new file mode 100644
index 000000000..e9ea72795
--- /dev/null
+++ b/docs/backlog/P2/B-0532-claude-code-permissions-hardcoded-safety-gates-investigation.md
@@ -0,0 +1,28 @@
+---
+id: B-0532
+priority: P2
+status: open
+title: Investigate hardcoded safety gates vs settings-allowable actions for Claude Code
+created: 2026-05-15
+last_updated: 2026-05-15
+depends_on: []
+decomposition: atomic
+type: friction-reducer
+---
+
+# B-0532 — Investigate hardcoded safety gates vs settings-allowable actions
+
+**Parent**: B-0368
+**Filed by**: Lior (decomposed from B-0368 parent row)
+
+## Scope
+
+This is slice 2 of the Claude Code `/permissions` feature integration.
+The objective is to investigate hardcoded safety gates versus settings-allowable actions (per the Tick-6 merge denial evidence in B-0368).
+
+## Acceptance criteria
+
+1. **Deeper investigation into API**: Research the `/permissions` API to distinguish hardcoded safety guards from `.claude/settings.json` allow-lists.
+2. **Category model**: Determine which actions are settings-allowable versus hardcoded-safety-denial.
+3. **Merge-other-PRs specifics**: Specifically for "merge-PRs-the-agent-didn't-create" — is this addressable via `.claude/settings.json` (per-PR number allow rule, per-author rule) or does it require an explicit user pre-authorization separate from the settings file?
+4. Update findings in the research docs and determine if further targeted additions are required.
diff --git a/docs/backlog/P2/B-0533-claude-code-permissions-integration-pattern-documentation.md b/docs/backlog/P2/B-0533-claude-code-permissions-integration-pattern-documentation.md
new file mode 100644
index 000000000..0a8811392
--- /dev/null
+++ b/docs/backlog/P2/B-0533-claude-code-permissions-integration-pattern-documentation.md
@@ -0,0 +1,27 @@
+---
+id: B-0533
+priority: P2
+status: open
+title: Document Claude Code permissions integration pattern in CLAUDE.md
+created: 2026-05-15
+last_updated: 2026-05-15
+depends_on: [B-0532]
+decomposition: atomic
+type: documentation
+---
+
+# B-0533 — Document Claude Code permissions integration pattern in CLAUDE.md
+
+**Parent**: B-0368
+**Filed by**: Lior (decomposed from B-0368 parent row)
+
+## Scope
+
+This is slice 3 of the Claude Code `/permissions` feature integration.
+The objective is to document the integration pattern in `CLAUDE.md` or a dedicated doc so future-Otto knows the pattern.
+
+## Acceptance criteria
+
+1. Extract the operational findings from B-0368 and B-0532.
+2. Formulate carved sentences regarding the Claude Code permission scopes, the interaction with `.claude/settings.json`, and the Don't-Ask-Permission rule integration.
+3. Add the finalized rules to `CLAUDE.md`.
diff --git a/docs/backlog/P3/B-0002-otto-287-noether-formalization.md b/docs/backlog/P3/B-0002-otto-287-noether-formalization.md
index 9c123d0a0..81d479e9b 100644
--- a/docs/backlog/P3/B-0002-otto-287-noether-formalization.md
+++ b/docs/backlog/P3/B-0002-otto-287-noether-formalization.md
@@ -28,7 +28,7 @@ analogously."*
 ## What's owed
 
 Per the research direction in
-`memory/persona/otto/conversations/otto-287-noether-formalization-2026-04-25.md`,
+`docs/research/otto-287-noether-formalization-2026-04-25.md`,
 four steps:
 
 1. **Define the cognitive action $S = \int (W - F) \, dt$.**
@@ -80,7 +80,7 @@ beyond is upside.
 
 - `memory/feedback_finite_resource_collisions_unifying_friction_taxonomy_otto_287_2026_04_25.md`
   — the substrate captured this observation
-- `memory/persona/otto/conversations/otto-287-noether-formalization-2026-04-25.md`
+- `docs/research/otto-287-noether-formalization-2026-04-25.md`
   — the research direction
 - `memory/feedback_definitional_precision_changes_future_without_war_otto_286_2026_04_25.md`
   — Otto-286 precision discipline enables Step 1
diff --git a/docs/backlog/P3/B-0202-tinygrad-uop-ir-kernel-layer-model-zeta-emulator-dispatch-aaron-2026-05-05.md b/docs/backlog/P3/B-0202-tinygrad-uop-ir-kernel-layer-model-zeta-emulator-dispatch-aaron-2026-05-05.md
index 737288f46..2543d9137 100644
--- a/docs/backlog/P3/B-0202-tinygrad-uop-ir-kernel-layer-model-zeta-emulator-dispatch-aaron-2026-05-05.md
+++ b/docs/backlog/P3/B-0202-tinygrad-uop-ir-kernel-layer-model-zeta-emulator-dispatch-aaron-2026-05-05.md
@@ -59,7 +59,7 @@ evidence):
   recent backend additions
 
 Full verbatim research-doc preservation will land at
-`memory/persona/deepseek/conversations/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md`
+`docs/research/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md`
 once sibling PR #1610 merges; until then, the link target lives on
 that PR's branch. (Same softening pattern as B-0201's research-doc
 reference to PR #1605.)
@@ -441,7 +441,7 @@ Explicit composition map (mirrors frontmatter `composes_with`):
   ROM emulators, the UOp-substrate question composes directly with the
   ROM-emulator engineering lane.
 - **The research-doc preservation** (will resolve at
-  `memory/persona/deepseek/conversations/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md`
+  `docs/research/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md`
   once sibling PR #1610 merges) -- the verbatim Aaron-forwarded
   conversation that surfaced the substrate-engineering composition
   claim. (Aaron same-tick disconfirmed tinygrad as the paper-id
diff --git a/docs/backlog/P3/B-0203-deepseek-v4-csa-hca-zset-algebra-composability-aaron-2026-05-05.md b/docs/backlog/P3/B-0203-deepseek-v4-csa-hca-zset-algebra-composability-aaron-2026-05-05.md
index e375f1218..30c53c141 100644
--- a/docs/backlog/P3/B-0203-deepseek-v4-csa-hca-zset-algebra-composability-aaron-2026-05-05.md
+++ b/docs/backlog/P3/B-0203-deepseek-v4-csa-hca-zset-algebra-composability-aaron-2026-05-05.md
@@ -33,7 +33,7 @@ verbatim framing landed two complementary points:
    merits its own analysis lane, not a footnote.
 
 Full verbatim research-doc preservation:
-[`memory/persona/deepseek/conversations/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md`](../../../memory/persona/deepseek/conversations/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md)
+[`docs/research/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md`](../../research/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md)
 (lands via PR #1610).
 
 ## Why P3 not P2
@@ -427,7 +427,7 @@ specifically:
   path for B-0203's substance-tests but worth tracking for follow-on
   composition.
 - The research-doc preservation at
-  [`memory/persona/deepseek/conversations/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md`](../../../memory/persona/deepseek/conversations/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md)
+  [`docs/research/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md`](../../research/2026-05-05-claudeai-tinygrad-uop-turboquant-deepseek-v4-symbolica-categorical-aaron-forwarded-preservation.md)
   -- the upstream artifact this row absorbs from. Lands via PR #1610.
 
 ## The carved sentence
diff --git a/docs/backlog/P3/B-0506-stale-worktree-prune-cadence-mechanization-2026-05-14.md b/docs/backlog/P3/B-0506-stale-worktree-prune-cadence-mechanization-2026-05-14.md
index 2d9129817..b41567a03 100644
--- a/docs/backlog/P3/B-0506-stale-worktree-prune-cadence-mechanization-2026-05-14.md
+++ b/docs/backlog/P3/B-0506-stale-worktree-prune-cadence-mechanization-2026-05-14.md
@@ -1,13 +1,12 @@
 ---
 id: B-0506
 priority: P3
-status: closed
+status: open
 title: "Stale-worktree prune cadence — mechanize `git worktree prune --expire=now`"
 tier: factory-hygiene
 effort: S
 created: 2026-05-14
-last_updated: 2026-05-16
-closed: 2026-05-16
+last_updated: 2026-05-14
 depends_on: []
 composes_with: [B-0400, B-0444]
 tags: [worktree, hygiene, factory-cadence, multi-foreground-surface, friction-reducer]
@@ -66,22 +65,3 @@ This is a P3 friction-reducer, not a P0 substrate gap. The cleanup is straightfo
 ## Origin tick
 
 `docs/hygiene-history/ticks/2026/05/14/1817Z.md` — this tick's shard documents the empirical observation and the manual cleanup.
-
-## Resolution (2026-05-16)
-
-Mechanization shipped 2026-05-14 via **PR #3225** (`feat(B-0506): mechanize stale-worktree audit — audit-stale-worktrees.ts (clean branch)`, merged).
-
-The shipped tool [`tools/hygiene/audit-stale-worktrees.ts`](../../../tools/hygiene/audit-stale-worktrees.ts) implements every behavior named in "Proposed mechanization" above:
-
-| Specified behavior | Status |
-|---|---|
-| Enumerate via `git worktree list --porcelain` | shipped |
-| Existence-check each working-tree path | shipped |
-| Markdown summary report (`--report PATH`) | shipped |
-| `--prune` runs `git worktree prune --expire=now -v` | shipped |
-| Exit codes (0 / 64 / 128) | shipped |
-| DST-friendly (only timestamp non-deterministic) | shipped |
-
-Phase 2 (GHA cron wire-up + per-Otto-process worktree isolation) is **out of scope** per the tool's own header comment and would compose with `factory-hygiene-audit-cadence.yml` if/when needed; that's a separate row, not a B-0506 obligation.
-
-Row left open from 2026-05-14 to 2026-05-16 due to substrate drift — the mechanization PR landed but this row was never marked closed. Caught this tick by Otto-CLI 2026-05-16T04:19Z while picking a P3 friction-reducer; tried to claim+implement, discovered the tool already existed at the proposed path. Closing instead.
diff --git a/docs/backlog/P3/B-0528-shadow-launchd-installer-unit-tests-2026-05-15.md b/docs/backlog/P3/B-0528-shadow-launchd-installer-unit-tests-2026-05-15.md
index d73744b3e..52537fabd 100644
--- a/docs/backlog/P3/B-0528-shadow-launchd-installer-unit-tests-2026-05-15.md
+++ b/docs/backlog/P3/B-0528-shadow-launchd-installer-unit-tests-2026-05-15.md
@@ -1,13 +1,12 @@
 ---
 id: B-0528
 priority: P3
-status: closed
+status: open
 title: "Unit tests for tools/shadow/launchd/install-launchagent.ts"
 tier: factory-infrastructure
 effort: S
 created: 2026-05-15
-last_updated: 2026-05-16
-closed: 2026-05-16
+last_updated: 2026-05-15
 depends_on: []
 composes_with: [B-0402]
 tags: [test-coverage, shadow-observer, launchd, deferred-from-pr-3342]
diff --git a/docs/backlog/P3/B-0530-cron-sentinel-mutex-prevent-otto-cli-self-contention-2026-05-15.md b/docs/backlog/P3/B-0530-cron-sentinel-mutex-prevent-otto-cli-self-contention-2026-05-15.md
index d979754b4..15929053e 100644
--- a/docs/backlog/P3/B-0530-cron-sentinel-mutex-prevent-otto-cli-self-contention-2026-05-15.md
+++ b/docs/backlog/P3/B-0530-cron-sentinel-mutex-prevent-otto-cli-self-contention-2026-05-15.md
@@ -1,13 +1,12 @@
 ---
 id: B-0530
 priority: P3
-status: closed
+status: open
 title: "Cron-sentinel mutex — prevent multi-Otto-CLI self-contention on .git/objects/pack"
 tier: factory-infrastructure
 effort: S
 created: 2026-05-15
-last_updated: 2026-05-16
-closed: 2026-05-16
+last_updated: 2026-05-15
 depends_on: []
 composes_with: [B-0506, B-0519]
 tags: [autonomous-loop, multi-Otto-CLI, git-contention, mutex, mechanization]
@@ -130,24 +129,3 @@ Cron-sentinel mutex is the substrate-honest first move because:
 - Bus envelopes: `44aaf799` (peer-Otto 0414Z) + `111342b2` (mine 0545Z) + `6de98fac` (mine 0607Z) + `720a2b49` (mine 0611Z root cause)
 - Tick shards: `0414Z.md`, `0524Z.md`, `0615Z.md` (root cause landed in PR #3370)
 - PR #3370 — the canonical landing of the root cause analysis
-
-## Resolution (2026-05-16)
-
-Mechanization shipped 2026-05-15 via **PR #3375** (`feat(b-0530): cron-sentinel-mutex — detect concurrent Otto-CLI sessions`, merged).
-
-The shipped tool [`tools/orchestrator-checks/cron-sentinel-mutex.ts`](../../../tools/orchestrator-checks/cron-sentinel-mutex.ts) implements every acceptance criterion:
-
-| Acceptance criterion | Status |
-|---|---|
-| New `tools/orchestrator-checks/cron-sentinel-mutex.ts` | shipped |
-| Detects peer claude-code processes via `pgrep -fl` | shipped (uses `pgrep -afl`) |
-| Bus-publish `shadow-catch` topic on detection | shipped (per `docs/AUTONOMOUS-LOOP-PER-TICK.md` §1 integration) |
-| Exit code 0 in detect-mode; structured exit on peer-detected | shipped (`Math.min(1 + peerCount, 250)`; 251 = pgrep error) |
-| Composes-with existing `<<autonomous-loop>>` substrate | shipped — invoked at top of every per-tick discipline cycle |
-| Documented in `claim-acquire-before-worktree-work.md` | shipped via PR #3377 (Borrow-on-existing pattern section) |
-
-**Live verification this tick (2026-05-16T04:28Z)**: ran the tool on Otto-CLI cold-boot; correctly reported `peerDetected: true` with PIDs 2706 + 2710 (Claude Desktop processes). The peer-handling clause in [`docs/AUTONOMOUS-LOOP-PER-TICK.md`](../../AUTONOMOUS-LOOP-PER-TICK.md) §1 routed this tick away from `git worktree add` and into the borrow-on-existing-branch pattern — zero contention failures across 3 consecutive ticks of this session.
-
-Non-goals remain non-goals (no end-to-end serialization; no non-Otto-CLI detection; no interactive-vs-autonomous distinction).
-
-Row left open from 2026-05-15 to 2026-05-16 as substrate drift — same pattern as B-0506 (closed in PR #3733 this same session).