chore(b-0368): decompose layer 1 - backlog only

[AceHack]

Decomposed from PR #3545. Peeling off the backlog changes into an atomic PR.

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Restore valid research links in backlog rows

This change rewires references from memory/persona/... to docs/research/..., but the new targets are not present in the repository (for example, docs/research/otto-287-noether-formalization-2026-04-25.md is missing while the previous memory path exists). That leaves dead substrate links in backlog items and makes cited evidence unreachable for review/audit workflows; either migrate/create the referenced research files in the same commit or keep the existing paths until that migration lands.

Useful? React with 👍 / 👎.

[chatgpt-codex-connector]

Keep parent children list in sync with child row

This removes B-0058.3 from B-0058's children list, but docs/backlog/P1/B-0058.3-candidate-failure-honesty-log.md still declares parent: B-0058. That creates a parent/child graph inconsistency that can hide unfinished slices from tooling that relies on declared children for status/closure checks, so the edge should be either preserved in both directions or removed in both directions.

Useful? React with 👍 / 👎.

[Copilot]

Pull request overview

This PR is a backlog-only change set that decomposes B-0368 into two child backlog rows (B-0532/B-0533) and then applies broad metadata/link edits across many existing backlog rows (status flips, last_updated edits, and path rewrites from memory/persona/... to docs/research/...).

Changes:

• Add new P2 child rows B-0532 and B-0533 and wire them as children of B-0368.
• Reopen multiple previously-closed backlog rows and delete their “Resolution” sections.
• Rewrite many backlog-row cross-references from memory/persona/... to docs/research/....

Reviewed changes

Copilot reviewed 32 out of 32 changed files in this pull request and generated 31 comments.

Show a summary per file

File	Description
docs/backlog/P3/B-0530-cron-sentinel-mutex-prevent-otto-cli-self-contention-2026-05-15.md	Reopens row and removes resolution section; updates frontmatter.
docs/backlog/P3/B-0528-shadow-launchd-installer-unit-tests-2026-05-15.md	Reopens row; updates frontmatter.
docs/backlog/P3/B-0506-stale-worktree-prune-cadence-mechanization-2026-05-14.md	Reopens row and removes resolution section; updates frontmatter.
docs/backlog/P3/B-0203-deepseek-v4-csa-hca-zset-algebra-composability-aaron-2026-05-05.md	Updates research-doc link target paths.
docs/backlog/P3/B-0202-tinygrad-uop-ir-kernel-layer-model-zeta-emulator-dispatch-aaron-2026-05-05.md	Updates research-doc link target paths.
docs/backlog/P3/B-0002-otto-287-noether-formalization.md	Updates research-doc link target paths.
docs/backlog/P2/B-0533-claude-code-permissions-integration-pattern-documentation.md	Adds new child row for documenting Claude Code /permissions integration pattern.
docs/backlog/P2/B-0532-claude-code-permissions-hardcoded-safety-gates-investigation.md	Adds new child row for investigating hardcoded vs settings-allowable permission gates.
docs/backlog/P2/B-0196-bigint-and-bignumber-integration-aaron-2026-05-05.md	Updates research-doc link target path.
docs/backlog/P2/B-0049.1-mystery-schools-stage1-eleusinian-bibliographic-scaffold.md	Reopens row; adjusts last_updated.
docs/backlog/P2/B-0046.1-economics-history-stage1-reading-list-scaffold.md	Reopens row; adjusts last_updated.
docs/backlog/P2/B-0045.1-biology-stage1-reading-list-scaffold.md	Reopens row; adjusts last_updated.
docs/backlog/P2/B-0001-example-schema-self-reference.md	Updates design-spec link target path.
docs/backlog/P1/B-0505-b0442-slice5c-docs-autonomous-loop-acceptance-close-2026-05-14.md	Reopens row; adjusts last_updated and closure metadata.
docs/backlog/P1/B-0504-b0442-slice5b-wire-auto-recover-into-pollonce-2026-05-14.md	Reopens row; adjusts last_updated and closure metadata.
docs/backlog/P1/B-0503-b0442-slice5a-open-recovery-pr-core-function-2026-05-14.md	Reopens row; rewrites acceptance criteria + design sketch; adjusts last_updated.
docs/backlog/P1/B-0502-b0441-slice-6-launchd-plist-autonomous-loop-docs-2026-05-14.md	Changes row status and resets acceptance checklist items.
docs/backlog/P1/B-0500-b0441-slice-3-queue-state-guard-poll-once-wiring-2026-05-14.md	Reopens row and resets acceptance checklist items.
docs/backlog/P1/B-0494-circuit-breaker-live-bus-snapshot-2026-05-14.md	Reopens row and removes resolution section; adjusts last_updated.
docs/backlog/P1/B-0463-wallet-immune-system-vaccine-spread-poucc-spec.md	Updates research-doc link target paths.
docs/backlog/P1/B-0442-missed-substrate-cascade-detector-background-service-2026-05-13.md	Reopens row; adjusts last_updated and closure metadata.
docs/backlog/P1/B-0441-backlog-row-ready-to-grind-notifier-background-service-2026-05-13.md	Resets acceptance markers + slice status table for the notifier service.
docs/backlog/P1/B-0401-demo-surface-circuit-breaker-hamiltonian-git-alignment-ui.md	Updates Alexa-conversation reference path.
docs/backlog/P1/B-0400-inter-agent-ephemeral-communication-bus-nats-protocol.md	Updates multi-agent review doc reference path.
docs/backlog/P1/B-0368-claude-code-permissions-feature-tight-integration-aaron-2026-05-02.md	Marks row decomposed and adds children list for B-0532/B-0533.
docs/backlog/P1/B-0313-wake-time-otto-nn-anchor-backfill.md	Updates slice research landing paths.
docs/backlog/P1/B-0247-ace-dlc-content-packs-kernel-extensions-package-manager-2026-05-07.md	Updates Alexa-feedback reference path.
docs/backlog/P1/B-0239-shadow-work-as-ai-debugger-for-regular-people-product-pitch-2026-05-06.md	Updates shadow-identity research reference path.
docs/backlog/P1/B-0159-refresh-github-worldview-cross-cutting-claudeai-2026-05-01.md	Reopens row and removes resolution section; adjusts last_updated.
docs/backlog/P1/B-0061-finish-monolith-to-per-row-migration-no-residue-aaron-2026-04-28.md	Updates design-spec reference path.
docs/backlog/P1/B-0058-ai-ethics-and-safety-research-track.md	Updates children list and edits section text; adjusts last_updated.
docs/backlog/P1/B-0003-alignment-md-rewrite.md	Updates Otto-287 research reference paths.

Comments suppressed due to low confidence (15)

docs/backlog/P3/B-0530-cron-sentinel-mutex-prevent-otto-cli-self-contention-2026-05-15.md:10

• last_updated was set to 2026-05-15, but this row is being edited in this PR. Per tools/backlog/README.md (last_updated is updated on every content edit), please bump last_updated to the date of this change instead of regressing it.
  docs/backlog/P3/B-0528-shadow-launchd-installer-unit-tests-2026-05-15.md:10
• last_updated was regressed to 2026-05-15, but this row is being modified in this PR. tools/backlog/README.md requires updating last_updated on every content edit—please bump it to the date of this edit.
  docs/backlog/P3/B-0506-stale-worktree-prune-cadence-mechanization-2026-05-14.md:10
• last_updated was regressed to 2026-05-14 even though the row is edited in this PR. Please update last_updated to reflect this edit (required by tools/backlog/README.md).

title: "Stale-worktree prune cadence — mechanize `git worktree prune --expire=now`"
tier: factory-hygiene
effort: S
created: 2026-05-14
last_updated: 2026-05-14
depends_on: []

docs/backlog/P3/B-0203-deepseek-v4-csa-hca-zset-algebra-composability-aaron-2026-05-05.md:431

• This second reference to docs/research/...tinygrad-uop...md also points to a non-existent file in docs/research/ on this branch. Please update it to the actual location (currently under memory/persona/deepseek/conversations/...) or add the missing doc so the link resolves.

  composition.
- The research-doc preservation at
  [`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.

docs/backlog/P3/B-0202-tinygrad-uop-ir-kernel-layer-model-zeta-emulator-dispatch-aaron-2026-05-05.md:445

• This later reference to docs/research/...tinygrad-uop...md is also broken because the target file isn’t in docs/research/ on this branch. Please update it to the actual existing path (currently under memory/persona/deepseek/conversations/...) or add the missing doc.

  ROM emulators, the UOp-substrate question composes directly with the
  ROM-emulator engineering lane.
- **The research-doc preservation** (will resolve at
  `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

docs/backlog/P3/B-0002-otto-287-noether-formalization.md:84

• This second reference to docs/research/otto-287-noether-formalization-2026-04-25.md is also broken because the target file doesn’t exist under docs/research/ on this branch. Please update it to the current location under memory/persona/otto/conversations/... (or add the missing doc).

- `memory/feedback_finite_resource_collisions_unifying_friction_taxonomy_otto_287_2026_04_25.md`
  — the substrate captured this observation
- `docs/research/otto-287-noether-formalization-2026-04-25.md`
  — the research direction

docs/backlog/P1/B-0313-wake-time-otto-nn-anchor-backfill.md:86

• This slice-2 research landing was updated to a docs/research/... path, but that file does not exist in docs/research/ on this branch. The slice docs exist under memory/persona/otto/conversations/ (e.g., otto-nn-principles-external-anchors-slice2-otto275-otto279-otto351-otto352.md). Please link to the existing location or add the missing research doc.

**Slice-2 research landing (2026-05-10):**
`docs/research/otto-nn-principles-external-anchors-slice2-otto275-otto279-otto351-otto352.md`

docs/backlog/P1/B-0463-wallet-immune-system-vaccine-spread-poucc-spec.md:98

• This second DeepSeek reference was also changed to a docs/research/... path, but the target file is not present in docs/research/ on this branch. The referenced artifact exists at memory/persona/deepseek/conversations/2026-05-11-deepseek-immune-system-ilife-redteam-qubic-bankerbot-simulations.md; please update the link accordingly (or add the missing research doc).

- `docs/research/2026-05-11-deepseek-hkt-clifford-e8-klein-bottle-beacon-smooth.md`
  (15-layer synthesis)
- `docs/research/2026-05-11-deepseek-immune-system-ilife-redteam-qubic-bankerbot-simulations.md`
  (attack simulations + vaccine spread)

docs/backlog/P1/B-0003-alignment-md-rewrite.md:179

• This second reference to docs/research/otto-287-noether-formalization-2026-04-25.md is also broken because the target file isn’t in docs/research/ on this branch. Please update it to the existing location under memory/persona/otto/conversations/... (or add the missing research doc).

  — the rigor foundation.
- `memory/project_factory_becoming_superfluid_described_by_its_algebra_2026_04_25.md`
  — the empirical calibration data.
- `docs/research/otto-287-noether-formalization-2026-04-25.md`
  — the formalization research that compounds rigor.

docs/backlog/P1/B-0500-b0441-slice-3-queue-state-guard-poll-once-wiring-2026-05-14.md:8

• This row was changed from closed → open and its acceptance checklist was reset, but the described behavior appears to already be implemented (tools/bg/backlog-ready-notifier.ts calls isAgentQueueEmpty(config.targetAgent, ...) and uses a targetAgent field). Reopening the row will make generated backlog views inaccurate unless the code is also being rolled back.

---
id: B-0500
priority: P1
status: open
title: "B-0441 slice 3 — wire isAgentQueueEmpty guard into pollOnce"
tier: factory-infrastructure
effort: XS
created: 2026-05-14

docs/backlog/P1/B-0502-b0441-slice-6-launchd-plist-autonomous-loop-docs-2026-05-14.md:8

• This row’s status was changed from shipped to in-progress and the acceptance checklist was reset, but the launchd plist exists at .gemini/launchd/com.zeta.backlog-ready-notifier.plist. Unless this PR also removes/invalidates that artifact, the backlog row should remain consistent with what’s already in-tree.

---
id: B-0502
priority: P1
status: in-progress
title: "B-0441 slice 6 — launchd plist for backlog-ready-notifier + AUTONOMOUS-LOOP.md update"
tier: factory-infrastructure
effort: XS
created: 2026-05-14

docs/backlog/P1/B-0503-b0442-slice5a-open-recovery-pr-core-function-2026-05-14.md:66

• The acceptance criteria + design sketch were changed to require buildRecoveryBranchName(prNumber, ts) and timestamped branch names, but the shipped implementation in tools/bg/missed-substrate-recovery.ts exports buildRecoveryBranchName(prNumber) and documents that determinism is load-bearing. Please keep this backlog row consistent with the current code, or include the corresponding code changes in the same PR so the spec and implementation don’t diverge.

    | { status: "error";          reason: string }
    ```
  - `buildRecoveryBranchName(prNumber: number, ts: Date) => string`
    — deterministic branch name `recovery/<prNumber>-<YYYYMMDDHHMMSS>`;
      pure function; no I/O.
  - `buildRecoveryPRBody(finding: CascadeFinding) => string`

docs/backlog/P1/B-0503-b0442-slice5a-open-recovery-pr-core-function-2026-05-14.md:145

• The design sketch now calls buildRecoveryBranchName(finding.prNumber, new Date()), which makes openRecoveryPR non-deterministic; the current implementation in tools/bg/missed-substrate-recovery.ts uses a deterministic branch name and relies on it for idempotency. If you really want timestamped names, the idempotency strategy in the shipped code/docs will need to be updated together (otherwise this row will mis-spec what’s actually deployed).

  finding: CascadeFinding,
  dryRun: boolean,
  adapters: RecoveryAdapters,
): RecoveryResult {
  const recoveryBranch = buildRecoveryBranchName(finding.prNumber, new Date());

  const exists = adapters.checkRecoveryPRExists(recoveryBranch);

docs/backlog/P1/B-0503-b0442-slice5a-open-recovery-pr-core-function-2026-05-14.md:203

• This explanatory section now says the timestamp is “not load-bearing for correctness,” but the shipped implementation’s comments explicitly treat determinism as load-bearing for the idempotency gate. Please reconcile the explanation with the actual implementation (or update the code to match this new rationale).

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 `openRecoveryPR` uses `new Date()` internally for the branch name

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.

docs/backlog/P1/B-0504-b0442-slice5b-wire-auto-recover-into-pollonce-2026-05-14.md:10

• last_updated was regressed to 2026-05-14 even though this row is being edited in this PR. Per tools/backlog/README.md, please bump last_updated to the date of this edit.

tier: factory-infrastructure
effort: S
created: 2026-05-14
last_updated: 2026-05-14
parent: B-0442

[AceHack]

Maji (Node 4) Entropy Reduction: This PR is a massive blob (32 files). It violates atomic PR constraints. I am unable to decompose it at this moment due to a stale .git/index.lock blocking local worktree operations. Decomposition will commence once the lock clears. Do not merge.