Record fresh LFS restore verification and final publication checksums

.gitattributes

@@ -1,3 +1,7 @@
 # Preserve historical source bytes and SHA-256 across platforms. No EOL conversion.
 * -text
 *.jsonl.gz binary
+artifacts/**/*.tar.zst filter=lfs diff=lfs merge=lfs -text
+artifacts/lfs-smoke/*.bin filter=lfs diff=lfs merge=lfs -text
+artifacts/public-resources-20261001/**/payload-*.bin filter=lfs diff=lfs merge=lfs -text
+artifacts/public-resources-20261001/**/*.jsonl.gz filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -34,3 +34,5 @@ id_ed25519*
 /registry/verification-runs/
 # Historical learned deltas/checkpoints are not source files.
 /models/learned/
+# Explicit publication exports only; original scientific directories stay ignored.
+!/artifacts/**/*.tar.zst

CURRENT.md

@@ -1,6 +1,29 @@
 # Digital Drosophila — 当前状态
 
-更新：2026-09-30。独立分支：`codex/lif-author-semantics-lab`。
+更新：2026-10-01。独立分支：`codex/lif-author-semantics-lab`。
+
+## 最新状态（取代下方历史摘要的“当前／下一步”表述）
+
+Phase 4AQ 已封存为 **PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。Phase 4AR 的普通嗅觉 acquisition 已登记并启动，仍在执行；学习成功尚未判定，没有新 learned candidate。
+
+2026-10-01 00:09:04（Asia/Shanghai）的只读账本观察：
+
+- 已提交 **411/30,000** 轮训练（包含每轮更新和独立 CPU 校验）。
+- 已提交 **62/3,920** 次独立 probe。
+- 实际进程检查确认监督器、协调器和一个子进程存在；该未提交子进程不计入上述完成量。
+- 无 stopped、最终退出或 execution-complete 记录。登记 SHA 和 16 个登记源码 SHA 全部匹配；没有执行全量输入或历史产物完整性审计。
+
+登记 SHA-256：`b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740`。登记科学源码提交：`80aeb2093db655329774eff7b32fb6e417b8b40b`。这与当前仓库文档提交是不同概念；后续文档提交不会替换已登记源码版本。
+
+CPU 常驻原型的小范围工程验证已完成，原型未接入当前实验，也不据此更改当前运行速度或完成时间估计。
+
+下一步保持原登记执行，不自动重试、不调参或读取中途学习指标。真实完整退出后，再独立进行科学 gate 和最终完整性审计。普通 acquisition 本身不自动授权后续 assay、游戏、RL、decoder 或 Web/3D。
+
+[AR 登记范围](docs/progress/phase4ar-normal-acquisition.md) · [AQ 封存结果](docs/progress/phase4aq-execution-boundary.md) · [最新运行快照](registry/phase4ar-runtime-observation-20261001T000904/snapshot.json) · [本次同步说明](docs/progress/repository-sync-20261001.md) · [CPU 原型边界](docs/progress/conditioning-cpu-residency-probe-20260930.md)
+
+Git 仍仅同步代码、文档和小证据。本次没有上传大型原始数据或完整运行轨迹，也没有启用 Git LFS；不代表完成全量异机备份。下方截至 Phase 4AP 的原文作为历史摘要保留，其中“尚未启动条件化”等状态已经由本节取代。
+
+## 以下为截至 Phase 4AP 的历史摘要
 
 ## 最近已封存结果
 

NOTICE.md

@@ -2,6 +2,14 @@
 
 本仓库整理既有项目，不改变原始数据和软件的权属。尚未为本项目原创代码选定统一公开许可证；不得将“可访问此 Git 仓库”等同于取得任意再分发授权。
 
+## 2026-10-01 公开资源发布补充
+
+用户已确认保留公开仓库，仅上传明确允许公开再分发的资源。[MaleCNS 官方下载页](https://male-cns.janelia.org/download/)已核实指向 [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)。据此，独立发布分支现在归档其已下载的数据及明确标注变更来源的既有派生数据；Cell Type Explorer、visualpathways、DoOR.data 和 Shiu 作者模型源码按各自原许可处理。作者署名、固定 commit、许可证据 SHA、排除项和恢复方法见 [本次发布说明](registry/publication-20261001/README.md)。FlyVis 不明确许可的资源、活动实验、环境和凭据不纳入。
+
+下表保留初始化时的历史审查状态，不代表本次已核实许可仍然未知。新发布只在 `artifacts/` 增加只读快照，不覆盖原始数据或此前冻结索引；不为整个仓库补授统一许可证。
+
+## 初始化审查记录（2026-09-29）
+
 | 外部资源 | 冻结副本中的许可证据 | 本仓库处理 |
 |---|---|---|
 | MaleCNS v1.0 官方数据 | 来源文件、原下载脚本和校验清单；统一再分发许可本次未确证 | 只登记路径、来源、大小、SHA-256；不上传数据 |

README.md

@@ -3,7 +3,9 @@
 面向 MaleCNS v1.0 的可审计连接组、LIF 模型、感觉接口与局部可塑性机制研究。
 **这是研究工程仓库，不是已经实现自主学习或游戏控制的果蝇。**
 
-截至 2026-09-29，最新封存阶段是 **Phase 4Z：COMPLETE-EVENT-RESOLVED-PN-AUDIT**。
+截至 2026-10-01 00:09（Asia/Shanghai），最新封存阶段是 **Phase 4AQ：PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。
+**Phase 4AR 普通嗅觉 acquisition 正在执行，科学结论未判定**：采样时已提交 411/30,000 轮训练及 CPU 校验、62/3,920 次独立 probe；不是实时自动更新计数。
+最新研发分支为 `codex/lif-author-semantics-lab`，远端默认分支仍为初始化分支。本页状态不表示已完成分支合并。
 项目顶层验收口径为 **5/10（50%）**；这不是生物学逼真度、工作量完成率或剩余工期。
 最新正式候选运行时为 `MaleCNS-LIF-runtime-v2-deterministic-candidate`。
 `MaleCNS-TemporalEligibility-v2-candidate` 与 `MaleCNS-OlfactoryEncoder-v1-candidate` 保留。
@@ -13,7 +15,8 @@
 
 | 主题 | 文档 |
 |---|---|
-| 当前状态、验收比例、下一步 | [项目状态](docs/00-overview/status.md) |
+| 最新运行状态、证据与下一步 | [当前状态](CURRENT.md)、[本次同步说明](docs/progress/repository-sync-20261001.md) |
+| 顶层验收比例与历史基线 | [项目状态](docs/00-overview/status.md) |
 | 目录和数据流 | [架构与目录](docs/00-overview/architecture.md) |
 | 科学数据定义和来源 | [数据契约](docs/10-data/data-contract.md)、[来源登记](docs/10-data/provenance.md) |
 | 模型边界 | [模型与冻结契约](docs/20-model/baseline.md) |
@@ -35,7 +38,7 @@
 
 服务器项目根目录：`/data/digital-drosophila/`。
 远程：`ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git`。
-初始化分支：`codex/project-bootstrap`。
+初始化／当前远端默认分支：`codex/project-bootstrap`；最新研发分支：`codex/lif-author-semantics-lab`。
 
 Git 保存源代码、配置、文档、书目、阶段证据副本和逐文件哈希清单。
 **Git 不保存原始 SWC/Feather、CSR、完整事件/状态、模型 checkpoint、虚拟环境或大型压缩包。**
@@ -45,7 +48,7 @@ Git 保存源代码、配置、文档、书目、阶段证据副本和逐文件
 ## 安全的首次检查
 
 ```bash
-git clone --branch codex/project-bootstrap ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git
+git clone --branch codex/lif-author-semantics-lab ssh://git@192.168.10.31:2222/qishizhe/digital-drosophila.git
 cd digital-drosophila
 python3 -B tools/repo_guard.py
 ```

artifacts/public-resources-20261001/celltype-explorer/catalog.json

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+  "license": {
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+  "provenance": {
+    "attribution": "Reiser Lab and Male CNS Cell Type Explorer contributors; retain upstream notices",
+    "changes": "Unchanged pinned working-tree file bytes; .git, environments, caches and credentials excluded. A source snapshot, not a full Git clone.",
+    "commit": "789cc6c105798ce2fd70ba85dab394f90899616b",
+    "repository": "https://github.com/reiserlab/celltype-explorer-drosophila-male-cns"
+  },
+  "schema": "lfs-publication-group-v1",
+  "secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules",
+  "source_bytes": 3957079583,
+  "source_files": 8973,
+  "source_paths": [
+    "experiments/phase4f-retinotopic-vision/external-resources/celltype-explorer"
+  ],
+  "source_root": "/data/digital-drosophila",
+  "verification_scope": "content snapshot, not a license grant or nested-archive secret audit"
+}

artifacts/public-resources-20261001/door-data/catalog.json

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+    "url": "https://creativecommons.org/licenses/by-sa/4.0/"
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+  "provenance": {
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+    "changes": "Unchanged pinned data package; .git omitted. ShareAlike terms remain attached to this package, not asserted over unrelated repository content.",
+    "commit": "eea72d64b42a4e91dafe822cf0b5204de33f8d34",
+    "papers": [
+      "https://doi.org/10.1038/srep21841",
+      "https://doi.org/10.1093/chemse/bjq042"
+    ],
+    "repository": "https://github.com/ropensci/DoOR.data",
+    "version": "2.0.1"
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+  "source_paths": [
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+  ],
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+}

artifacts/public-resources-20261001/malecns-processed/catalog.json

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+    "changes": "Existing Phase 3 all-body and Phase 3B neuron-only tables, index mappings, CSR and audit reports, copied byte-for-byte. These were previously derived by filtering/reindexing official data, not new preprocessing. Phase 3 historical outputs are not the approved SNN input; use neuron-only for current runtime.",
+    "dataset": "male-cns:v1.0",
+    "source_page": "https://male-cns.janelia.org/download/"
+  },
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+}

artifacts/public-resources-20261001/malecns-raw-core/catalog.json

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artifacts/public-resources-20261001/malecns-swc/catalog.json

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artifacts/public-resources-20261001/malecns-synaptic-partners/catalog.json

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+}