From 8772db75649145bc5dc7a71cf5d1050def503c3f Mon Sep 17 00:00:00 2001 From: Lior Date: Thu, 28 May 2026 13:40:42 -0400 Subject: [PATCH] docs(archive): Preserve merged PRs 5892, 5891, 5890, 5878, 5877 --- ...table-route-map-for-github-pages-b-0302.md | 38 ++++++++ ...giene-parse-env-option-shebang-operands.md | 91 +++++++++++++++++++ ...00-emulator-generate-join-over-emulator.md | 61 +++++++++++++ ...s-substrate-as-controller-variant-for-b.md | 68 ++++++++++++++ ...wer-superorganism-perez-ding-2025-compl.md | 80 ++++++++++++++++ 5 files changed, 338 insertions(+) create mode 100644 docs/pr-discussions/PR-5877-docs-site-create-stable-route-map-for-github-pages-b-0302.md create mode 100644 docs/pr-discussions/PR-5878-fix-hygiene-parse-env-option-shebang-operands.md create mode 100644 docs/pr-discussions/PR-5890-feat-b-0924-custom-2600-emulator-generate-join-over-emulator.md create mode 100644 docs/pr-discussions/PR-5891-feat-b-0925-c-elegans-substrate-as-controller-variant-for-b.md create mode 100644 docs/pr-discussions/PR-5892-research-c-elegans-tower-superorganism-perez-ding-2025-compl.md diff --git a/docs/pr-discussions/PR-5877-docs-site-create-stable-route-map-for-github-pages-b-0302.md b/docs/pr-discussions/PR-5877-docs-site-create-stable-route-map-for-github-pages-b-0302.md new file mode 100644 index 0000000000..8375dc04b1 --- /dev/null +++ b/docs/pr-discussions/PR-5877-docs-site-create-stable-route-map-for-github-pages-b-0302.md @@ -0,0 +1,38 @@ +--- +pr_number: 5877 +title: "docs(site): Create stable route map for GitHub Pages (B-0302)" +author: "AceHack" +state: "MERGED" +created_at: "2026-05-28T16:50:58Z" +merged_at: "2026-05-28T17:08:06Z" +closed_at: "2026-05-28T17:08:06Z" +head_ref: "lior/B-0302-pages-routes" +base_ref: "main" +archived_at: "2026-05-28T17:40:42Z" +archive_tool: "tools/pr-preservation/archive-pr.ts" +--- + +# PR #5877: docs(site): Create stable route map for GitHub Pages (B-0302) + +## PR description + +This PR implements backlog item B-0302 by creating the stable URL route map for the GitHub Pages site. This file defines the URL structure before indexing begins. + +## Reviews + +### COMMENTED — @copilot-pull-request-reviewer (2026-05-28T16:53:44Z) + +## Pull request overview + +This PR adds a single new documentation file, `docs/site/routes.md`, establishing the frozen URL route map for the planned Zeta GitHub Pages site per backlog item B-0302. It defines five core public routes (root, vision, alignment, glossary, contributing) mapped to existing source documents, calls out the future `/research/` route as deferred to B-0304, and states the URL scheme is frozen before indexing without an accompanying redirect strategy. + +**Changes:** +- Adds a new `docs/site/routes.md` route-map document with policy preamble, core routes table, and deferred-routes table. +- Establishes pre-indexing URL freeze policy with explicit redirect-required clause for any future changes. +- Calls out `/research/` as deferred and tied to B-0304 as prerequisite. + +## General comments + +### @chatgpt-codex-connector (2026-05-28T16:51:02Z) + +You have reached your Codex usage limits for code reviews. You can see your limits in the [Codex usage dashboard](https://chatgpt.com/codex/cloud/settings/usage). diff --git a/docs/pr-discussions/PR-5878-fix-hygiene-parse-env-option-shebang-operands.md b/docs/pr-discussions/PR-5878-fix-hygiene-parse-env-option-shebang-operands.md new file mode 100644 index 0000000000..859d4a8d24 --- /dev/null +++ b/docs/pr-discussions/PR-5878-fix-hygiene-parse-env-option-shebang-operands.md @@ -0,0 +1,91 @@ +--- +pr_number: 5878 +title: "fix(hygiene): parse env option shebang operands" +author: "AceHack" +state: "MERGED" +created_at: "2026-05-28T16:51:56Z" +merged_at: "2026-05-28T17:02:07Z" +closed_at: "2026-05-28T17:02:07Z" +head_ref: "claim/codex-loop-bash-retirement-env-option-shebang-20260528" +base_ref: "main" +archived_at: "2026-05-28T17:40:41Z" +archive_tool: "tools/pr-preservation/archive-pr.ts" +--- + +# PR #5878: fix(hygiene): parse env option shebang operands + +## PR description + +## Summary + +- skips operand-bearing `env` options before selecting the shebang command +- covers `env -u NAME`, `env --unset NAME`, `env -P PATH`, `env --chdir DIR`, and `env -a ARG` before shell-family commands +- commits the Codex claim file for the background-service pickup + +## Tests + +- `bun test tools/hygiene/check-bash-retirement-inventory.test.ts` +- `bun tools/hygiene/check-bash-retirement-inventory.ts --enforce` +- `tsc --noEmit -p tsconfig.json` blocked locally: isolated worktree lacked `node_modules`; shared install then failed on unrelated missing `@nats-io/*` dependencies; `bun install --frozen-lockfile` is rejected by local Bun 1.0.11 lockfile mismatch. + +Agency-Signature-Version: 1 +Agent: Vera +Agent-Runtime: OpenAI Codex heartbeat +Agent-Model: GPT-5 +Credential-Identity: AceHack +Credential-Mode: shared +Human-Review: none +Human-Review-Evidence: none +Action-Mode: autonomous-fail-open +Task: none + +## Reviews + +### COMMENTED — @copilot-pull-request-reviewer (2026-05-28T16:54:11Z) + +## Pull request overview + +Updates the bash-retirement hygiene tool’s `env` shebang parsing so `#!/usr/bin/env ...` lines that include operand-bearing `env` options still correctly identify the underlying shell interpreter, keeping the repo’s “retained shell surface” inventory accurate. + +**Changes:** +- Teach `parseEnvCommand` to skip `env` options that consume a following operand (and `--opt=value` forms) before selecting the command. +- Add regression coverage for `env -a/-P/-u/--unset/--chdir` shebang variants in the hygiene tests. +- Add a Codex claim file describing the work scope (but currently not released/slugged per protocol). + +### Reviewed changes + +Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments. + +| File | Description | +| ---- | ----------- | +| tools/hygiene/check-bash-retirement-inventory.ts | Extend `env` shebang parsing to skip operand-bearing `env` options before command selection. | +| tools/hygiene/check-bash-retirement-inventory.test.ts | Add test fixtures asserting `env` option+operand shebangs are classified correctly. | +| docs/claims/codex-loop-bash-retirement-env-option-shebang-20260528.md | Adds a live claim record for this work (needs protocol compliance before merge). | + +## Review threads + +### Thread 1: docs/claims/codex-loop-bash-retirement-env-option-shebang-20260528.md:9 (resolved) + +**@copilot-pull-request-reviewer** (2026-05-28T16:54:10Z): + +P1: This claim file appears intended as a live claim, but the slug does not follow the documented slug rules (must be `backlog-`, `bug-`, `issue-`, or `task-`). As written (`codex-loop-bash-retirement-env-option-shebang-20260528`), it violates `docs/AGENT-CLAIM-PROTOCOL.md` §“Slug rules” (around lines 290-306). Rename the claim (and file/heading) to a valid slug (e.g. `task-bash-retirement-env-option-shebang-20260528`) or tie it to an existing backlog/issue ID. + +### Thread 2: docs/claims/codex-loop-bash-retirement-env-option-shebang-20260528.md:7 (resolved) + +**@copilot-pull-request-reviewer** (2026-05-28T16:54:11Z): + +P1: Claim files are required to be released (deleted) in the same PR that lands the work; otherwise `docs/claims/` accumulates stale “live” claims on `main`. This PR adds a claim file but does not include the release step (`git rm docs/claims/.md`), which conflicts with `docs/AGENT-CLAIM-PROTOCOL.md` TL;DR step 5 and `docs/claims/README.md`. Add a release commit that deletes this claim file before merge (or keep the claim only on a pushed `claim/` branch and omit it from the PR). + +## General comments + +### @chatgpt-codex-connector (2026-05-28T16:52:01Z) + +You have reached your Codex usage limits for code reviews. You can see your limits in the [Codex usage dashboard](https://chatgpt.com/codex/cloud/settings/usage). + +### @AceHack (2026-05-28T16:56:25Z) + +Vera review-fix update: pushed `039e8ea03` to release the live claim file from the PR diff, addressing the two claim-protocol review comments. + +Focused checks rerun after the removal: +- `bun test tools/hygiene/check-bash-retirement-inventory.test.ts` +- `bun tools/hygiene/check-bash-retirement-inventory.ts --enforce` diff --git a/docs/pr-discussions/PR-5890-feat-b-0924-custom-2600-emulator-generate-join-over-emulator.md b/docs/pr-discussions/PR-5890-feat-b-0924-custom-2600-emulator-generate-join-over-emulator.md new file mode 100644 index 0000000000..c3b60d71ea --- /dev/null +++ b/docs/pr-discussions/PR-5890-feat-b-0924-custom-2600-emulator-generate-join-over-emulator.md @@ -0,0 +1,61 @@ +--- +pr_number: 5890 +title: "feat(B-0924): custom 2600 emulator + generate+join over emulator scene + IScheduler DST bit-perfect-consensus + B-0917 hardware interrupts + ARC3-AGI (operator 2026-05-28)" +author: "AceHack" +state: "MERGED" +created_at: "2026-05-28T17:18:58Z" +merged_at: "2026-05-28T17:20:56Z" +closed_at: "2026-05-28T17:20:56Z" +head_ref: "otto-cli/b0924-emulator-generate-join-2600-arc3-2026-05-28" +base_ref: "main" +archived_at: "2026-05-28T17:40:40Z" +archive_tool: "tools/pr-preservation/archive-pr.ts" +--- + +# PR #5890: feat(B-0924): custom 2600 emulator + generate+join over emulator scene + IScheduler DST bit-perfect-consensus + B-0917 hardware interrupts + ARC3-AGI (operator 2026-05-28) + +## PR description + +Substrate-engineering substrate-target row per operator 2026-05-28 `(shadow*)` authorization: `file the backlog row (shadow*)`. + +## Substrate-engineering substrate-target + +Three composing operational targets: + +1. **Custom Atari 2600 emulator** — minimal-substrate starting point (TIA + RIOT + 6507; small state-space tractable for full-fidelity DST + z-sets) +2. **Generate+Join over emulator scene** (vs imitation-learning) — substrate-shift: DST seed + z-set join for consensus instead of training-data pattern-copy +3. **IScheduler DST bit-perfect-consensus test** — multiple emulator instances under DST agree on game-state evolution; consensus = bit-perfect-substrate test + +## Composes-with + +- **B-0917** (today's Kleisli interrupt substrate; hardware interrupts VBlank / WSYNC / cartridge-IRQ map cleanly to IntrCtx) +- **B-0865** (parent: ARC-AGI-3-style benchmark; this extends emulator-as-substrate scope) +- **B-0761** (Zeta cluster as ARC-AGI training reference) +- **B-0052, B-0053** (retractable-emulators design + emulator-ideas absorption clean-room) +- **B-0202** (tinygrad-uop-ir kernel layer emulator dispatch) +- **B-0867** (workflow-engine substrate) +- **B-0703** (multi-oracle BFT consensus → multi-instance bit-perfect-test) +- **B-0904** (GitHub-as-free-accelerator; emulator generation+join can run as GitHub Actions substrate) + +Plus framework rule composition: +- DST-omniscience (PR #5841), pilot-wave-MWI (PR #5842), Cayley-Dickson canonical-form (PR #5843), particle-as-locus (PR #5846), Clifford-underwater (PR #5850), asymmetric-authorship + monad-propagation + OPLE-T-TFeedback + function-as-control-flow-generator + algebra-owner z-sets skill substrate + +## Operator framing (verbatim) + +> *"we are buding our own emulaters starting with 2600 to train for ARC3-AGI benchmark and also test our consensus is bit perfect IScheduler DST by testing emulators in zsets, i was worried it was going to be terrible but we can simulate interrupts maybe we could go full generte+join on the emlator scene instead of trying to copy patterns that are there just ideas."* + +The substrate that worried operator IS now substrate-engineering-substrate-engineering substrate via today's B-0917 landing. + +## Substrate-honest scope + +Substrate-engineering substrate-target row; not single-PR shipping target. Provides substrate-anchor for future implementation (custom F# 2600 emulator + B-0917 IntrCtx integration + IScheduler DST harness + z-set game-state representation + generate+join scaffolding + smallest-scope deterministic-boot test). + +Cooperative-emulator gaming substrate-target (operator-Otto coop play once USB cluster + GitHub accelerator ship) composes per the cognitive-profile user-memory extension. + +🤖 Generated with [Claude Code](https://claude.com/claude-code) + +## General comments + +### @chatgpt-codex-connector (2026-05-28T17:19:04Z) + +You have reached your Codex usage limits for code reviews. You can see your limits in the [Codex usage dashboard](https://chatgpt.com/codex/cloud/settings/usage). diff --git a/docs/pr-discussions/PR-5891-feat-b-0925-c-elegans-substrate-as-controller-variant-for-b.md b/docs/pr-discussions/PR-5891-feat-b-0925-c-elegans-substrate-as-controller-variant-for-b.md new file mode 100644 index 0000000000..ef50f4c43d --- /dev/null +++ b/docs/pr-discussions/PR-5891-feat-b-0925-c-elegans-substrate-as-controller-variant-for-b.md @@ -0,0 +1,68 @@ +--- +pr_number: 5891 +title: "feat(B-0925): C. elegans-substrate as controller variant for B-0924 \u2014 OpenWorm 302-neuron connectome + generate+join + DST-omniscience + mirror-tier research (operator 2026-05-28)" +author: "AceHack" +state: "MERGED" +created_at: "2026-05-28T17:23:32Z" +merged_at: "2026-05-28T17:26:07Z" +closed_at: "2026-05-28T17:26:07Z" +head_ref: "otto-cli/b0925-celegans-controller-b0924-2026-05-28" +base_ref: "main" +archived_at: "2026-05-28T17:40:39Z" +archive_tool: "tools/pr-preservation/archive-pr.ts" +--- + +# PR #5891: feat(B-0925): C. elegans-substrate as controller variant for B-0924 — OpenWorm 302-neuron connectome + generate+join + DST-omniscience + mirror-tier research (operator 2026-05-28) + +## PR description + +Substrate-engineering substrate-target row per operator 2026-05-28 `(shadow*) mirror it too` authorization. + +## Substrate-engineering substrate-target + +C. elegans-substrate as controller variant for B-0924 (custom 2600 emulator + generate+join + DST + z-sets). + +## Substrate-rhyme + +Both substrates fit the SAME tractability class — small-enough for full-fidelity DST + z-set + generate+join scaffolding: + +| Substrate | State-space | Tractability | +|---|---|---| +| Atari 2600 (B-0924) | 256-byte RAM + TIA + PIA + 6507 | Full state-space enumerable from boot-seed | +| C. elegans (B-0925) | 302 neurons + ~7000 synapses + complete connectome (Cook et al. 2019) | OpenWorm c302 bit-perfect-simulatable | + +## Operator framing (verbatim) + +> *"i bet it maps to and this dude could beat both of us at ti Caenorhabditis elegans"* +> *"file as B-0925 (shadow*) mirror it too"* +> *"damn we gonna emulate a worm playing atari games thats fucking next level"* + +## What ships + +1. **Backlog row** B-0925 (composes with B-0924 + B-0917 + B-0865 + B-0761 + B-0202 + B-0703) +2. **Mirror-tier research note** `docs/research/2026-05-28-c-elegans-substrate-rhyme-...md` per "mirror it too" directive (substrate-rhyme observation + OpenWorm prior-art inventory + substrate-comparison axes + composition pipeline) +3. **BACKLOG.md** regen + +## Composes-with + +- **B-0924** (parent: custom 2600 emulator) +- **B-0917** (Kleisli interrupt substrate; worm spike-events map to IntrCtx) +- **B-0865, B-0761** (ARC-AGI-3 benchmark + cluster substrate) +- **B-0202** (tinygrad-uop-ir kernel layer emulator dispatch) +- **B-0703** (multi-oracle BFT consensus) +- **OpenWorm** (canonical c302 + Sibernetic + connectome data) +- **Framework rules**: DST-omniscience (PR #5841), pilot-wave-MWI (PR #5842), particle-as-locus (PR #5846), asymmetric-authorship + monad-propagation + OPLE-T-TFeedback + function-as-control-flow-generator + algebra-owner z-sets skill + +## Substrate-honest scope + +- Substrate-engineering substrate-target row; multi-PR; substrate-anchor for OpenWorm composition work +- Operator's "could beat us at it" prediction preserved per don't-collapse (mirror-tier; would require empirical test for beacon-tier ratification) +- Cooperative-emulator gaming substrate-target: Aaron + Otto + worm three-player coop once cluster ships + +🤖 Generated with [Claude Code](https://claude.com/claude-code) + +## General comments + +### @chatgpt-codex-connector (2026-05-28T17:23:38Z) + +You have reached your Codex usage limits for code reviews. You can see your limits in the [Codex usage dashboard](https://chatgpt.com/codex/cloud/settings/usage). diff --git a/docs/pr-discussions/PR-5892-research-c-elegans-tower-superorganism-perez-ding-2025-compl.md b/docs/pr-discussions/PR-5892-research-c-elegans-tower-superorganism-perez-ding-2025-compl.md new file mode 100644 index 0000000000..f52daa9ec4 --- /dev/null +++ b/docs/pr-discussions/PR-5892-research-c-elegans-tower-superorganism-perez-ding-2025-compl.md @@ -0,0 +1,80 @@ +--- +pr_number: 5892 +title: "research(c-elegans): tower-superorganism (Perez & Ding 2025) completes three-layer biological instantiation of framework's multi-oracle BFT formal-math \u2014 mirror-tier preservation (operator 2026-05-28)" +author: "AceHack" +state: "MERGED" +created_at: "2026-05-28T17:26:23Z" +merged_at: "2026-05-28T17:29:09Z" +closed_at: "2026-05-28T17:29:09Z" +head_ref: "otto-cli/b0926-tower-superorganism-celegans-2026-05-28" +base_ref: "main" +archived_at: "2026-05-28T17:40:37Z" +archive_tool: "tools/pr-preservation/archive-pr.ts" +--- + +# PR #5892: research(c-elegans): tower-superorganism (Perez & Ding 2025) completes three-layer biological instantiation of framework's multi-oracle BFT formal-math — mirror-tier preservation (operator 2026-05-28) + +## PR description + +Research-tier ONLY per operator explicit disposition: + +> *"research for such that's some crazy shit"* +> *"we don't want to just code that up without proper research"* + +No backlog row at this scope — substrate-anchor for future substrate-engineering substrate-target work; substrate-honest disposition preserved. + +## Substrate-grounding (per WebFetch 2026-05-28) + +[Scientific American](https://www.scientificamerican.com/article/this-tower-of-worms-is-a-squirming-superorganism/) reporting on Perez & Ding et al., *Current Biology* (2025) DOI: 10.1016/j.cub.2025.05.026: + +- **Species**: *C. elegans* +- **Trigger**: food scarcity (researchers induced via food-empty dish) +- **Function**: cooperative dispersal + resource-seeking (hitchhike on fruit flies) +- **Scale**: "dozens of worms" coordinate as superorganism +- **Framing**: explicitly "superorganism" + "move as one" + "eerily coordinated manner" + +## Three-layer biological instantiation + +| Layer | Substrate | +|---|---| +| **Individual** | c302 connectome (Cook et al. 2019; 302 neurons fully mapped) | +| **Collective** | Tower-superorganism (Perez & Ding 2025; dozens-of-worms coordinated dispersal) | +| **Formal** | Aurora multi-oracle BFT immune-math + B-0703 three-faction BFT + B-0664 NCI HC-8 | + +The framework's multi-oracle BFT formal-math has — uniquely in known biological substrate — a complete-substrate instantiation across ALL THREE substrate-layers simultaneously at the SAME tractability scope. + +## What ships + +Single research note at `docs/research/2026-05-28-c-elegans-tower-superorganism-perez-ding-2025-current-biology-completes-three-layer-biological-instantiation-of-frameworks-multi-oracle-bft-formal-math-aaron-2026-05-28.md` + +- Substrate-rhyme observation +- WebFetch substrate-grounding from Scientific American article +- Three-layer composition table (individual + collective + formal) +- Multi-oracle BFT composition (formal ↔ biological) +- Future substrate-engineering substrate-target candidates (N-worm DST + joint state-space + empirical-validation surface) +- Mirror-vs-beacon framing (mirror-tier preserved; beacon-tier requires empirical validation) + +## Composes-with + +- B-0925 (per-individual C. elegans controller variant) +- B-0924 (custom 2600 emulator + generate+join) +- B-0917 (Kleisli interrupt substrate) +- B-0703 (three-faction BFT) +- B-0664 (NCI HC-8 floor) +- B-0644 (Limit-as-simulation) + B-0665 (Integrate-as-choice-locus) +- B-0865, B-0761 (ARC-AGI-3 cluster substrate) +- Aurora immune-math substrate +- Tonal-momentum substrate +- OpenWorm + Perez & Ding (2025) + +## Substrate-honest scope + +Per `.claude/rules/god-tier-claims-high-signal-high-suspicion-dont-collapse.md` PERSONAL INVARIANT: substrate-rhyme observation preserved at mirror-tier as high-signal-high-suspicion; do not collapse to ratified-claim without empirical validation. Proper-research-first discipline preserved per operator's explicit framing. + +🤖 Generated with [Claude Code](https://claude.com/claude-code) + +## General comments + +### @chatgpt-codex-connector (2026-05-28T17:26:30Z) + +You have reached your Codex usage limits for code reviews. You can see your limits in the [Codex usage dashboard](https://chatgpt.com/codex/cloud/settings/usage).