Merge pull request 'docs: add bilingual repository summary and topics' (#1) from codex/repository-metadata-20261019 into main

.gitattributes

@@ -1,3 +1,8 @@
 # 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
+artifacts/acceleration-20261001/*.tar.zst 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 +1,50 @@
 # 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。统一成果入口：`main`。
+
+## 仓库整理（不是科学实验）
+
+CPU/GPU 加速成果与公开 LFS 资源按保留双亲的合并历史整合到 `main`。旧 7 个分支先按精确 SHA 创建 `archive/2026-10-01/*` 标签，再核验并清理远端分支；不改旧工作树、不修改已封存数据或模型。完整映射见[分支说明](docs/40-operations/branches-20261001.md)，执行结果以 `registry/branch-consolidation-20261001/` 的实际回执为准。
+
+历史 registry 文档保留原字节，其旧分支恢复命令由[统一恢复指南](docs/30-reproducibility/main-restore.md)取代。
+
+## 最新状态：暂停研究，CPU/GPU 两套方案保留
+
+用户要求保存并上传现有成果，以后再继续。没有恢复训练、没有启动新实验，没有切换正式科学实现。
+
+- Phase 4AR 按真实已提交账本停在 **1,033/30,000 轮训练及 CPU 校验、138/3,920 probes**；末个未完成提交不算完成，也不自动重试。
+- 原科学登记 SHA 为 `b63e6281b6505ca3b60acb467dd0b3fae274cf513dcbfd653649ba52e9ba9740`，注册源码为 `80aeb2093db655329774eff7b32fb6e417b8b40b`。
+- CPU 原方案、独立 CPU 校验和常驻进程方案全部保留；GPU eligibility/update 原型在两张 V100 与 4090 的固定回放上通过逐位比较，没有替换原 CPU 代码。
+- 全脑常驻回放保持原 4090 环境、原始数学与 fresh state，42/42 次逐位一致。13 组稳态配对：原运行函数中位 5.9825 → 3.7222 秒，配对倍率中位 1.6201×；不是整轮训练加速，也不是学习成功。
+- 原实验 64,034 文件/16 源码、前一轮 659 产物/13 源码均保持一致。完整历史 Phase 1–4AQ 没有重跑。
+- 公开原始/参考数据已在独立 LFS 发布分支保存；本次另保存 CPU/GPU 科学回放结果，不包含环境、编译缓存或未确认许可的软件包。
+
+[CPU/GPU 方案、结果、恢复与限制](registry/acceleration-20261001/README.md) · [为什么有多个分支](docs/40-operations/branches-20261001.md)
+
+以下全部是历史状态，不能据此恢复任务或认为仍在运行。
+
+## 2026-10-01 00:09 的历史快照（已被上文停止状态取代）
+
+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

@@ -1,9 +1,23 @@
 # Digital Drosophila / MaleCNS 全脑模型研究
 
+<!-- repository-metadata:start -->
+**中文简介**：围绕连接组、神经动力学与可塑性的数字果蝇研究。
+
+**English summary**: Digital fruit-fly research covering connectomics, neural dynamics and plasticity.
+
+| 中文标签 | English topic |
+| --- | --- |
+| 研究 | `research` |
+| 连接组 | `connectomics` |
+| 神经仿真 | `neural-simulation` |
+<!-- repository-metadata:end -->
+
 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，最新正式封存科学阶段仍是 **Phase 4AQ：PASS-EXACT-UPDATED-BOUNDARY-ENGINEERING-NOT-LEARNING**。
+**Phase 4AR 已按用户要求停止，暂不恢复**：已提交 1,033/30,000 轮训练及 CPU 校验、138/3,920 次独立 probe；执行尚未完成，学习成功未判定。
+统一入口为 **`main`**，包含注册科学代码、CPU/GPU 两套方案及已公开的 LFS 数据。7 个旧分支的精确版本通过 `archive/2026-10-01/*` 标签保留，见[分支与恢复说明](docs/40-operations/branches-20261001.md)。这次只是仓库整理，不是生产运行时升级，也没有恢复训练。
 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。
@@ -13,12 +27,13 @@
 
 | 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)、[CPU/GPU 保存说明](registry/acceleration-20261001/README.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) |
 | 论文、引用与证据用途 | [参考文献入口](references/README.md)、[证据边界](references/evidence-map.md) |
-| 环境与复现 | [环境](docs/30-reproducibility/environment.md)、[恢复](docs/30-reproducibility/restore.md) |
+| 环境与复现 | [环境](docs/30-reproducibility/environment.md)、[统一恢复入口](docs/30-reproducibility/main-restore.md) |
 | Git 同步、大数据备份与安全 | [同步说明](docs/40-operations/git-sync.md)、[备份](docs/40-operations/backup.md) |
 | 每个阶段的原始证据副本 | [阶段索引](registry/catalog-20260929/stages.json) |
 | 全部科学文件路径/大小/SHA-256 | [快照说明](registry/README.md) |
@@ -35,17 +50,17 @@
 
 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`。
+统一主分支：`main`。历史版本由归档标签保留；原注册科学源码仍固定为 `80aeb2093db655329774eff7b32fb6e417b8b40b`，不随主分支移动。
 
 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。**
+普通 Git 不直接保存大型科学二进制。**Git LFS** 保存获准公开再分发的原始/参考数据，以及本次 CPU/GPU 回放结果；两套原归档指针均原样整合到 `main`。没有上传虚拟环境、SDK 编译缓存、凭据或其他服务的数据。
 原项目实占约 29.72 GB（十进制、初始化前统计），不会因为初始化 Git 被删除、搬移或重写。
-仅 clone 本仓库不能恢复全数据；按[恢复说明](docs/30-reproducibility/restore.md)配置单独的数据副本。
+只取得 Git pointer 不能恢复全数据；需按[统一恢复指南](docs/30-reproducibility/main-restore.md)下载所需 LFS 对象并验证内部成员。已封存报告中的旧分支命令仅作历史记录；不要据此重新运行实验。这不是全服务器灾备。
 
 ## 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_LFS_SKIP_SMUDGE=1 git clone --branch main 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

@@ -0,0 +1,52 @@
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+    "sha256": "c1bca109b61e53327fa7e01128a411d8ea328972593168c3ad6e1202dfdddc9c"
+  },
+  "group_id": "celltype-explorer",
+  "license": {
+    "evidence_file": "LICENSE",
+    "evidence_sha256": "9ba9550ad48438d0836ddab3da480b3b69ffa0aac7b7878b5a0039e7ab429411",
+    "upstream": "CC-BY-4.0",
+    "url": "https://creativecommons.org/licenses/by/4.0/"
+  },
+  "members": {
+    "bytes": 421593,
+    "sha256": "8a51d3b4138bad12a520f8d1a12d54673416017d15fd1b1bcc49ed385da005bb"
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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

@@ -0,0 +1,51 @@
+{
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+  "archive_format": "tar.pax+zstd",
+  "archive_sha256": "64d415a1ea9f5c2fe09005ce1c2bb27eb45510fad27ad3c39cf0001e6f525fd1",
+  "chunk_bytes": 67108864,
+  "chunks": [
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+      "sha256": "64d415a1ea9f5c2fe09005ce1c2bb27eb45510fad27ad3c39cf0001e6f525fd1"
+    }
+  ],
+  "exclusion_records": 1,
+  "exclusions": {
+    "bytes": 147,
+    "sha256": "82627a482fd6adfc3abf4f83a30158fd8371b4532f425f7eb3b03044eb7e1367"
+  },
+  "group_id": "door-data",
+  "license": {
+    "evidence_file": "DESCRIPTION",
+    "evidence_sha256": "27db2a92eb651d67969de94959990d51668a5857a33c4750a3b6ef49c5880504",
+    "upstream": "CC-BY-SA-4.0",
+    "url": "https://creativecommons.org/licenses/by-sa/4.0/"
+  },
+  "members": {
+    "bytes": 9486,
+    "sha256": "ef13db49577b3b3d1c7c31aab117d911a2decc5a80ead66b6a350c43d16374b4"
+  },
+  "plan_sha256": "a20a61821c504e8315171a5fd14afbac011b934709af344045175bdda9fcba71",
+  "provenance": {
+    "attribution": "Daniel Münch, C. Giovanni Galizia, Shouwen Ma, Martin Strauch, Anja Nissler; see upstream DESCRIPTION and data-source references",
+    "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"
+  },
+  "schema": "lfs-publication-group-v1",
+  "secret_scan": "UTF-8 files <=2 MiB, known binary suffixes excluded; fail closed on matching rules",
+  "source_bytes": 6534522,
+  "source_files": 189,
+  "source_paths": [
+    "experiments/phase4l-olfactory-grounding/external-resources/DoOR.data"
+  ],
+  "source_root": "/data/digital-drosophila",
+  "verification_scope": "content snapshot, not a license grant or nested-archive secret audit"
+}

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

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+  "chunk_bytes": 67108864,
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+    {
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+    },
+    {
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+    },
+    {
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+    },
+    {
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+    {
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+}