reviewer-response-sci - SKILL.md Agent Skill

name: reviewer-response-sci description: 用于SCI审稿意见逐条回复的全流程技能，适用于期刊大修/小修阶段，只出回复包（HTML），不改主稿。触发词：审稿意见回复、回复审稿人、回复reviewer、response letter、回复信、rebuttal、逐条回复、Response to Reviewer、revise and resubmit、R&R、reviewer comments。路由说明：与revise-sci区分，本技能只出回复包不改主稿，需同时改主稿并出修订稿docx请用revise-sci；与reviewer-simulator区分，本技能针对已收到的意见写回复，后者是模拟生成审稿意见。

Reviewer Response SCI

Scope

Default mode is one-shot full package with atomic storage. Two secondary modes also exist: Re-Render（手改 unit JSON 后单独重渲，见 Re-Render Workflow）和 skeleton/prewrite 预览（出占位符草稿，命令见 Scripts 段）。

Required Inputs

参数	必需	说明
`comments_docx_path`	✅	审稿意见文件
`manuscript_docx_path`	✅	论文正文
`si_docx_path`	可选	补充材料
`project_root`	✅	输出根目录
`output_html_path`	✅	最终 HTML 路径

Outputs（one-shot 产物）：

Atomic JSON pages — units/ 目录（每条意见一个 JSON + 邮件 JSON）
Atomic manuscript units — manuscript_units/
Atomic SI units — si_units/（有SI时）
One final hierarchical HTML（主交付物，见 Output Contract）

Save Path Confirmation (Mandatory)

Before running the pipeline, first ask the user where output files should be saved.

环境预检（软门禁，确认 project_root 后、跑 pipeline 前）： python3 scripts/env_preflight.py <project_root> --cli esearch --py docx，写 env_status.json，末行 PRECHECK: OK|ASK|BLOCKED。BLOCKED（Python 过低）→ 停并引导升级；ASK（缺 esearch/python-docx 等可选工具）→ 逐项问用户是否安装并给指引，用户答"已装/不装"后才继续；OK → 继续。回退靠 state_manager.py snapshot（不建 git 检查点）。

Default behavior if user does not specify a custom location:

Use the current project directory.
Create a dedicated subfolder for this run (for example: projects/<task_name_or_date>/).
Write all artifacts into that subfolder (units/, manuscript_units/, si_units/, logs/, final HTML).

Output Contract (One-Shot)

主交付 = 回复包（给编辑的总览邮件 + 各审稿人 point-by-point 回复，最终渲染为单文件分层 HTML）。 修改稿 track-changes 需用户手工补：本技能生成回复文档，不产出 Word track-changes 版本；用户应以 manuscript_edit_plan.md 为操作指南，在 Word 中手动启用修订模式完成改稿。若用户要求 track-changes 稿件，解释此限制并推荐使用 manuscript_edit_plan.md。

主交付物 = 单文件分层 HTML（左侧层级 TOC + 右侧内容，单页可见）。TOC 顶层节点为 Editor（若有）+ Reviewer #1/#2/...，Editor 排在所有 Reviewer 之前；编辑信里的 editor comment（字数/格式/伦理声明/数据可用性/利益冲突/统计复核等）作为独立顶层 Editor 节点呈现，与各 Reviewer 并列，不得并入任何 Reviewer。全部 UI 由 scripts/build_full_package.py 的 render_html() 生成，TOC 层级、严重度背景色、折叠/展开、可拖拽分割线、复制 按钮、localStorage 持久化、各 box 布局均已硬编码，AI 无需手工实现 HTML。完整 UI 验收对照细则见 references/output-template.md。

AI 真正要产出的是每条 comment unit 的内容字段（脚本只写占位符，AI 填真值）：

审稿人意图：原始意见(EN) + 中文直译（直译不意译）+ 中文意图理解（摘要，非粘贴英文原文）。直译/中文回应必须由当前模型直接产出，脚本不自动出译文、只留占位符。
Response：中文回复 + 对应英文（非逐字翻译）。
修改候选：revised EN 段落（聚焦匹配句周围片段）+ 中文译文；无修改写 无；定位字段（unit_id/路径/段落与句子 index）随 unit 写入。
修改说明：动作列表（添加/删除/修改+原因）+ 🔴 Core/🟡 Support 汇总。
证据/图片：Figure Prompt Block，审稿人明确要求改/新增图片时，按 references/figure-prompt-template.md 生成结构化提示词，存入对应 comment unit JSON 的 content.figure_prompt。

Atomic JSON Contract

Project layout:

project_root/project_state.json
project_root/index.json (hierarchical TOC source)
project_root/citation_registry.json (new references added during response; see Step 2)
project_root/manuscript_edit_plan.md (ordered revision plan; see Step 5)
project_root/units/000_email.json
project_root/units/*.json (one file per comment)
project_root/manuscript_units/*.json (one section-level block per unit: heading + corresponding body text + corresponding figure captions when present)
project_root/si_units/*.json (one section-level block per unit: heading + corresponding body text + corresponding figure captions when present)

Each unit follows references/atomic-unit-schema.json. Each comment unit should carry content.atomic_location and must be renderable in HTML section 3. Source atomic units (manuscript_units / si_units) must include:

section-level units (unit_type=section_block, optionally preamble_block)
section text and corresponding figure captions in the same section-level unit when available
force split back-matter sections into independent units: Author Contributions, Acknowledgements, Conflicts of Interest, References (supports numbered headings like 6. AUTHOR CONTRIBUTIONS and inline heading patterns)
if no figure exists, figure-caption units can be absent
optional image attachment extraction is allowed but not mandatory; section text + corresponding figure caption text is mandatory

Rules

Do not fabricate experiments, statistics, or references.
If evidence is missing, explicitly mark Not provided by user.
Keep tone professional and non-defensive.
English reviewer responses must be fluent and natural, with low AI-style phrasing.
Prefer short sentences for clear, natural rhythm; avoid long complex sentences by default, but do not split mechanically.
If a reviewer comment requires adding references, literature retrieval follows topic-dependent routing: ① determine field — life science/medicine → PubMed CLI first (esearch/efetch, ~/edirect/, < /dev/null, proxy http://127.0.0.1:<PROXY_PORT>); CS/AI/engineering → paper-search MCP first (mcp__paper-search-mcp__search_arxiv etc.) ② fallback to the other when primary yields no results. Auto-install PubMed CLI if ~/edirect/esearch missing: sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)". Windows: the sh/curl installer and < /dev/null are not available in native cmd/PowerShell — run PubMed CLI under WSL, or skip it and use the paper-search MCP fallback instead.
严禁使用 tavily、websearch 或 openalex（pyalex）进行文献检索。
Serial Search (MANDATORY): Execute all retrieval calls sequentially (PubMed CLI and paper-search MCP alike). Never parallelize search requests. Enforce ≥1s interval between consecutive calls.
Do not create ad-hoc fixer scripts (e.g., fix_gate_errors.py, temporary patch scripts) during normal runs.
When gate checks fail, directly edit the failing project_root/units/*.json fields and re-run checks.
Keep one-page-per-comment structure.
All copy buttons in the UI must use Chinese label 复制.
Frontend design specifications are hardcoded in scripts/build_full_package.py's render_html(); AI does not need to write HTML. Full spec is in references/output-template.md.
Quality gates must fail when:
- revised_excerpt_en is placeholder/empty (unless explicitly running with a relaxed gate mode)
- revised_excerpt_en is identical to original_excerpt_en
- unit status indicates needs_manual_revision
If comments_docx fails to parse (corrupt file, encoding error), abort immediately and report the exact error; do not proceed to atomization.
If a reviewer comment cannot be matched to any manuscript paragraph (location confidence below threshold), set atomic_location.confidence = "low" and mark the unit needs_manual_revision; do not fabricate a location.
Gate fix loop must not exceed 3 iterations; if gate still fails after 3 direct JSON edits, halt and report remaining failures to the user with a list of unresolved unit IDs.
AI Style Control: English responses must avoid AI-typical phrasing patterns:
- Hedging overuse: "it is important to note that", "it should be noted that", "notably", "importantly"
- Empty appreciation: "we greatly appreciate your insightful comments", "this is an excellent suggestion"
- Filler phrases: "in order to", "we would like to point out that", "as the reviewer rightly noted"
- Structural repetition: ≥3 responses must not open with the same template sentence
- English sentence length hard cap: each sentence in response_en and revised_excerpt_en must be ≤30 words. If a sentence exceeds 30 words, split it. Do not achieve this by removing necessary content; restructure instead.
- -ing participial clause ban: do not attach a dangling -ing clause to the main clause with a comma (e.g., ", reflecting our commitment to…", ", ensuring that…", ", highlighting the importance of…"). Rewrite as a separate sentence or use a coordinating conjunction.
- Decorative em-dash ban: do not use —/——/em-dash as a pause, parenthetical, or emphasis marker (e.g., "This result—while preliminary—suggests…"); use a comma, period, or split sentence instead. Hyphens in compound terms ("dose-response") and numeric ranges are not affected. Applies to both English and Chinese outputs.
- Scare-quote ban: do not use quotation marks around coined words or ordinary phrases to imply novelty or irony (e.g., "robust" findings, "novel" approach). Retain quotes for: first-time term definitions, direct verbatim quotations from reviewer comments, and established idiomatic expressions.
- Explanatory-colon ban: do not use the pattern "concept: explanation" as a decorative sentence structure (e.g., "Main revision: we added a new control group"). Legitimate colons include ratios (2:1), clock times, list lead-ins, section headings, and figure labels ("Figure 3A:").
- risk_check.py scans for these patterns automatically (including sentence length and -ing clause detection); WARN-level issues should be fixed before delivery
Chinese response style (中文回复规则):
- 单句 ≤50 字硬上限。 超 50 字的句子必须拆分；不得为凑长度补充冗余内容。
- 从句嵌套 ≤2 层。 禁止三重嵌套（"因为…由于…鉴于…"类结构）。
- risk_check.py 对 response_zh 执行中文句长检测（WARN 级，>50 字告警）

Domain Edge Cases

Reviewer recommends acceptance without comments ("I have no major/minor concerns"): create a single email-only response acknowledging the reviewer; do not generate an empty Major/Minor section.
Two reviewers give contradictory suggestions (e.g., R1 says "remove Section 3" vs R2 says "expand Section 3"): flag the conflict explicitly in both units' notes_core_zh; in the English response, acknowledge the divergence and state which direction is adopted with evidence-based justification. Add a [CONFLICTING ADVICE] marker in manuscript_edit_plan.md.
Reviewer writes comments in a non-English language: translate the original comment into English first (store in reviewer_comment_en), then produce the Chinese translation from the original language (not from the English translation). Note the original language in a source_language annotation in the unit JSON.
Manuscript lacks standard section headings (e.g., Letter/Communication format): atomize by paragraph breaks instead of headings; set unit_type=paragraph_block for manuscript units; use paragraph index as the primary location anchor.
Same paragraph targeted by 5+ comments: in manuscript_edit_plan.md, merge all into one block sorted by reviewer priority (Editor > R1 > R2 > R3). If modifications conflict within the same paragraph, flag [INTRA-PARAGRAPH CONFLICT] and present alternative revision options for user decision.

One-Shot Workflow

执行模型（先读这段）： 本流程是两段式自动化 + AI 填空，不是线性手工 13 步。

scripts/build_full_package.py（pipeline 内部自动调用）一次性完成 Step 3/4/5/6/8 的机械部分：atomize 论文/SI 段落、在 units/*.json 写好占位符骨架（【待AI...】 / [AI_FILL_REQUIRED]）、生成 index.json、并由 render_html() 渲出完整 HTML。不要手工 atomize，也不要手写 index.json。
AI 的核心工作只有两件：①Step 7 把 units/*.json 里的占位符字段填成真实内容；②gate 失败时按报告直接改对应 units/*.json 再重跑。
两种调用时机，二选一：
1. 分步：先 build_full_package.py 出骨架（无条件写占位符、不跑 gate）→ AI 填 units/*.json → 再 run_pipeline.py 跑全部 gate；
2. 串起：一条 run_pipeline.py 走完 build→gate（首轮占位符会被门禁拦下，按报告填 units 后重跑）。
下列编号步骤是逻辑顺序说明，多数由脚本代劳；User Checkpoint 之间 AI 需停下确认。
跨平台命令说明（一次性）： 本节及后续所有 python3 scripts/... 命令在 Windows 上请用 python 或 py 代替 python3（macOS/Linux 保持 python3）。

Parse all reviewer comments from comments_docx_path. The parser (split_reviewer_blocks) recognizes both Reviewer #N blocks and Editor blocks (Editor:, Editor Comments, Comments from the Editor, Editorial Comments, 编辑意见, 编辑要求 等) as top-level nodes. Editor comments become an independent reviewer="Editor" group, never merged into a reviewer. 1.5. [User Checkpoint] Print parsed comment summary table:
- Top-level node count (Editor + Reviewers)
- Per-node breakdown: Major / Minor / General comment counts (Editor comments usually fall under General)
- Full list: reviewer × section × comment index × first 20 words of each comment Ask the user: "Comment parsing complete. Does this match the reviewer letter? (yes / abort / correct:N)" Do not continue to step 1.7 until user confirms.

1.7. [Strategy Planning] Build a rebuttal strategy table before writing any responses:

Reviewer	#	Section	Strategy	Rationale	Data Needed
R1	1	Major	Accept	Valid concern, easy fix	None
R1	2	Major	Partial	Agree on X, push back on Y	New ref for Y
R2	1	Minor	Push back	Misunderstanding, cite existing evidence	None

Strategy options:

Accept: fully agree, will revise as requested
Partial: agree on some points, provide evidence/rationale for others
Push back: respectfully disagree with evidence-based justification
Acknowledge: thank reviewer for the suggestion, explain why not adopted (e.g., scope, data limitation)

Rules:

Every comment must have a strategy assignment before proceeding
Push back requires at least one concrete evidence item (existing data, published precedent, or methodological rationale)
If strategy requires new literature, flag in Data Needed column for Step 2
Print the strategy table and ask user: "Strategy plan ready. Approve? (yes / adjust:R1.2 → Accept / abort)"
Do not proceed to Step 2 until user confirms
用户确认后，将每条 comment 的 strategy 写入对应 units/*.json 的 content.strategy 字段（脚本建骨架时留空字符串，由 AI 在此步骤填入）

If any comment needs additional citations (identified in Step 1.7 Data Needed), run retrieval per the Rules section's topic-dependent routing spec.
- After retrieval, build citation_registry.json in project_root/:
```
{
  "original_ref_count": 42,
  "entries": [
    {
      "ref_number": 43,
      "title": "...",
      "doi": "10.xxxx/...",
      "pmid": "12345678",
      "authors": "First A, Second B",
      "year": 2023,
      "journal": "...",
      "source_provider": "pubmed-cli",
      "source_id": "esearch:query_string",
      "added_for_units": ["003_R1_major_01"],
      "retrieved_at": "2024-..."
    }
  ]
}
```
- original_ref_count: total references in the original manuscript (count from References section)
- New reference numbers must start from original_ref_count + 1, sequential, no gaps
- Each entry must record source_provider (e.g., pubmed-cli, paper-search-mcp) for traceability
Atomize manuscript and SI into section-level units (heading + body + corresponding figure captions). 3.5. [User Checkpoint] Print a summary table:
- Total section-level units extracted (manuscript count / SI count)
- Any sections that failed to split or produced empty units Ask the user: "Atomization complete. Proceed to build comment units? (yes / abort)" Do not continue to step 4 until user confirms.
Build comment atomic units in project_root/units/ and attach anchor-based links to manuscript/SI units. Also build email page JSON at project_root/units/000_email.json with the following content:
- subject: Response to Reviewers — [Manuscript Title]
- opening: thank the editor; state that a point-by-point response and revised manuscript are attached
- change_summary: one bullet per reviewer, ≤2 sentences per bullet, summarizing major revisions made
- closing: restate willingness to provide further revisions if needed
- Tone: professional, concise, non-defensive; English only; no Chinese in email body
Build manuscript_edit_plan.md skeleton in project_root/ (Step 5 = 建骨架；Step 7 后回填真值，见下).
- The plan must be sorted by manuscript original order (ascending manuscript_paragraph_index).
- Each row must include:
  - comment_unit_id / reviewer and major-minor info
  - target document (manuscript / SI / both)
  - section heading
  - paragraph index
  - one Word-search key sentence (Word Find key sentence)
  - exact to-be-replaced snippet (if available)
  - revised text to insert (EN, and ZH if provided)：此列 Step 5 时留占位符 [PENDING Step 7]；Step 7 完成后运行 python3 scripts/state_manager.py aggregate-edit-plan --project-root <root> 自动聚合回填。
  - action type (添加 / 删除 / 修改)
- When multiple comments map to the same paragraph, merge into one ordered block with sub-items.
- If a comment is global (language polishing, full-figure consistency), put it in a separate Global edits section and explicitly mark as non-localized.
Build hierarchical index in project_root/index.json.
Fill all AI-required fields in each comment unit JSON. Execute in sub-steps:

改坏可回滚： 每次大改 units/*.json 前先 python3 scripts/state_manager.py snapshot --project-root <root> 建还原点；改坏用 python3 scripts/state_manager.py rollback --project-root <root>（默认还原最近一次快照）。快照存于 logs/snapshots/units_<时间戳>/。

7a. 排序与分批：
- 按 reviewer 分组，每组内先 major 后 minor 后 general
- 如 comment 总数 ≤15，一次性处理；>15 条时分批（每批 ≤10 条），每批完成后写盘再继续下一批
- 每条 comment unit 需填写以下 8 组字段（参照 references/atomic-unit-schema.json）：
7b. 逐条填写（每条 comment unit）： 0. 读取 content.strategy 字段（Step 1.7 已写入），据此选定回复基调：Accept→直接致谢+落实；Partial→分点肯定+部分推回；Push back→证据先行+礼貌否定；Acknowledge→解释为何未采纳。
1. content.reviewer_comment_zh：直译审稿意见（中文，不改写不概括）
2. content.reviewer_intent_zh：理解审稿人真实意图（中文摘要，≤3 句）
3. content.response_en：英文回复（遵循 references/decision-rules.md 的基调选择和句式规范；短句优先见 Rules）
4. content.response_zh：中文回复（与英文回复对应，非逐字翻译，需自然通顺）
5. content.revised_excerpt_en：修改后的英文正文段落（如无需修改写 无）
6. content.revised_excerpt_zh：修改后的中文翻译（如无需修改写 无）
7. content.modification_actions：修改动作列表（每条含 action_type + target + reason）
8. content.notes_core_zh + content.notes_support_zh：核心🔴和辅助🟡修改说明
7c. 质量标准：
- 英文回复：≥3 句、≤300 词；必须包含致谢 + 具体行动描述
- 中文回复：与英文回复信息等价，但措辞独立，不是机械翻译
- revised_excerpt：必须与 original_excerpt_en 有实质差异（不能只改标点）
- 禁止虚构实验、统计、引用（遵循 Rules 中的红线）
Step 7 Mini-Gate（填写完成后，进入 Step 8 前执行）：
- 抽取前 3 个 comment unit，检查以下字段是否已填（非占位符）：
  - content.reviewer_comment_zh（非 待AI / AI_FILL_REQUIRED）
  - content.response_zh（非空、非占位符）
  - content.revised_excerpt_en（非空、非与 original_excerpt_en 相同）
- 如发现任何占位符或空值，停止并列出未填字段，等待修复后再继续
- 抽查通过后方可进入 Step 7.5
7.5. [User Checkpoint — Quality Review] 展示回复质量摘要供用户审查：
- 打印表格：每条 comment 的 unit_id | reviewer | section | response_en 前 50 字 | revised_excerpt 状态（有修改/无/needs_manual）
- 标记需人工关注的条目：needs_manual_revision 的 unit、confidence=low 的定位、revised_excerpt_en 为 无 但 comment 明确要求改文的
- 问用户："Response content ready for rendering. Review OK? (yes / fix:unit_id / abort)"
- 用户可指定修改特定 unit，修改后重新展示该 unit 摘要
- 确认后方可进入 Step 8
Step 7 后 → edit_plan 回填（在进入 Step 8 前执行）：
```
python3 scripts/state_manager.py aggregate-edit-plan --project-root <root>
```
脚本遍历 units/*.json，把每个 unit 的 revised_excerpt_en（以及 revised_excerpt_zh，若有则以 ／ 拼接）写入 manuscript_edit_plan.md 对应行的 revised text to insert 列，替换 [PENDING Step 7]。revised_excerpt_en == "无" 的 unit 写入 无改动，不计为 PENDING。输出含两行关键信息：filled: N（已回填数）和 still PENDING: N（未填数）；若有 PENDING，脚本列出具体 unit_id 并以退出码 2 提示，需补填后重跑。回填完成后 edit_plan 即为可直接用于手工 track-changes 的完整操作清单。
Render single HTML with left hierarchical TOC + right content pane from updated atomic JSON.
Run hard gate checks, citation checks, and HTML checks before delivery.
- 判读： scripts/run_pipeline.py 串行自动执行全部 gate（顺序与职责详见 Scripts 段）；退出码 0 = 全部通过；非零时 stdout 打印 PIPELINE: FAIL (step=..., code=...) 及失败 unit。按失败信息直接改对应 units/*.json（≤3 次上限，见 Rules）后重跑。Do not run gates manually one-by-one; do not generate extra fixer scripts.
- 注： citation_ref_tracker / citation_guard 在 pipeline 内为 WARN 级（未带 --fail-on-undefined / --fail-on-unverified，仅撤稿引用会直接 FAIL），PIPELINE: PASS 不代表引文零缺陷，RR1/RR2 须在 DoD 委托盲检阶段单独确认。
Run final consistency report.
Write checkpoint + transaction logs to project_root/logs/.
Sync unit state map to project_root/logs/unit_state.json.
Write reproducibility snapshot to project_root/logs/version_snapshot.json (hashes for key scripts + outputs).

❌ 反例黑名单（Anti-Patterns）

❌ 越界改主稿或生成 Word track-changes 稿，本技能只出回复包（HTML），改稿一律落到 manuscript_edit_plan.md 由用户手工执行。
❌ 虚构实验、统计或引用来回应意见；证据缺失时不写 Not provided by user 而是编造数据。
❌ response_en 里承诺的动作（we added／clarified／revised）在 modification_actions 或 revised_excerpt_en 找不到落点（承诺↔落点不一致，consistency_check WARN 必须消除）。
❌ 主 agent 自评承诺↔落点一致性与 DoD 清单，必须委托独立上下文子代理盲检，delegate_review verify 未 exit 0 就出具回复信。
❌ 漏回任何一条意见，尤其把 Editor 意见并入某个 Reviewer，而非作为独立顶层节点。
❌ 用 tavily、websearch 或 openalex（pyalex）查文献；生命医学不走 PubMed CLI、CS/AI 不走 paper-search MCP。
❌ 并行发起检索请求，必须串行且相邻调用间隔 ≥1s。
❌ 把 revised_excerpt_en 留作占位符、留空、或与 original_excerpt_en 完全相同（仅改标点也算未改），strict_gate 必拦。
❌ 交付时残留 待AI / AI_FILL_REQUIRED / [PENDING Step 7] 占位符，或 Step 7 后漏跑 aggregate-edit-plan 回填 edit_plan。
❌ 去 AI 三禁未过：装饰性破折号、scare quotes、解释性冒号；英文单句 >30 词或挂 -ing 分词从句，中文单句 >50 字或从句嵌套 >2 层。
❌ 英文回复堆套话：空致谢（we greatly appreciate your insightful comments）、对冲词（it is important to note that）、≥3 条回复用同一模板开头。
❌ 意见无法匹配到任何段落时硬编一个 location，而非置 confidence=low 并标 needs_manual_revision。
❌ gate 失败时新建临时修复脚本（fix_gate_errors.py 之类）或逐个手跑 gate，应直接改 units/*.json 重跑且修复循环 ≤3 次。
❌ Push back 策略的 unit 没有任何具体证据（引文／数据／方法学依据）就硬顶审稿人。

Definition-of-Done: 回复包收口自检清单

硬规则：清单未逐项确认通过，不得向用户声明"回复包完成"。 能脚本核的项直接跑对应 gate；人工项逐条确认。

🔴 委托盲检（不得主 agent 自评）：你刚写完回复包，自评会失真地默认通过、且易漏项。承诺↔落点一致性尤其如此，主 agent 写了回复再自核"承诺有没有落地"几乎必然失真。run_pipeline.py 退出码 0 后、声明完成前，必须把 DoD 清单委托给独立上下文的子代理盲检，自己不直接打勾：

🔴 出具前置闸口：delegate_review verify 必须 exit 0（含 RR14 结构完整性），否则不得向用户出具 response letter。

生成任务包：python scripts/delegate_review.py pack --checklist references/dod_checklist.json --gate response-dod --files <project_root>/units/*.json（Windows PowerShell/cmd 不展开 *.json，需把 units/ 下的 json 显式逐个列在 --files 后，或在 WSL/bash 里运行）
派一个独立子代理（Claude Code 用 academic-blind-reviewer；其他平台派通用子代理），把任务包原样给它、不要给它回复包的写作上下文，要求按任务包返回 JSON 数组。
校验返回：python scripts/delegate_review.py verify --checklist references/dod_checklist.json --gate response-dod --return <子代理返回.json>；退出码非 0（任一缺项/fail/无证据）= fail-closed，据子代理证据修复后重跑，未过不得声明完成。

下列清单与 references/dod_checklist.json 逐项对应（改清单先改 JSON，此处仅供人工对照；能脚本核的项子代理会先跑脚本）：

通用 6 项（全技能必过，对应 RR1–RR6）

① 引文 [N] ↔ 参考列表一一对应（无孤儿、无缺号、编号连续）→ citation_ref_tracker.py
② 本次新增引用已过 citation_guard.py（status == "pass" 或无新增引用）
③ 全部回复内容符合投稿论文主线（无跑题、无与原稿结论矛盾的表述）→ 人工
④ 占位符清零（无 待AI / AI_FILL_REQUIRED / [PENDING Step 7]）→ final_content_gate.py
⑤ 去 AI（英文单句 ≤30 词、无 -ing 分词挂句、无套话禁词；中文单句 ≤50 字、从句 ≤2 层）→ risk_check.py + 人工
⑥ 字数达标（每条 response_en ≥3 句且 ≤300 词；response_zh 信息等价）→ 人工

reviewer-response 特有项（对应 RR7–RR13）

逐条覆盖：每条审稿意见（含 Editor 意见）均有对应 unit，无遗漏 → 人工对照 Step 1.5 解析表
Editor 层独立：Editor 意见为独立顶层节点，未并入任何 Reviewer → HTML TOC 人工核对
Strategy 基调已定：每个 comment unit 的 content.strategy 字段均非空 → 人工（Step 1.7 确认后）
承诺 ↔ 落点一致：response_en 里承诺的动作能在 modification_actions 或 revised_excerpt_en 找到对应落点 → consistency_check.py（WARN 需消除）[此项必须由独立子代理核，主 agent 不得自评]
edit_plan 已聚合回填：manuscript_edit_plan.md 无 [PENDING Step 7] 行 → aggregate-edit-plan 脚本退出码 0
反驳有据：所有 Push back 策略的 unit 均有至少一条具体证据（引文 / 数据 / 方法学依据）→ 人工
Citation registry 已核验：citation_registry.json 存在且 citation_guard.py 通过；若无新增引用，确认 citation_registry.json 的 entries 为空数组 → citation_guard.py
各 gate 全通：各独立 gate 脚本退出码均为 0（strict_gate / final_content_gate / consistency_check / risk_check / citation_guard / citation_ref_tracker）→ 见 RR13
结构完整性（RR14）：每个 response unit 结构完整（审稿意见原文 + 回复正文 + 修改证据/落点定位三要素齐全），无空 unit；letter 整体覆盖每条意见无遗漏 → 人工

Re-Render Workflow

After manual editing of any unit JSON:

Keep index.json unchanged unless hierarchy changes.
Rebuild HTML only using scripts/render_from_atomic_json.py.
- If render fails (JSON parse error / missing required field): fix the offending units/*.json directly, then re-run. Do not regenerate from scratch.
- If render fails (script not found / import error): check scripts/ directory exists and dependencies are installed; fall back to scripts/run_pipeline.py --allow-placeholder as last resort.
Sync state using scripts/state_manager.py sync --project-root ..
- If sync fails: run scripts/state_manager.py show --project-root . to identify out-of-sync units; fix manually, then retry sync.
Run scripts/final_content_gate.py and scripts/html_format_check.py on the newly rendered HTML.
- Gate checks are mandatory even for single-unit edits.
- If gate fails, fix the offending units/*.json directly and re-run from step 2. Do not skip.

Scripts

入口： scripts/run_pipeline.py，一站式串行执行 preflight → build → 全部 gate → consistency report → html gate。5 个必需参数：--comments / --manuscript / --si（可选）/ --project-root / --output-html。

最小可执行示例（占位符首轮预览，加 --allow-placeholder 放宽内容门禁出骨架；正式交付去掉该 flag）：

python3 scripts/run_pipeline.py \
  --comments /path/to/reviewer_comments.docx \
  --manuscript /path/to/manuscript.docx \
  --si /path/to/supplementary.docx \
  --project-root /path/to/project_root \
  --output-html /path/to/project_root/reviewer_response.html \
  --allow-placeholder

无 SI 时省略 --si。AI 填完 units/*.json 后，去掉 --allow-placeholder 重跑同一命令即为正式交付。

各 gate 由 run_pipeline.py 串行自动调用，正常运行无需手动单独跑。按执行顺序：

strict_gate.py：硬门禁，检查 revised_excerpt_en 非空/非占位符/与原文有实质差异、needs_manual_revision 状态
final_content_gate.py：内容完整性，检查所有 待AI / AI_FILL_REQUIRED 占位符是否已填（--allow-placeholder 仅骨架预览阶段）
consistency_check.py：① 禁用词/冲突术语检查；② 承诺↔落点一致性（WARN）：response_en 中承诺的动作动词（we added/clarified/revised + 对象）须能在同 unit 的 modification_actions 或 revised_excerpt_en 找到对应，否则 WARN（非阻断）
final_consistency_report.py：生成统计报告（units 数量、链接率、缺失 excerpt 计数）
html_format_check.py：HTML 结构完整性
risk_check.py：检测虚构实验/统计、过度承诺、AI 式套话、跨 unit 结构重复
citation_guard.py：验证 citation_registry.json 新增引用真实性（DOI/PMID/撤稿检测）；--offline 跳过在线验证。报告写入 logs/citation_guard_report.json，顶层结构为 {"status": "pass"|"warn", "verified": N, "failed": N, "retracted": N, ...}（注意：无 report.ok 嵌套层；判断通过用 status == "pass"，判断撤稿用 retracted > 0）
citation_ref_tracker.py：交叉验证 [N] 引用编号一致性（未定义引用、编号间隙）

Re-Render 单独脚本：render_from_atomic_json.py（重渲）、state_manager.py（状态同步 sync/show/set/init；改 units 前后用 snapshot/rollback 建还原点与回滚）。

References

按需加载，不要全部预加载：

Atomic schema: references/atomic-unit-schema.json，单元 JSON 结构定义（原子化构建时参考）
Atomic workflow: references/atomic-workflow.md，原子化流程详细说明（首次使用或遇到异常时）
HTML structural skeleton: references/html-template-full.html，主交付物布局骨架（grid + sidebar + content 结构）；实际渲染由 scripts/build_full_package.py 的 render_html() 生成完整 UI（含折叠/展开、拖拽分割线、复制按钮、severity 背景色、localStorage 持久化）
Single-comment fill template: references/html-template.html，单条 comment 的占位符填充骨架，仅配合 html-fill-guide.md 手工填单页时使用；与上面的整包骨架 html-template-full.html 不同
Output contract: references/output-template.md，输出规范（核对交付物结构时）
Decision rules and sentence patterns: references/decision-rules.md，回复措辞决策规则（撰写英文回复时）
HTML filling notes: references/html-fill-guide.md，html-template.html 占位符填写注意事项（手工填单页或渲染异常时）
Figure prompt template: references/figure-prompt-template.md，图片修改/新增时的结构化提示词模板（Output Contract 第3块图片需求时）
Consistency rules: references/consistency-rules.json，consistency_check.py 默认加载的一致性规则集（无需手动引用，gate 自动读取）