@hongmaple0820/med-scale-research-os 0.43.0

package/dist/workflows/presets.js.map

@@ -0,0 +1 @@
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package/docs/README.md

@@ -0,0 +1,105 @@
+# SCALE Engine 文档地图
+
+这个目录同时包含用户指南、治理能力说明、架构参考、历史规划和推广素材。新用户应优先阅读入门入口和当前治理能力文档，历史规划仅作为背景材料。
+
+## 新用户入口
+
+| 文档 | 说明 |
+| --- | --- |
+| [start/README.md](start/README.md) | 入门路径总览 |
+| [start/quickstart.md](start/quickstart.md) | 3 分钟快速开始 |
+| [start/agent-governance-demo.md](start/agent-governance-demo.md) | 官方 demo walkthrough |
+| [start/artifact-lifecycle.md](start/artifact-lifecycle.md) | Artifact 生命周期完整 walkthrough |
+| [../README.md](../README.md) | 项目主页和能力总览 |
+
+## 仓库维护入口
+
+| 文档 | 说明 |
+| --- | --- |
+| [guides/GETTING_STARTED.md](guides/GETTING_STARTED.md) | `scale-engine` 仓库维护者的 15 分钟上手路径 |
+| [guides/DEVELOPMENT_WORKFLOW.md](guides/DEVELOPMENT_WORKFLOW.md) | 本仓库日常开发工作流 |
+| [workflow/README.md](workflow/README.md) | 仓库门禁、分支策略和 workflow 命令面 |
+
+## 当前治理能力
+
+| 文档 | 说明 |
+| --- | --- |
+| [SHIELD.md](SHIELD.md) | **Scale Shield** — 退出码钩子拦截引擎，YAML 策略编译，40+ 危险命令阻断 |
+| [ORCHESTRATOR.md](ORCHESTRATOR.md) | **Scale Orchestrator** — 声明式编排守护进程，git worktree 隔离，协调循环 |
+| [CORTEX.md](CORTEX.md) | **Scale Cortex** — 证据驱动持续进化，Instincts 提取，SessionStart 注入，治理 ROI |
+| [RESOURCE_GOVERNANCE.md](RESOURCE_GOVERNANCE.md) | 文档、报告、媒体、脚本、临时产物的生命周期治理 |
+| [ENGINEERING_STANDARDS.md](ENGINEERING_STANDARDS.md) | 日志、安全、ORM、框架、测试、部署等工程规范 |
+| [BACKGROUND_HUNTER.md](BACKGROUND_HUNTER.md) | Background Hunter 只读主动巡检、诊断交接和 ignore baseline |
+| [DEPENDENCY_AUDIT.md](DEPENDENCY_AUDIT.md) | 供应链依赖审计、G7 dependency 子门禁和 dependency policy |
+| [TOOL_ORCHESTRATION.md](TOOL_ORCHESTRATION.md) | skills、MCP、CLI、浏览器、桌面自动化的编排策略 |
+| [RUNTIME_EVIDENCE.md](RUNTIME_EVIDENCE.md) | 会话 ledger、运行时证据和最终交付检查 |
+| [MEMORY_FABRIC.md](MEMORY_FABRIC.md) | Runtime evidence、session events、knowledge recall 和 graph status 的预算化上下文包 |
+| [MEMORY_BRAIN.md](MEMORY_BRAIN.md) | 证据驱动的长期记忆、矛盾检测、dream 整理和 failure replay 沉淀 |
+| [CONTEXT_BUDGET.md](CONTEXT_BUDGET.md) | Context Budget、Progressive Governance、Lazy Loading 和 Governance ROI |
+| [CODE_INTELLIGENCE.md](CODE_INTELLIGENCE.md) | CodeGraph、Graphify 和显式 fallback 的代码智能与探索 ROI |
+| [WORKFLOW_EVAL.md](WORKFLOW_EVAL.md) | Workflow Eval、pass@k 指标、Failure Replay 和改进候选 |
+| [SKILL_RADAR.md](SKILL_RADAR.md) | Skill Radar、能力置信度、证据要求和供应链安全检查 |
+| [AI_ENGINEERING_OS_POSITIONING.md](AI_ENGINEERING_OS_POSITIONING.md) | Agent Governance Runtime / AI Engineering OS 方向、`scale ai-os plan/run/status/dashboard/benchmark/migrate/adopt/doctor` runtime 入口、`0.28.0` 可用闭环增强和 3-12 个月远景路线 |
+| [THIRD_PARTY_SKILLS.md](THIRD_PARTY_SKILLS.md) | 第三方 skill 致谢、授权边界、引用方式和 vendoring 策略 |
+| [EXTERNAL_REFERENCES.md](EXTERNAL_REFERENCES.md) | 外部项目、skills、MCP、CLI 和适配器引用的完整清单 |
+| [UPGRADE_MANAGEMENT.md](UPGRADE_MANAGEMENT.md) | SCALE CLI、governance pack、skills、MCP 和 CLI 工具的安全升级流程 |
+| [GOVERNANCE_DASHBOARD.md](GOVERNANCE_DASHBOARD.md) | Runtime、eval、memory、resource、HTML artifact 的统一治理面板 |
+| [RELEASE_READINESS.md](RELEASE_READINESS.md) | 发版前质量门槛、官方 demo 和真实项目落地验收 |
+| [DOCUMENT_STANDARDS.md](DOCUMENT_STANDARDS.md) | 文档编写与维护规范 |
+| [GITLAB_FLOW.md](GITLAB_FLOW.md) | GitLab Flow 分支、发版、tag 和临时 worktree 生命周期规范 |
+| [SKILL-REPOSITORY.md](SKILL-REPOSITORY.md) | 受治理 skill repository 和安装安全策略 |
+| [VIBE-TEMPLATES.md](VIBE-TEMPLATES.md) | 可复制的 Vibe Coding 提示词模板 |
+| [LEADERSHIP-PRESETS.md](LEADERSHIP-PRESETS.md) | CEO、CTO、PM、Architect 等内置领导者角色预设 |
+
+## 当前规划与执行蓝图
+
+这些文档描述计划中的架构演进，不代表当前 CLI 已全部实现。进入实现前应按文档中的验收标准和红线逐项拆分任务。
+
+| 文档 | 说明 |
+| --- | --- |
+| [plans/2026-05-20-scale-engine-v2-final-architecture-plan.md](plans/2026-05-20-scale-engine-v2-final-architecture-plan.md) | SCALE Engine V2.0 最终架构落地方案：Prompt Cache、Dashboard 聚合、Background Hunter、供应链门禁、动态/视觉验证和 Evolution Shadow Mode |
+
+## 架构与参考
+
+| 文档 | 说明 |
+| --- | --- |
+| [00-OVERVIEW.md](00-OVERVIEW.md) | 系统概览 |
+| [01-ARCHITECTURE.md](01-ARCHITECTURE.md) | 架构设计 |
+| [02-DATA-MODEL.md](02-DATA-MODEL.md) | 数据模型 |
+| [03-CORE-MODULES.md](03-CORE-MODULES.md) | 核心模块 |
+| [04-INTEGRATION.md](04-INTEGRATION.md) | 平台与集成 |
+| [06-DECISIONS.md](06-DECISIONS.md) | 架构决策记录 |
+
+## 历史规划和过程记录
+
+这些文档是历史上下文，不一定代表当前产品入口：
+
+| 文档 | 说明 |
+| --- | --- |
+| [05-ROADMAP.md](05-ROADMAP.md) | 路线图 |
+| [OPTIMIZATION_PLAN.md](OPTIMIZATION_PLAN.md) | 历史优化计划 |
+| [WEEK1-2-REPORT.md](WEEK1-2-REPORT.md) | 阶段报告 |
+| [TASK_GUARD_SUMMARY.md](TASK_GUARD_SUMMARY.md) | Task Guard 总结 |
+| [TASK_GUARD_WORKFLOW_DEMO.md](TASK_GUARD_WORKFLOW_DEMO.md) | 早期 workflow demo |
+| [plans/2026-05-19-agent-engineering-os-upgrade-plan.md](plans/2026-05-19-agent-engineering-os-upgrade-plan.md) | Agent Engineering OS 升级审核稿：Context Budget、CodeGraph、Memory Brain、Skill Radar、HTML Artifact 和 Eval Harness |
+| [plans/](plans/) | 规划方案和技术方案归档 |
+| [superpowers/](superpowers/) | 外部方法论对照和计划归档 |
+
+## 推广和素材
+
+| 文档 | 说明 |
+| --- | --- |
+| [promote-article-v2.md](promote-article-v2.md) | 推广文章草稿 v2 |
+| [promote-article-v2.html](promote-article-v2.html) | 推广文章 HTML v2 |
+| [promote-article-v3.md](promote-article-v3.md) | 推广文章草稿 v3 |
+| [promote-article-v3.html](promote-article-v3.html) | 推广文章 HTML v3 |
+| [imgs/](imgs/) | 社群二维码和推广图片 |
+
+## 维护规则
+
+- 面向新用户的文档优先放在 `docs/start/`。
+- 面向本仓库维护者的 workflow 文档优先放在 `docs/guides/` 和 `docs/workflow/`。
+- 当前可执行能力放在根 README 和当前治理能力文档中。
+- 历史规划不要混入新手教程，避免用户把旧计划当成当前事实。
+- 如果 CLI 行为变化，必须同步更新 `README.md`、`docs/start/quickstart.md` 和相关 reference 文档。
+- 如果新增 governance pack，必须同时更新 `README.md`、`docs/start/README.md` 和对应测试。

package/docs/guides/DEVELOPMENT_WORKFLOW.md

@@ -0,0 +1,99 @@
+# SCALE Engine 开发工作流
+
+这份文档说明日常如何在 `scale-engine` 仓库里按最新工程化工作流工作。
+
+## 标准闭环
+
+```text
+探索 -> 规划 -> 执行 -> 验证 -> 沉淀
+```
+
+## 1. 探索
+
+目标：先弄清真实仓库状态，再动手。
+
+```bash
+make new-task NAME=task-slug LEVEL=M
+make plan NAME=task-slug LEVEL=M
+make explore FILES='AGENTS.md CLAUDE.md README.md package.json src/api/cli.ts' MSG='main contradiction'
+make gate-workflow
+```
+
+最低要求：
+
+- 至少读 3 个相关文件。
+- 写清主矛盾，而不是只列文件名。
+- 对不确定项明确标出，不靠猜。
+
+## 2. 规划
+
+在 `.planning/tasks/<task>/plan.md` 里至少补齐这些信息：
+
+- scope / boundary
+- acceptance criteria
+- exception / failure path
+- rollback / fallback
+- verification commands
+
+如果任务改动发布、权限、安全、凭据、npm 发版或破坏性行为，按 `CRITICAL` 处理。
+
+## 3. 执行
+
+原则：
+
+- 最小必要修改。
+- 优先复用现有脚本和 `npm` 命令，不再发明第二套命令。
+- 改 `src/` 行为时，原则上同步改 `tests/`，否则会被 G3 拦下。
+
+## 4. 验证
+
+推荐顺序：
+
+```bash
+make gate-workflow     # G1, G2, G3, G16
+make gate-quality      # G0, G4, G5, G6, G7, G8, G17, G18, G19, G20
+make verify PROFILE=default  # 完整验证
+git diff --check
+```
+
+门禁分三层（共 23 个），详见 [GATES_AND_SCORE.md](../workflow/GATES_AND_SCORE.md)：
+
+**核心门禁（G0-G8）** — 每次提交必须通过：
+- `G0` 构建必须通过
+- `G1` 探索至少读 3 个文件并记录主矛盾
+- `G2` 计划包含边界、异常、回滚
+- `G3` `src/` 行为改动必须伴随测试
+- `G4` lint 必须通过
+- `G5` 测试必须通过
+- `G6` 覆盖率和任务证据（profile 级）
+- `G7` 安全和依赖检查（profile 级）
+- `G8` 产品冒烟（profile 级）
+
+**元治理门禁（G9-G15）** — 治理有效性检查：
+- `G9` 知识库使用、`G11` 护栏有效性、`G12` 工作流完整性（默认启用）
+- `G10` 改进证据、`G13` 多 Agent 协调、`G14` skill 使用、`G15` 自我改进（可选）
+
+**增强门禁（G16-G22）** — 提交纪律和运行时质量：
+- `G16` 未提交文件阈值和大文件检查（阻断）
+- `G17` 文档链接卫生（advisory）
+- `G18` 运行时证据记录（阻断）
+- `G19` 代码审查（L/CRITICAL 任务阻断）
+- `G20` 供应链安全（阻断）
+- `G21` 上下文 token 预算（advisory）
+- `G22` 会话健康：worktree 泄露检查（advisory）
+
+## 5. 沉淀
+
+应该留下：
+
+- `verification.md`
+- `review.md`
+- `summary.md`
+- 必要的长期规则文档更新
+
+不应该留下：
+
+- 临时日志
+- worktree 状态
+- 截图、trace、缓存
+- 只对一次任务有意义的中间文件

package/docs/guides/GETTING_STARTED.md

@@ -0,0 +1,93 @@
+# SCALE Engine 仓库上手
+
+这份文档面向要开发 `scale-engine` 仓库本身的人，不是面向安装 CLI 的最终用户。
+
+## 15 分钟路径
+
+1. 先读根目录 [README.md](../../README.md)。
+2. 跑本仓库 workflow 预检：
+
+```bash
+make preflight
+```
+
+3. 看当前可用验证面：
+
+```bash
+make verify-list
+```
+
+4. 建一个任务骨架并记录探索：
+
+```bash
+make new-task NAME=example LEVEL=M
+make plan NAME=example LEVEL=M
+make explore FILES='AGENTS.md CLAUDE.md README.md package.json' MSG='main contradiction'
+make gate-workflow
+```
+
+5. 做完改动后跑质量面：
+
+```bash
+make gate-quality
+make verify PROFILE=default
+git diff --check
+```
+
+如果改动影响安装、第三方能力、skills、记忆或知识库入口，还要跑安装烟测：
+
+```bash
+make setup-smoke
+npm run smoke:setup
+npm run smoke:providers
+```
+
+`smoke:setup` 负责安装入口和配置路径；`smoke:providers` 负责真实 gbrain/graphify 回放。没有远端 gbrain 或大项目 Graphify 环境时，默认报告 `blocked` 并给出修复命令；如果要把它作为强制门禁，使用 `npm run smoke:gbrain` 或 `npm run smoke:graphify -- --large-project <path>`。
+
+准备发版本仓库时，直接跑完整发布门禁：
+
+```bash
+npm run release:check
+```
+
+如果全量测试卡住或需要定位顺序相关问题，再用 `npm run test:serial` 做排障；不要把它当成默认发布门禁。
+
+如果失败和本机 shell、PATH、Python、Bun、Cargo 或第三方 CLI 有关，先跑：
+
+```bash
+scale doctor env --json
+```
+
+## SCALE 2.0 引擎开发
+
+三引擎开发时的常用命令：
+
+```bash
+# Shield: 编译策略 → hook 脚本
+scale shield compile
+scale shield test
+
+# Orchestrator: 启动编排 daemon (开发调试)
+scale orch start
+scale orch status
+scale orch stop
+
+# Cortex: 从失败日志提取学习
+scale cortex extract
+scale cortex inject --minimal
+```
+
+## 你应该看到什么
+
+- `.scale/workspace.json` 明确了 `dev -> master` 的仓库分支策略。
+- `.agent/project.json` 定义了本仓库的 Node/TypeScript 验证命令。
+- `scripts/gates/*` 和 `scripts/workflow/*` 不是说明文档，而是可执行入口。
+- `.planning/tasks/<date>-<task>/` 用于任务级证据，不再把临时过程写进 `docs/`。
+
+## 常见误区
+
+- `make gate-workflow` 通过，不代表代码质量通过。
+- `make gate-quality` 通过，也不代表你已经记录了风险、回滚和未验证项。
+- `G8` 会检查改动过的 Markdown 和工作流文档卫生，不替代业务验证。
+- `--dry-run` 只能证明入口存在，不能写成“测试通过”。
+- 不要把 `.claude/worktrees/`、`.agent/state/`、日志或截图提交进仓库。

package/docs/guides/MEDICAL_AGENT_OPERATING_GUIDE.md

@@ -0,0 +1,61 @@
+# 医学研究者 × Agent 操作手册
+
+## 角色分工
+
+| 角色 | 职责 |
+|------|------|
+| **医学研究者** | 提出研究问题、确认靶点/疾病、解读结论 |
+| **AI Agent** | 执行命令、汇总数据、生成报告草稿 |
+| **SCALE 工作流** | 约束 Agent 必须验证、留证据、不幻觉 |
+
+## 标准工作流
+
+```
+研究者提问 → Agent 澄清参数 → scale target analyze → scale target status → 解读报告
+```
+
+## Agent 必遵规则
+
+1. **先诊断后执行**：任何分析前运行 `scale target doctor`
+2. **证据优先**：只引用 `output/` 和 `--json` 返回的字段，禁止编造 p 值、临床试验数
+3. **失败即停**：任一 stage 失败时报告 `stages_failed`，不继续编造后续结论
+4. **验证声明**：没有实际命令输出，不说「已通过」或「分析完成」
+
+## 常用命令
+
+```bash
+# 环境检查
+scale target doctor
+
+# 完整分析（Agent 用 JSON 模式）
+scale target analyze TP53 --disease "lung cancer" --cancers LUAD --json
+
+# 查看状态
+scale target status --json
+
+# 打包研究者交付包
+scale target package --target TP53 --disease "lung cancer" --json
+
+# 启动医学研究工作台：http://127.0.0.1:18766/
+scale target dashboard
+```
+
+## 参数说明
+
+| 参数 | 示例 | 说明 |
+|------|------|------|
+| `target` | CDK4 | 基因符号 |
+| `--disease` | "breast cancer" | 疾病名称（引号包裹） |
+| `--cancers` | BRCA,LUAD | TCGA 癌种代码 |
+| `--modality` | small_molecule | 药物形式 |
+| `--risk-level` | medium | 风险等级 |
+
+## 结果解读要点
+
+Agent 向研究者汇报时应包含：
+
+- 表达显著性（Stage 1）
+- 成药性评分与排名（Stage 2）
+- 竞品临床试验数量与阶段分布（Stage 3）
+- 里程碑周期与成本估算（Stage 4）
+- 每个结论对应的 JSON/MD 文件路径

package/docs/guides/MEDICAL_RESEARCH_DELIVERY.md

@@ -0,0 +1,217 @@
+# 医学研究工作流 — 今日交付指南
+
+> **适用对象**：医学研究工作者（操作 Agent）+ 技术支持同事  
+> **交付版本**：v0.43.0 + 靶点研究管线 Beta  
+> **最后更新**：2026-06-10
+
+---
+
+## 5 分钟上手（研究者视角）
+
+### 第一步：环境检查
+
+```bash
+scale target doctor
+```
+
+看到 `总体: 可运行` 即可继续。若失败：
+
+```bash
+cd target-research-platform
+pip install -r requirements.txt
+```
+
+### 第二步：运行完整分析
+
+```bash
+scale target analyze CDK4 --disease "breast cancer" --cancers BRCA
+```
+
+预计 5–15 分钟，会依次完成四个阶段：
+
+| 阶段 | 内容 |
+|------|------|
+| Stage 1 | 表达全景（GTEx / TCGA / HPA） |
+| Stage 2 | 靶点筛选与成药性评分 |
+| Stage 3 | 文献与竞品格局 |
+| Stage 4 | 商业计划书与里程碑 |
+
+### 第三步：生成期刊论文草稿
+
+```bash
+scale target manuscript --target CDK4 --disease "breast cancer"
+```
+
+该命令基于已有四阶段结果生成中文 IMRaD 草稿、中华肿瘤杂志格式稿、Word 草稿、图表和元数据，并写入 `dashboard_runtime/live_status.json`，供 Dashboard 展示。
+
+严格交付或 CI 场景可加质量门禁：
+
+```bash
+scale target manuscript --target CDK4 --disease "breast cancer" --fail-on-quality --json
+```
+
+`--fail-on-quality` 会在稿件质量门禁存在硬错误时返回非零退出码；普通运行仍会生成稿件并在 JSON 中输出 `quality_gate` 详情。
+
+### 第四步：查看结果
+
+```bash
+# 命令行状态
+scale target status
+
+# 医学研究工作台（浏览器打开 http://127.0.0.1:18766）
+scale target dashboard
+
+# 研究者交付包
+scale target package --target CDK4 --disease "breast cancer"
+```
+
+濡傛灉瑕佹妸鏈鍖诲浜や粯娌夋穩鍒伴粯璁よ蹇嗕緵搴斿晢锛堟帹鑽?`gbrain`锛夛紝鍙洿鎺ヨ繍琛岋細
+
+```bash
+scale target remember --target CDK4 --disease "breast cancer"
+scale target package --target CDK4 --disease "breast cancer" --seed-memory
+scale target package --target CDK4 --disease "breast cancer" --seed-memory --settle-learning --ingest-memory-brain
+```
+
+`remember` / `--seed-memory` 浼氬皢稿浠躲€佷腑鍗庤偪鐦ゆ潅蹇楁牸寮忕銆乵eta銆乹uality銆乫act_check銆乴iterature evidence銆丄gent review cache 鍜?delivery manifest staging 鎴愬彲妫€绱㈡枃妗ｏ紝鍐嶅鍏?`gbrain`銆傞粯璁や粛浣跨敤 `--no-embed` 鏈湴瀵煎叆妯″紡锛屼笉浼氶粯榛樻墦寮€澶栭儴鍐欏叆銆?
+```
+
+---
+
+## 给 Agent 的操作指令（复制即用）
+
+在 Cursor / Codex 中，研究者可以直接发送：
+
+```
+请分析靶点 CDK4 在乳腺癌中的成药性，执行：
+scale target doctor
+scale target analyze CDK4 --disease "breast cancer" --cancers BRCA --json
+分析完成后运行 scale target status 并总结关键结论。
+```
+
+Agent 必须：
+1. 先跑 `doctor`，失败则停止并报告修复步骤
+2. 用 `--json` 获取结构化结果，禁止编造数据
+3. 引用产物路径（`artifacts` 字段）作为证据
+4. 未跑验证前不得声称「分析通过」
+
+---
+
+## 交付范围说明
+
+### 今日可交付（Beta）
+
+| 能力 | 状态 |
+|------|------|
+| 四阶段靶点分析管线 | 可用 |
+| 权威 API 数据溯源 | 可用 |
+| `scale target analyze` 统一入口 | 可用 |
+| 本地 Dashboard 可视化 | 可用 |
+| Agent 操作指令模板 | 可用 |
+| SCALE 工作流门禁（define/verify/ship） | 可用 |
+
+### 今日不承诺（Beta 后续）
+
+| 能力 | 状态 |
+|------|------|
+| 多用户 / 权限 / 审计合规 | 未实现 |
+| 云端部署 | 未实现 |
+| FDA 21 CFR Part 11 | 未实现 |
+| 非医学类 Agent 步骤的真实 LLM 调用 | 仍为模拟 |
+
+---
+
+## 产物位置
+
+分析完成后，产物在：
+
+```
+target-research-platform/output/
+├── stage1/   # 表达分析 JSON
+├── stage2/   # 筛选排序 JSON
+├── stage3/   # 深度调研 JSON
+├── stage4/   # 商业计划书 MD + JSON
+├── manuscripts/  # 期刊论文草稿（中文 IMRaD + 图表 + 逐篇评述）
+│   ├── {TARGET}_{disease}_manuscript.md
+│   ├── {TARGET}_{disease}_manuscript_zhongliu.md   # 中华肿瘤杂志格式
+│   ├── {TARGET}_{disease}_manuscript.docx
+│   ├── {TARGET}_{disease}_manuscript_meta.json
+│   ├── {TARGET}_{disease}_manuscript_quality.json      # 质量门禁报告
+│   ├── {TARGET}_{disease}_manuscript_fact_check.json  # 医学事实核查报告
+│   ├── {TARGET}_{disease}_delivery_manifest.json      # 交付清单与 hash
+│   ├── {TARGET}_{disease}_memory_summary.md           # 记忆摘要
+│   ├── {TARGET}_{disease}_memory_seed.json            # 记忆播种记录
+│   ├── {TARGET}_{disease}_memory_learning_candidate.md   # 学习候选摘要
+│   ├── {TARGET}_{disease}_memory_learning_candidate.json # 学习候选记录
+│   └── figures/   # 热图、桑基图等 PNG
+├── deliveries/
+│   └── {TARGET}_{disease}_delivery.zip                # 研究者交付包（含 memory artifacts）
+└── dashboard_runtime/live_status.json  # Dashboard 实时状态
+```
+
+---
+
+## 医学 Skills 富化（论文生成）
+
+论文管线已接入三层证据增强（对标 AIPOCH Evidence Insight 逻辑）：
+
+| 能力 | 实现 | 环境变量 |
+|------|------|----------|
+| PubMed 完整摘要 + MeSH | `PubMedClient.fetch_details`（efetch） | 默认开启；`MANUSCRIPT_ENRICH_PUBMED=0` 关闭 |
+| 被引次数（免费） | `OpenAlexClient` | 默认开启，**无需 Key** |
+| AMiner 引用链/期刊信号 | `AMinerClient.enrich_by_title` | 可选 `AMINER_TOKEN` |
+| **Agent 平台评述（推荐）** | `{slug}_agent_reviews.json` | Cursor Agent 写入，**无需 Key** |
+| SCALE 本地模型评述 | `SCALE_LOCAL_BASE_URL` | 默认探测 Ollama `localhost:11434` |
+| 外部 LLM 评述 | `LiteratureReviewer` | 可选 `OPENAI_API_KEY` |
+
+为避免外部学术 API 长尾阻塞交付，论文富化有默认时间边界：`MANUSCRIPT_ENRICH_BUDGET_SECONDS=45`、`MANUSCRIPT_ENRICH_OPENALEX_TIMEOUT=5`、`MANUSCRIPT_ENRICH_PUBMED_TIMEOUT=10`、`MANUSCRIPT_ENRICH_AMINER_TIMEOUT=8`。超时不会中断论文生成，只会降级使用已有 Stage3/缓存元数据，并在 manuscript metadata 的 `literature_reviews.enrichment` 中记录 `deadline_exceeded` 与 `budget_seconds`。
+
+论文 PNG 图表会自动选择可用中文字体（如 Microsoft YaHei / SimHei / Noto Sans SC）。如部署环境字体选择不理想，可用 `MANUSCRIPT_CHART_FONT` 指定 matplotlib 可识别的字体名。
+
+**方式 A — Agent 平台（推荐，无需 API Key）**
+
+```text
+1. python main.py manuscript --target CDK4 --disease "breast cancer"
+   → 生成 CDK4_breast_cancer_review_tasks.json（待办）
+2. 在 Cursor 中对 Agent 说：「请根据 review_tasks 生成 agent_reviews.json」
+   → 写入 CDK4_breast_cancer_agent_reviews.json
+3. 再次运行 manuscript 命令 → 自动合并 Agent 评述
+```
+
+**方式 B — SCALE 本地模型（Ollama）**
+
+```powershell
+$env:SCALE_LOCAL_BASE_URL = "http://localhost:11434/v1"
+$env:SCALE_LOCAL_MODEL = "qwen2.5:7b"
+python main.py manuscript --target CDK4 --disease "breast cancer" --json
+```
+
+**方式 C — 外部 API（可选）**
+
+```powershell
+$env:OPENAI_API_KEY = "sk-..."
+python main.py manuscript --target CDK4 --disease "breast cancer" --json
+```
+
+> 当前未安装 AIPOCH 550+ skills 包；已将 `study-design-identifier`、`paper-to-claim-verifier`、`drug-target-evidence-landscape` 的核心规则编码在 `medical_skills_bridge.py`。完整技能库见 [medical-research-skills](https://github.com/aipoch/medical-research-skills)。
+
+---
+
+## 故障排查
+
+| 现象 | 处理 |
+|------|------|
+| `未找到 target-research-platform` | 在仓库根目录 `e:\project\yixue-scale-engine` 运行 |
+| Python 不可用 | 安装 Python 3.10+，确保 `python --version` 可用 |
+| API 超时 | 检查网络，重试；缓存目录 `target-research-platform/cache/` 会加速二次查询 |
+| Dashboard 空白 | 先完成一次 `scale target analyze`，再启动 dashboard |
+
+---
+
+## 技术支持联系清单
+
+交付时向研究者说明：
+
+1. 本版本为 **Alpha**，结果仅供研究参考，不构成申报依据
+2. 所有数据来自公开 API，带完整溯源记录
+3. 遇到问题先跑 `scale target doctor`，将输出截图给技术支持