docs: add bilingual repository summary and topics

.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

@@ -1,55 +1,131 @@
-# 当前研究状态 — Phase 4AC
+# Digital Drosophila — 当前状态
 
-最新结果：**COMPLETE-SEMANTICS-AUDIT / LEARNING-NOT-ACHIEVED**。
-学习可用的总目标尚未达到，不把审计 PASS 当成学习 PASS。
-初始化 README/registry 保留原字节，最新结论从本页进入。
+更新：2026-10-01。统一成果入口：`main`。
 
-- [中文机制结论及限制](docs/progress/phase4ac-interpretation.md)
-- [完整小回路/单细胞结果](docs/progress/phase4ac-lif-semantics.md)
-- [预先声明的诊断方案](models/male-cns-lif/lif-semantics-audit-v1/PROTOCOL.md)
-- [新阶段校验清单](registry/phase4ac-lif-semantics/seal-verification.json)
-- [上一轮末梢作用范围诊断](docs/progress/phase4ab-terminal-scope.md)
-- [小回路与全脑背景的只读复核](docs/progress/feedback-context-review-20260930.md)
+## 仓库整理（不是科学实验）
 
-## 后续只读复核的重要限制
+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。
 
-所选五节点只贡献三个 ALLN 晚期正到达权重的 7.57%–8.99%；达到各自80%正输入需要49–52个来源。
-因此孤立小回路可以自持，不意味着它是全脑唯一原因。回路外输入也可能受该回路反馈影响，不是已证明独立的外源驱动。
-对旧数据的派生分解没有新模拟或训练；正输入比例不能当因果责任比例。
-独立新模型分支尚待用户确认，不把持续目标自动当作改变冻结动力学的许可。
+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。
 
-## 新增机制证据
+## 最新状态：暂停研究，CPU/GPU 两套方案保留
 
-只施加一次初始 spike，使用原有冻结动力学：
+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。
 
-| 真实小回路 | 1 s 内总 spike | 500–1,000 ms spike |
-|---|---:|---:|
-| 2 个 ALLN | 473 | 238 |
-| 3 个 ALLN | 1,064 | 535 |
-| 3 ALLN + VA6 PN + KC | 1,483 | 747 |
-| 真实前向边对照 | 3 | 0 |
-| 无初始刺激 | 0 | 0 |
+- 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。
 
-最小回路：body 11478 → 11620（235 contacts），11620 → 11478（283 contacts），两者为 lLN1_bc / ACh。
-单次输入足以在隔离小回路中产生持续到观察期末的活动；不代表已证明全脑必要性，也不代表真实果蝇该回路必然如此。
+[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)
 
-## 原作者实现与本项目适配差异
+以下全部是历史状态，不能据此恢复任务或认为仍在运行。
 
-固定作者代码在 spike 后清零 g，对不应期内 g 更新/输入设限，并有不同积分、阈值和刺激时序。
-本项目冻结版本明确保留 g，继续衰减/接收输入。这是建模语义差异，不是本轮发现的 GPU 回归错误。
-单细胞组件测试证明这些选择会改变响应，但真实连接强度的一次输入下，reset-only 并未改变 spike 数。
-因此 **g reset 不得直接称为学习修复**，也不能仅据放电减少自动选择新模型。
+## 2026-10-01 00:09 的历史快照（已被上文停止状态取代）
 
-## 验证与下一步
+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。
 
-7 项单元测试、17×4 单细胞 fixture、5 个真实小回路 CPU/GPU 全状态/事件精确对照通过。
-五组 deterministic-v2 全脑冻结参考 trial 精确一致。
-原快照 230,239 项及 Phase 4AA / 4AB 模型与实验前后校验无变化。
-新产物有独立 manifest/SHA-256；未训练、未生成 learned candidate。
-ComfyUI 保持驻留，不停用、不卸载、不升级依赖。
+2026-10-01 00:09:04（Asia/Shanghai）的只读账本观察：
 
-后续需要明确授权的独立动力学模型分支：先验证原作者 oracle 和局部机制，再检查输入区别与学习功能。
-仍要求独立 evaluation seeds、A 对 B 的特异性、MBON/downstream readout 和完整 conditioning controls。
-不调整学习率/阈值或扩大 mask，不进入游戏、RL、decoder、视觉；不修改已冻结版本。
+- 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。
 
-Git 仅同步代码、小报告、官方小型源代码及校验清单。大数据/完整 spike 输出仍在服务器，不等于完整异机备份。
+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
+
+Phase 4AP：**PASS-EXACT-PROCESS-ISOLATED-DELTA-INTERFACE-NOT-LEARNING**。
+
+12/12 个槽位完成（明确导入 1 条 AO 轨迹，新增 11 次神经运行）；复用原两组输入，未重新抽样。
+6/6 reference/light 比较与 6/6 跨 arm 对照精确通过；D0/frozen 保持零更新，D1 两轮分别有 90/79 条目标 compartment 边更新，跨 compartment 为 0。第二轮实际安装第一轮 90 条非零 delta。旧 28 套完整性与 AO/诊断/AN/AM 封存前后通过，原 AO 失败记录不变。
+
+40/40 服务器接口测试及 14/14 发布工具测试通过；无 NaN/Inf。仍没有 A/B 功能学习评估或 learned candidate，两个 A epoch 的总放电数也没有展示对照差异。下一步集中完成 retention 更新边界、完整学习门与端到端预算准备，再进入真实正常 acquisition；不再以接口 PASS 替代学习。
+
+[AP 正式结果与下一步](docs/progress/phase4ap-interface-status.md) · [正式状态](registry/phase4ap-conditioning-interface-v2/evidence/audit/final-status.json)
+
+## 前一项接口中止
+
+Phase 4AO：**FAIL-POSTPROCESS-MODULE-IDENTITY**，学习效果尚未判断。
+
+登记 12 条两轮 delta 衔接验证，仅第一条 reference 神经轨迹完成并封存（120 ms、36,539 spikes、无 NaN/Inf）；随后因两个同源 loader 的缓存归属冲突停止，完整流程完成数为 0/12。未重跑轨迹、未覆盖源码、未启动完整 conditioning。
+
+独立 CPU 进程后处理诊断已通过：同一轨迹产生 90 条目标 compartment 非零 delta，跨 compartment 改动为 0；未安装新权重，不能据此认定学习成功。AN/AM 封存与 28 套旧完整性再次通过。下一步单独登记进程隔离协调器，不能恢复或改写本次已封存 AO。
+
+[AO 结果、原因与后续边界](docs/progress/phase4ao-interface-status.md) · [正式失败状态](registry/phase4ao-conditioning-interface/evidence/audit/final-status.json)
+
+## 前一项工程验证
+
+Phase 4AN：**PASS-EXACT-LIGHT-CONTINUATION-ENGINEERING-NOT-LEARNING**。
+
+固定 zero/static25 输入下，32/32 次运行及 74 项比较通过；分段续跑保留精确事件、末态和延迟队列，独立 CSR 审计覆盖真实非零跨段到达。AM 双封存及 28 套旧完整性记录再次通过。没有训练，未生成 learned candidate；结论只覆盖注册的 100 ms 输入及固定切点，不是普遍动力学证明。
+
+light 的 100 ms 核心模拟约 2.15–2.19 s，单条输出约 2.60 MB，尚未达到实时。整个 32-call 执行流程约 433.97 s；首次编译、校验和保存都包含在该流程时间内。
+
+[AN 结果及预算边界](docs/progress/phase4an-interpretation.md)。注册 SHA：`7317441126f191ccc6e6d28438870b3921537ebe282a6acb163716a690057945`；实验 manifest SHA：`e8952a48cd3ea6a93c811a1183a1f7b79e19646299924e7688e5f393737a9aa2`。
+
+## 全脑固定权重接口
+
+Phase 4AM：**PASS-EXACT-WHOLEBRAIN-PLASTIC-INTERFACE-NOT-LEARNING**。
+
+独立建立 D18 whole-brain plastic-overlay 接口，不覆盖或替换旧 reference/runtime。
+75/75 服务器单元测试通过；完整性链 28 个根运行前后全部通过，五组旧参考重新运行全部精确。
+预注册 SHA-256：`465886b78ada08092c2c83de278844707499718977fb6dc6a7608391da0e5304`。
+
+- 零 delta 门完成：120 个固定主输入及 24 次技术重复，共 **144/144 与 Phase 4AK D18 精确一致**。
+- 同一库存 static25 的 144 次闭环运行完成，24 次技术重复精确一致；真实反馈重新计算，不钳制源事件。
+- static25 是原 float32 候选权重的 25% floor 经明确 SI 精度桥接，不是学习结果，也不声称等于 float64 基础权重的精确 25%。
+- 120/120 主试验的 MBON、实际 downstream、descending、motor 事件序列及逐细胞计数有变化；12 个 mask 目标的计数变化为 119/120、事件变化为 120/120；KC 事件变化 120/120、计数变化 32/120。这不是每个细胞都变化，也不是学习或行为 PASS。
+- 两阶段都不训练，未产生 learned candidate。zero/static25 阶段墙时分别约 1665.34/1471.04 秒；主试验最大已分配显存 526,523,392 bytes。
+
+运行目录：`experiments/phase4am-wholebrain-plastic-interface/`。
+[AM 结果解释](docs/progress/phase4am-interpretation.md) · [正式状态](registry/phase4am-wholebrain-plastic-interface/evidence/audit/final-status.json) · [预注册设计](models/male-cns-lif/wholebrain-plastic-interface-v1/PROTOCOL.md)
+
+## 前序结论保持不变
+
+Phase 4AL：**PASS-CONDITIONAL-CREDIT-TRANSFER-AUDIT-NOT-LEARNING**。
+
+固定 D18 的 120 条主轨迹及 24 次重复全部 MBON 基线逐位复现；60 组气味对都有各自特有的 KC/候选边。固定 25% 减弱在 120/120 主试验中改变了 MBON count 或首次 latency，但那是钳制源事件的条件性回放，不是真实全脑反馈、不代表气味特异记忆或响应上界。
+
+14,232 条 mask 边、12 个 mask-recipient MBON 和全部 97 个 MBON 保留。
+Phase 4AK D18 表征验证 PASS 原样保留。1.8 ms 为工程 APL 时序假设，不是实测延迟；matched_energy 匹配预期而非每次实际事件数；旧 1212 条非 KC fast-APL 出边未被 graded 路径替代的限制仍存在。
+
+[AL 结果解释](docs/progress/phase4al-interpretation.md) · [AL 正式状态](registry/phase4al-mb-credit-transfer/evidence/audit/final-status.json) · [AK 结果解释](docs/progress/phase4ak-interpretation.md)
+
+## 当前准备与学习边界
+
+Phase 4AN 的有限工程门已封存；21 份实际使用源码已按 SHA 锁定。AO 进一步登记了包含科学准备代码的 51 份源快照，实验以接口失败封存。AP 使用独立目录的 5 份新源码完成进程隔离门，旧 51 源不变；lab 整个目录仍未封存，完整科学条件化协议尚未登记执行，没有学习候选。
+
+评估清单和完整条件化政策仍是科学草案；完整 63 位输入、单轮更新桥及 fresh-reset 跨轮 delta 实际安装已通过有限 AO/AP 证据链，不能等同于完整学习。历史准备记录见[条件化准备进度与限制](docs/progress/conditioning-preparation-2026-09-30.md)，当前接口结果以 AP 报告为准。
+
+服务器 CPU 合成测试 119/119 通过，0 跳过；21 个 AN 注册源测试前后 SHA 均未变。当前续跑器禁止父子段更换 overlay，因此“保留末态并使用新 delta”的 retention 更新边界仍需新增接口验证，不是现有工程 PASS 已覆盖的能力。
+
+完整 conditioning 草案为 68,000 epochs、10,760 生物秒（含 idle），新显式评估政策再列出 9,440 次 probes / 1,132.8 生物秒，总计 11,892.8 生物秒。这是未执行的条件性计划库存，不是工期预算。真实 CUDA 输入检查在 AO 通过，后处理冲突由独立 AP 接口解决。仍需反转/连续保持功能门、实际末态与新 delta 衔接及完整端到端资源预算，不直接启动大批量训练。
+
+目标仍是“学习可以使用”，当前没有达到。接口验证或静态权重效果不能替代真实条件化。
+后续须预注册固定 olfactory A/B、具体 DAN type/compartment、至少五个互不重叠训练种子流及独立 evaluation streams；保留原 eligibility-v2、人工 US 与实际 DAN 放电的明确区分，以及配对/控制、反转、延迟奖励、保持等功能验证。
+
+继续冻结 raw/base CSR/W_syn/sign、既有 APL 参数、eligibility-v2、14,232-edge mask 和全部已封存产物。不调参挽救结果，不接游戏、视觉、decoder、RL 或 Web。
+
+AM 已正式封存并在服务器发布 3,020 份小证据；本地已按发布收据逐项验收 3,040 个文件（含控制与清单文件）。AN 的 599 个小证据文件已逐项本地验收；620 个实际 Git blobs 校验通过并推送为 `aeccb7d0ccdcf6788e0a8de60e7ab96f70dbe734`。Git 同步范围仅为源码、文档及小证据。大型轨迹保留在服务器，小证据同步不等于全量异机备份。
+
+模型 manifest SHA-256：`7edeb251ecbeac5a64805fefe171a0a0bf8bba2675919ef922cc1a329c203ea8`。
+实验 manifest SHA-256：`9e24b682935a9b18e05db7a933080c5f63ddbeb8a0c85cc0df1cfe1d06d88ab4`。
+正式状态 SHA-256：`18b12c832e156bd6e5ba950f48a49fb908c62104b91bb3e78213f523c8fdc8f9`。
+
+AP 新登记源码 commit：`0bcce983324ecfe1c75826a23e94ff932ad5e883`。
+AP 实验 manifest SHA：`a40e433541a6c02f7ad95622e96646da9a90a93e4e43cb3abfde3846b2554f00`。
+AP registry 共 356 份小文件已本地逐项 SHA 验收。Git 只同步源码、文档和小证据，不包含服务器大型轨迹。

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

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+  "group_id": "celltype-explorer",
+  "license": {
+    "evidence_file": "LICENSE",
+    "evidence_sha256": "9ba9550ad48438d0836ddab3da480b3b69ffa0aac7b7878b5a0039e7ab429411",
+    "upstream": "CC-BY-4.0",
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+  "provenance": {
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+    "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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+  "chunk_bytes": 67108864,
+  "chunks": [
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+  ],
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+  },
+  "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/"
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+  "members": {
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+  "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"
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+    "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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+    "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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+  "license": {
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+    "local_manifests_scripts": "Project-authored provenance; no new blanket software license",
+    "url": "https://creativecommons.org/licenses/by/4.0/"
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+  "provenance": {
+    "attribution": "Male CNS collaboration: FlyEM (HHMI Janelia), University of Cambridge Department of Zoology, MRC Laboratory of Molecular Biology, Google Research; retain original dataset author credits",
+    "changes": "Data file bytes unchanged; archival compression and path manifest only. Download logs excluded.",
+    "source_page": "https://male-cns.janelia.org/download/",
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+  ],
+  "source_root": "/data/digital-drosophila",
+  "verification_scope": "content snapshot, not a license grant or nested-archive secret audit"
+}

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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+}