| name | revise-sci |
| version | 2.23.2 |
| description | 退稿/返修全管道，同时出逐条回复信+修改后正文docx+Patch修订。触发词：改稿、修改稿子、修订正文、退稿改进、返修、revise manuscript、major revision、minor revision、revise and resubmit、point-by-point response、revised manuscript。路由说明：与reviewer-response-sci区分，本技能同时改主稿+出回复包，后者只出回复不改稿；与gsw区分，gsw写新稿，本技能专处理已有稿子的审稿意见驱动修改。 |
Revise-Sci
Overview
Use this skill to turn reviewer comments, the original manuscript, SI, and attachments into two deliverables: a revised manuscript and a structured Response to Reviewers. Both come out in Markdown and Word.
The workflow is script-gated. Do not skip steps. Do not fabricate experiments, data, statistics, or references.
The comment parser accepts both atomic comment-unit HTML and reviewer-simulator style report HTML with critique lists.
The manuscript atomizer recognizes numbered section headings such as 1, 1.1, and 2.3.4 even when the source Word paragraph style is not a formal heading style.
开场监工卡（每次启动必打印，逐字给用户）
返修改稿最容易在这几处翻车，AI 会做但只有你能核对是不是真做到了。启动本技能时必须原样打印这张卡：
- 拆意见别信 AI 说全了：拆完 AI 应给你一份意见清单，你拿原始审稿信数条数：有没有被合并成一条、有没有整条漏掉。数目对不上就是漏了。
- 改原意要逐处盯：每一处改动，AI 应贴「原句 → 改后句」，你确认意思没变、没夹带你没同意的新结论。看不到对照就别放行。
- 覆盖看对照表：交付前 AI 应给「意见 × 是否回复 × 是否改稿 × 结局」对照表。「改稿」列为空**但结局标
push_back（有意驳回不改）**的是正常的，不是漏；真正的漏是：某条既没回复、结局又不是 completed/push_back/需作者确认。分清「有意不改」和「漏改」。
- 缺证据写"需作者确认"是正常的：AI 没有你的数据/实验时应写「需作者确认」等你补，这不是 bug，请你补齐，别当故障报错。
- 门禁 PASS 只保形式：门禁只查格式/覆盖/红线这类机械项，改得对不对、说理通不通，得你自己核，别把 PASS 当"改对了"。
跨会话接续（每次开局先跑，与监工卡是两件事）
监工卡是「启动提醒」，接续报告是「续上上一会话的进度」。每次进入本技能、且 project_root 已存在时，先跑接续命令再动手：
python "<技能>/scripts/session_journal.py" resume --root <project_root>
env_preflight.py 会把这条打印为 RESUME_CMD（连同 LOG_CMD / CITATION_CHECK_CMD，均为解析好的绝对路径）。读完接续报告后，据它跟用户打接续握手：复述当前 phase、已处理的 comment、以及 decisions_log.md 里用户历次要求，问「我接着做 <下一步>，对吗？还是先插新要求？」等用户确认再继续。
用户在会话中途插入任何临时要求（改哪节、换策略、加/撤某条意见的处理方式）时，当场 log，后续会话必读必守：
python "<技能>/scripts/session_journal.py" log --root <project_root> --note "<用户要求原话>"
Mandatory Intake Before Any Full Pipeline Run
When the user provides a comments_path, a manuscript_docx_path, or both, do not jump straight into run_pipeline.py.
First, env precheck (soft gate, before any pipeline run): python scripts/env_preflight.py <project_root> --cli esearch --py docx; it writes env_status.json, and the last line prints PRECHECK: OK|ASK|BLOCKED. BLOCKED (Python too old) → stop and guide upgrade; ASK (missing optional tools like esearch/python-docx) → ask the user per tool whether to install, give guidance, continue only after the user answers installed/skip; OK → continue. Rollback uses state_manager.py snapshot + Patch-hash (no git checkpoints).
Always run:
python scripts/intake_router.py --comments <comments_path> --manuscript <manuscript_docx_path>
Before any substantive revise work, report to the user:
- which
comments_input_mode was detected;
- which branch-specific workflow will be used next;
- that the workflow preserves the same atomicization, fragment-only rewrite, anti-AI polish, state-window, anti-forgetfulness, and hard-gate rules;
- then ask the user to confirm that routing decision together with the desired
project_root / output path.
If the input does not match any supported branch:
- do not proceed silently;
- ask the user whether to map the input to an existing branch or create a new branch;
- any new branch must still preserve the same atomicization, fragment-only rewrite, anti-AI polish, state-window, anti-forgetfulness, and hard-gate rules.
If the user has no reviewer comments and only provides the manuscript:
- run
python scripts/intake_router.py --manuscript <manuscript_docx_path>;
- ask whether to use
reviewer-simulator first to generate reviewer comments;
- check global availability using
python scripts/ensure_global_skill.py --skill-name reviewer-simulator;
- if the skill is missing and the user confirms installation, install it from your own skills backup repository (reviewer-simulator subdirectory) before invoking that branch.
Comment Input Modes
docx-review-comments: ordinary reviewer comments exported from email or web into a .docx. The parser expects reviewer / major-minor / numbered-comment structure and keeps multiline comments inside one unit.docx-review-letter: ordinary decision-letter style .docx files where the structure is usually editor email -> Reviewer #N overall statement -> numbered comments. The parser now distinguishes editor statements, reviewer overall statements, and actionable numbered comments instead of collapsing them into a single comment stream.reviewer-simulator-html: HTML generated by reviewer-simulator. The parser reads critique-section / critique-list blocks and preserves comment_title, problem_description, evidence_anchor, root_cause, and author_strategy.reviewer-response-sci-html: HTML generated by reviewer-response-sci. The parser extracts the original reviewer comment plus seeded response_en/zh, original_excerpt, revised_excerpt, and revision_location, then feeds those seeds back into localization and response drafting.atomic-comment-html: already-atomic HTML with comment-unit nodes. Existing comment_id values are preserved.no-comments-manuscript-only: manuscript exists but reviewer comments are not provided yet. This is not a revise branch by itself; it is an intake state that must first ask whether to bootstrap comments via reviewer-simulator.
For docx-review-letter, the workflow must:
- distinguish top-of-letter editor statements from numbered editor action items;
- capture reviewer-level
Overall statement / General assessment / Reviewer statement text as reviewer-summary seeds, not as the first numbered comment;
- preserve those statement seeds into downstream response rendering so the exported response package can still show editor/reviewer context explicitly.
For reviewer-response-sci-html, do not trust the incoming response package at face value:
- treat seeded response/revision content as structured hints rather than auto-approved final output;
- prioritize seeded location/original-excerpt hints when localizing the target paragraph;
- still rerun
revise -> polish -> literature/reference checks -> strict_gate before delivery.
Required Inputs
comments_pathmanuscript_docx_pathproject_rootoutput_md_pathoutput_docx_path
Optional but supported:
si_docx_pathattachments_dir_pathreference_docx_pathjournal_stylepaper_search_results_pathreferences_source_pathexpected_comments_modecontext_token_budgetcontext_tail_lines
Output Contract
Always produce:
response_to_reviewers.mdresponse_to_reviewers.docx- revised manuscript markdown at
output_md_path
- revised manuscript Word at
output_docx_path
- 默认 in-place 保原稿格式：当原稿是
.docx 时，改后稿基于原始 manuscript docx 编辑，未被改的段落、表格、图片、样式、对齐原样保留，只替换被点名改写的段落的文字，并按行内标记（*斜体*/**粗**/<sup>/<sub>）重建 run、继承原段落基础字体（font.name/size/eastAsia）。定位/身份对不上时 fail-closed 硬停：export_docx.py 退出码 3，把拒绝原因和两个选项（① 重跑加 --allow-rebuild-fallback 接受重排版本；② 修锚点后用未改动原稿重跑）显式打给用户，不再默认静默降级为 md 全量重建（那会丢原稿表格/图位/对齐并按期刊模板重排，用户却不知情）。只有显式传 --allow-rebuild-fallback（run_pipeline 同名 flag 透传）才回退 md 全量重建。原稿非 docx 或无原稿时正常走 md 全量重建（legacy fallback，非降级）。导出模式记录在 project_state.json 的 outputs.manuscript_export_mode（in-place / in-place-tracked / md-rebuild）。response_to_reviewers.docx 不受影响，维持现有固定样式脚本（含 eastAsia）。
- 可选
--track-changes 词级修订痕迹（默认关闭，仅 in-place 生效）：改动段落按 original vs current 的词级 diff 写成带 Word 红蓝增删痕迹的 docx（<w:ins>/<w:del>，仅包住真正变化的词，行内斜体/上下标/粗体在痕迹两侧保留），导出模式记为 in-place-tracked。关闭时行为与原 clean in-place 完全一致。详见 Pipeline 段 export_docx.py 的 --track-changes 说明。
precheck_report.mdissue_matrix.mdmanuscript_edit_plan.mdfinal_consistency_report.mddata/literature_index.jsondata/revision_claims.jsondata/synthesis_matrix.jsondata/synthesis_matrix_audit.jsondata/reference_registry.jsondata/reference_coverage_audit.jsonfigure_index.json / reference_index.json,反向抽取的图、参考交叉索引(每项含 cited_by 与 orphan_type)abbreviation_index.json,反向抽取的缩略语交叉索引(每项含 defined_count / used_count / orphan_type:undefined_use / duplicate_definition / title_abbreviation 为硬错,defined_unused 为软警告)manuscript_index.md,人读版图/参考/缩略语索引与孤儿汇总。启发式抽取,作审查辅助而非红线核验figures/figure_NN.<ext> + figures/image_manifest.json,从源 docx word/media/ 解出的内嵌图(按 zip 出现顺序命名),供最终返修 docx 嵌回。仅二进制搬运,不做 OCR/图像识别;非 docx 输入则目录可能为空manuscript_section_index.json 每个 section 条目含 figures 字段:该节图注/裸图标题锚定的图清单(figure_id / caption / image_file / source)。图注文本落在哪节该图即归哪节(definitive);图号→图片文件走 manifest idx 启发式(zip 顺序 ≈ 阅读顺序),故图片绑定标 image_binding: ordinal_heuristic
Pipeline
Run the scripts in this exact order:
python scripts/intake_router.py ...
python scripts/preflight.py ...
python scripts/atomize_comments.py ...
python scripts/atomize_manuscript.py ...
python scripts/manuscript_index.py --manuscript <manuscript_docx_path> --project-root <project_root> --units-dir units
python scripts/extract_docx_images.py --manuscript <manuscript_path> --project-root <project_root>
python scripts/build_issue_matrix.py ...
python scripts/state_manager.py --project-root <project_root> refresh
python scripts/citation_guard.py ...
python scripts/revise_units.py --project-root <project_root> [--paper-search-results <paper_search_validated.json>] [--comment-id <comment_id>]
python scripts/build_literature_index.py --project-root <project_root> [--seed-index <writing_project_literature_index.json>]
python scripts/matrix_manager.py bootstrap ...
python scripts/matrix_manager.py audit ...
python scripts/merge_manuscript.py --project-root <project_root> --output-md <output_md>
python scripts/reference_sync.py --project-root <project_root> --output-md <output_md>
python scripts/build_reference_registry.py --project-root <project_root> --output-md <output_md> [--references-source <ref_source>] [--reference-search-decision ask|approved|declined]
python scripts/export_docx.py --project-root <project_root> --output-md <output_md> --output-docx <output_docx> [--reference-docx <ref_docx>] [--manuscript-docx <original_manuscript_docx>] [--no-inplace] [--allow-rebuild-fallback] [--track-changes] [--author revise-sci] [--date <ISO8601>] [--journal-style journal-manuscript|nature-review|cell-press|lancet-review]
python scripts/final_consistency_report.py ...
python scripts/strict_gate.py ...
Or use the single entrypoint:
python scripts/run_pipeline.py --comments <comments_path> --manuscript <manuscript_docx_path> --project-root <project_root> --output-md <output_md_path> --output-docx <output_docx_path> [--journal-style journal-manuscript|nature-review|cell-press|lancet-review] [--expected-comments-mode <comments_input_mode>] [--context-token-budget 4200] [--context-tail-lines 80] [--paper-search-results <paper_search_results_path>] [--resume] [--resume-from <step>] [--resume-keep-unaffected] [--force-rebuild] [--allow-rebuild-fallback]
--expected-comments-mode is strongly recommended after the user confirms the branch chosen by intake_router.py. preflight.py will block execution if the confirmed mode and the detected mode do not match.
[意见清单核对·必停]（拆意见后、改写前的强制关卡）
位置：atomize_comments.py 拆完审稿意见之后、revise_units.py 开始改写之前。这是流程内部的硬关卡，与开场监工卡不同：监工卡是启动时提醒，这一步是拆完意见后的当场核对。
拆完审稿意见后，立即停下，把每条 comment_id + 该条前 30 字列成清单打给用户，并原样问：
「请拿原始审稿信对照数一遍，条数对不对？有没有哪条被合并成一条、或整段漏掉？（尤其审稿人用连续散文、(i)(ii)、罗马数字、或一段里塞多个要求时最容易漏）」
用户确认"都在、没漏"后才继续改写。用户指出漏掉或被合并的，回去把它补成独立 comment（补进 units/、重新原子化）后再继续，不得跳过这一步直接跑 revise_units.py。
[通读定策略·前置阶段]（清单核对通过后、逐条改写前）
真人返修的第一件事不是逐条动手，而是先把所有意见通读一遍、定下每条的应对策略。这里也一样：意见清单核对通过后、revise_units.py 开始逐条改写之前，先做一轮 triage，不要从 atomize 直接跳到逐条改。
对每条 comment 定四选一的策略，并写进该 unit 的 revision_strategy 字段（units/*.json）：
| 策略 | revision_strategy 值 | 含义 | 结局 |
|---|
| 照做 | comply | 认可意见，按要求改正文 | 走正常改写 → completed / needs_author_confirmation |
| 部分让 | partial | 部分采纳，改一部分并说明取舍 | 正常改写 + 回复信说明界限 |
| 驳回 | push_back（或 驳回/reject） | 不采纳、正文不动，在回复信据理反驳 | 一等结局 push_back（见下节） |
| 补数据 | needs_data | 需新增实验/数据/图，当前材料不足 | 落 needs_author_confirmation，等作者补 |
硬规则：revise_units.py 逐条改写前，每条 unit 的 revision_strategy 必须先填（该字段已存在也要强制先确认/覆盖，不能留空跳过）。通读定策略是本阶段的产出，把结论落到字段里再进逐条改写。
[驳回/不改] 是一等合法结局（不是漏改）
除 completed / needs_author_confirmation 外，新增第三个合法结局 push_back：认定某条意见不应采纳，正文一个字不动，只在回复信里据理反驳。这是真实返修的常态（审稿人误解、超范围要求、与本文定位冲突等），不是缺陷。
- 怎么触发：该 unit 的
revision_strategy 设为 push_back（或 驳回/reject 等，见上表）。revise_units.py 即把该条 status 置为 push_back：正文不改、revised_excerpt 记为「N/A — manuscript unchanged」、回复信生成据理反驳的中英回应。反驳理由填 unit 的 push_back_rationale_zh / push_back_rationale_en（不填则回复信留占位提示作者补）。
- 覆盖判定别误报：
issue_matrix.md 的「修改动作」列会显示「不改（驳回）」、状态列显示 push_back；监工卡第 3 条的对照表里，某条「改稿」列为空但结局是 push_back 的，是「有意不改」，不得判成「漏改」。判漏改的唯一标准是：status 既非 completed、又非 push_back、又非 needs_author_confirmation，或该 comment_id 在回复信里根本没有回应。
- 不阻断交付：
push_back 是已决结局，delivery_status 只被 needs_author_confirmation 卡；push_back 计入 project_state.json 的 counts.push_back，不进待办。
- 红线仍在：驳回≠可以不回应。回复信里该条必须有据理反驳的 response（中英），否则仍算漏回。
[合并意见] 允许多条相关意见协调回应
原子架构默认每条意见一个密封 state window，但相关意见（同一处、同一诉求的不同侧面）应允许合并成一处协调回应 + 交叉引用，而不是各写各的、自相矛盾。
- 最小用法：给相关的几条 unit 设同一个
merge_group（任意稳定 id，如 MG-limitations），并指定其中一条为 merge_lead（主回应所在的 comment_id）。主条写完整协调回应；其余成员条的 response 里交叉引用主条（如「详见 R2.3 的统一回应」/ "see our unified response to R2.3"），不重复长篇。
- 窗口不封死：
state/comment_windows/<id>.json 会带上 merge_group / merge_lead，据此从 comment_registry.json 找到同组兄弟条一起看，避免协同时上下文被切断。
- 不拆原子架构：合并只是「分组 + 交叉引用」，每条仍是独立 unit、独立 comment_id、独立覆盖核验，绝不把多条塞进一条。
Anti-Forgetfulness And Token-Budget Protocol
revise-sci does not load the entire manuscript and all comments into one context window. It uses the same approach as article-writing, review-writing, and sci2doc, adapted for revise work:
- Intake-first routing: route the comment source first, then lock the branch before loading anything large.
- Section-paragraph atomicization: only the target section and target paragraph are used for rewrite scope.
- Comment-scoped state windows: every processed
comment_id gets its own context package under state/comment_windows/<comment_id>.json.
- Section digests, not full reloads: cross-section consistency uses
state/section_digests.json, which stores only headings, paragraph counts, and key sentences, rather than full section text.
- Token budget compaction:
state_manager.py write-cycle estimates token load and compacts related digests / reviewer context / neighboring paragraphs if the bundle exceeds the configured budget.
- Cycle log persistence: every revise action appends to
state/comment_cycle_log.json and state/comment_memory/<comment_id>.md, so a future agent does not need to reconstruct local history from scratch.
- Snapshot safety:
state_manager.py snapshot writes state snapshots so runs can be resumed with smaller context and lower drift risk.
Recommended per-comment loading command:
python scripts/state_manager.py --project-root <project_root> write-cycle --comment-id <comment_id> --token-budget 4200 --tail-lines 80 --json-summary
This command is the revise-sci equivalent of the section-scoped state loading in article-writing, review-writing, and sci2doc. It is the preferred context entry before any manual or AI-assisted change to a specific comment-linked paragraph.
Patch 修订协议（可选的确定性修订路径）
This is an optional, additive deterministic path for applying scope-locked edits. It does not replace the atomize -> issue-matrix -> revise_units -> strict_gate flow. Use it when you need a hard guarantee that only the touched blocks can change and every other block stays byte-for-byte identical, rather than having the model regenerate whole sections (the main source of scope creep and drift).
Protocol (four phases):
- anchorize: split the target draft into blank-line blocks, assign each a stable anchor id (
block-NNNN-<hash8>), and write a block manifest (anchor -> exact original bytes + sha256 + byte offsets):
python scripts/anchorize_draft.py --draft <draft.md> --manifest <project_root>/block_manifest.json
- patch: for each reviewer comment that needs a block changed, author a patch entry
{anchor_id, expected_hash, new_content} where expected_hash is the block's sha256 from the manifest. Patch only the blocks that must change; never touch other anchors. The patch file is a JSON array of such entries.
- apply (deterministic, fail-closed): locate each block by anchor id, verify its current sha256 equals the patch's
expected_hash, then splice only the patched byte-spans:
python scripts/apply_revision_patch.py --manifest <block_manifest.json> --patch <patch.json> --output <revised.md>
If any entry's hash does not match (the block already changed) or the source draft drifted since anchorize, the whole patch set is rejected, nothing is written, and the script exits non-zero. There is no silent partial apply.
- finalizer:
apply_revision_patch.py reassembles the full draft from the original source, copying every unpatched byte verbatim (blocks, separators, and trailing-newline state preserved). Feed <revised.md> back into the normal polish -> literature/reference checks -> strict_gate flow before delivery.
Rules:
- The patch path is fail-closed: a hash mismatch or source drift must abort and write nothing; never coerce or auto-relocate a patch onto a changed block.
- The patch path is an increment on top of the existing pipeline, not a replacement:
atomize_comments.py, build_issue_matrix.py, the state-window protocol, and strict_gate.py all still apply to the resulting draft.
缩略语首展一致性(Abbreviation Consistency)
改稿最易破坏缩略语一致性:改某句时删掉了首展、在首展之前的位置裸用 ABBR、或新增术语未首展。规则:
- 首展格式:英文
Full Name (ABBR);中文正文 中文全称（English Full Name, ABBR）。同一缩写全文只首展一次,之后裸用 ABBR,不重复展开。
- Title 禁缩写(DNA/RNA/PCR 等通用词除外);Abstract 独立,即使正文已定义,Abstract 内首次出现仍应重新展开。
- 改稿守则:替换/删除句子时若该句承载某缩写的唯一首展,须把首展移到改后稿中该缩写的新首现处;新引入的术语必须在首现处首展。
- 核查:
manuscript_index.py 对改后稿产 abbreviation_index.json。undefined_use(裸用未定义)/duplicate_definition(重复首展)/title_abbreviation(Title 含缩写)为硬错须修;defined_unused(定义后未再用)为软警告,人工取舍。通用缩写见脚本 UNIVERSAL_ABBREVIATIONS 白名单,自动跳过。索引为启发式辅助,可疑项人工复核。
Response Format
response_to_reviewers must use this hierarchy:
# 回复审稿人的邮件- optional
## Editor Statement when the decision letter contains editor-only overall instructions but no numbered editor comments
- optional
# Editor when there are numbered editorial action items
# Reviewer #N## Major / Minor### Comment k
Each comment must contain:
审稿意见与中文理解Response to Reviewer（中英对照）可能需要修改的正文/附件内容（中英对照）修改说明（中文）Evidence Attachments
Rules
- Missing information must be written as
Not provided by user or 需作者确认.
- If a reviewer asks for new literature, only
paper-search is allowed as the external provider family.
paper_search_results_path may be used to ingest confirmed paper-search results into citation-oriented comment handling.paper_search_results_path is not trusted directly. It must first pass citation_guard.py, which performs dual verification using provider trace and identifier/title consistency evidence before citations can auto-complete a comment.- 新增文献真实性双验（B②，不许 --offline 交付）：审稿要求补新文献时，全部新引文献必须过
citation_guard.py 的 在线真实性双验（DOI/PMID 解析、撤稿检测、逐源标题一致性）。有已 completed 的 citation 类意见时，strict_gate.py 会读 paper_search_guard_report.json：summary.online_check 非 true（即用 --offline 或没加 --live 跑的）或 all_rows_guard_verified 非 true，一律 fail-close。交付前必须 python scripts/citation_guard.py --live ... 重跑，不许 --offline 跳过。
- 新引文献↔它支撑的回复论点，须过引文核证（B④）：真实性通过只说明该文献存在，不说明它真支撑你借它下的结论。对每条「新引文献 → 它在回复信/正文里支撑的论点句」，用该文献检索到的真实 abstract 判支撑度，落
claim_evidence.json（每条含 claim_sentence / is_load_bearing / ref_id / retrieved_abstract / verdict∈support/weak/contradict/unknown / user_confirmed），再跑共享 citation_claim_check.py（CITATION_CHECK_CMD）。跨批复用由脚本自动完成，AI 不必手动记账。脚本在核证前从项目根 ref_evidence_cache.json 自动回填缺失字段，核证后强制落盘。已在别处验过 abstract 的文献，本批该行 retrieved_abstract 可留空，脚本按 ref_id 回填。同一篇文献且完全同一论点句此前已人工确认过的，脚本自动复用其 verdict 与 user_confirmed，不再重复反向验证与逐条确认。只有新的 (文献, 论点) 组合才需要你补 abstract、判支撑度并逐条人工确认。门禁强度不变，承重句被判 contradict/unknown、缺 abstract、或 support/weak 但未确认一律硬拦，新 (文献, 论点) 无 verdict 仍 fail-close。同一篇文献换去支撑另一句论点，不复用旧确认，须独立判定。有 completed citation 意见时，strict_gate.py 复用共享 citation_claim_check._row_blockers 核验 claim_evidence.json，文件缺失或任一承重句阻断即 fail-close。abstract 的检索走工作流subagent（本脚本不含 MCP）。
build_literature_index.py must convert validated citation support into review-writing style canonical artifacts: data/literature_index.json and data/revision_claims.json.build_literature_index.py accepts an optional --seed-index <path> to reuse the writing project's existing literature_index.json (produced by gsw/review-writing) as a seed. Seed entries keep their original global_id; revision-found references that match a seed entry (dedup key: normalized DOI > PMID > normalized title) reuse the seed number instead of getting a new one, and truly new references continue numbering from max(seed global_id) + 1. The seed is read-only; the merged result is written only to revise-sci's own data/literature_index.json, never back to the writing project (seed-extension semantics). The seed reader tolerates the looser gsw schema (global id under any of global_id/citation_number/id/number/ref_number, back-filled by array order when absent) and a seed located either at the project root or under data/. Omitting --seed-index keeps the original rebuild-from-1 behavior unchanged.matrix_manager.py must derive data/synthesis_matrix.json from the canonical literature index and emit data/synthesis_matrix_audit.json before delivery.build_reference_registry.py must extract the final manuscript reference list into canonical data/reference_registry.json and audit body-to-reference coverage into data/reference_coverage_audit.json.build_reference_registry.py may import a fallback reference seed from references_source_path when the manuscript reference list is empty or absent.- If a manuscript already has a partial numeric
References section, build_reference_registry.py should try to merge missing numbered entries from the detected legacy reference source instead of failing immediately.
- If unresolved reference gaps still remain after registry rebuild,
build_reference_registry.py must emit reference_recovery_request.md so the author knows exactly which source formats to provide next.
- If no original or legacy reference source is available, ask the user whether to start a new literature-search-and-fill cycle; default state is
reference_search_decision=ask, not silent auto-search.
- If the user approves new reference search, the search-and-fill path must follow the
review-writing discipline: paper-search retrieval only, immediate citation_guard.py after each import batch, update canonical data/literature_index.json, then refresh data/synthesis_matrix.json / data/synthesis_matrix_audit.json before any new references can enter the manuscript.
- If
reference_search_decision=approved and reference gaps still exist, the skill must generate reference_search_manifest.json and reference_search_task.md so the approved search cycle is executable and auditable rather than implicit.
- The approved search cycle should also emit
reference_search_strategy.json and reference_search_status.json so search scope, provider policy, round model, and step status remain explicit and machine-checkable.
- The approved search cycle should also emit
reference_search_rounds.json, containing concrete query batches for Round 1 / Round 2 / Round 3 under review-writing governance.
- The approved search cycle must explicitly declare
workflow=review-writing, allowed_provider_families=["paper-search"], forbidden_provider_families containing websearch, and verification_policy.dual_verification_required=true.
- The approved search cycle must keep a three-round structure in both
reference_search_manifest.json and reference_search_strategy.json, and must record citation_guard.py as the mandatory verification command.
build_reference_registry.py should audit both numeric citations and author-year citations; unresolved gaps in either style must block delivery.- Confirmed citation support must include an explicit anchor such as
target_section_heading, target_paragraph_index, or target_text; otherwise the item stays in needs_author_confirmation.
- If current materials are insufficient, keep the item in
needs_author_confirmation instead of inventing a resolution.
- Treat
completed as a narrow state: only conservative text-only clarification or limitation edits with reliable paragraph localization may be auto-completed.
- If paragraph localization is ambiguous and multiple candidates score similarly, fall back to
needs_author_confirmation rather than selecting a paragraph aggressively.
- If a comment contains an explicit structured section hint such as
Section 4.2 or 4.2 节 but that hint cannot be matched to an existing section, do not fall back to lexical matching; keep the item in needs_author_confirmation.
- For Chinese-source reviewer comments, keep the original Chinese comment as the authoritative source block and render a separate English working summary instead of mislabeled bilingual fields.
preflight.py must record comments_input_mode so downstream steps and audit reports know whether the current run came from raw reviewer comments, reviewer-simulator HTML, reviewer-response-sci HTML, or already-atomic HTML.preflight.py must also record expected_comments_mode, context_token_budget, and context_tail_lines; these values become part of the resume fingerprint.preflight.py must fail fast when the user runs the full pipeline on an unsupported or unclassified comments source, rather than silently guessing a branch.reviewer-response-sci HTML inputs must be treated as response-rich seeds: atomize_comments.py should preserve the seeded response/revision fields, and revise_units.py should reuse them conservatively for localization and draft response blocks without bypassing manuscript rewrite constraints or hard gates.- Citation-only comments may be auto-completed only when confirmed
paper-search results and formatted citation text are explicitly provided.
- Citation-only comments may be auto-completed only when the row is
confirmed, the citation guard marks it guard_verified=true, and the target anchor is explicit.
- After manuscript merge,
reference_sync.py must append or update the References/参考文献 section using canonical data/literature_index.json and emit reference_sync_report.json.
- When
author_confirmation_reason is rendered into English, the translated reason must remain fully English with no leftover Chinese fragments.
- For substantive requests such as new mechanism explanations, new evidence, new figures, or unresolved section matches, stop at
needs_author_confirmation and do not auto-complete.
strict_gate.py must verify comment coverage, response/manuscript/edit-plan consistency, atomic location completeness, provider-family policy, and per-comment evidence blocks before delivery.- 📢 交付前半成品提醒（非阻断）：
strict_gate.py 每次运行都统计最终 response 正文里 需作者确认 的出现次数、以及非默认的 Not provided（排除每个 unit 的 Image/Table 默认模板行 Not provided by user，避免狼来了）；命中就打印醒目 banner「还有 N 处待你处理」。这不判 FAIL（需作者确认 是合法输出），只响亮提醒，防止半成品被当成成品直接投稿。
- 🧭 PASS 诚实化：
STRICT_GATE: PASS 后追加一行真话：PASS 仅覆盖形式层（引文编号/去 AI/结构/占位符/文件完整性），改写是否改变原意、科学结论是否正确、数据是否一致均未自动核验，须作者逐条核对。
strict_gate.py must verify that every auto-completed citation comment is covered by reference_sync_report.json; otherwise delivery fails.strict_gate.py must verify that every auto-completed citation comment is present in both data/literature_index.json and data/synthesis_matrix.json, and that data/synthesis_matrix_audit.json reports no unresolved matrix gaps.strict_gate.py must fail delivery when data/reference_coverage_audit.json reports unresolved numeric citation gaps, even if the comment-level workflow itself completed.strict_gate.py must parse response_to_reviewers.docx and verify that comment headings, response-section headings, and evidence-section headings are present for every comment block.strict_gate.py must verify that reference_search_manifest.json, reference_search_strategy.json, and reference_search_status.json are internally consistent with actual approved-search artifacts such as paper_search_validated.json, paper_search_guard_report.json, data/literature_index.json, data/synthesis_matrix_audit.json, and reference_sync_report.json.references_source_path is optional. If not provided explicitly, the pipeline may auto-detect likely sources such as a same-title sibling manuscript docx with a populated References block, <comments_dir>/data/literature_index.json, attachment files named like reference*/bibliography*, or project-local seed files.references_source_path auto-discovery should also inspect nearby versioned manuscript docx files inside shallow subdirectories of the manuscript folder when they share the same title and contain a usable References block.references_source_path may also be a .ris file exported from a reference manager.- Keep
Evidence Attachments in every comment block, even when no image or table is available.
--resume skips already-materialized upstream artifacts so a rerun does not silently overwrite previously curated units.--resume also checks stored input fingerprints; if comments/manuscript/SI/attachments/reference/paper-search inputs changed, the rerun fails fast instead of trusting stale artifacts. 失败提示里会引导用户改用 --resume-keep-unaffected。--resume-keep-unaffected：返修一作常天天改稿，一处改动即触发上面的全量重建、丢弃已 curated units。加此 flag 后，若本次改动仅涉及内容输入（comments/manuscript/SI）且未触及任何已定位的 comment unit（重新原子化到临时目录后比对：无 comment 文本增删改、且没有 unit 锚定的 section 正文变化），则保留全部 curated units、更新输入指纹后续跑；若有 unit 受影响则列出受影响的 comment_id 并 fail（curation 与原子化耦合，无法只重生成受影响 units 而不清空其它 curation，须重新 curation 后 --force-rebuild）；若改动涉及非内容输入（journal_style/runner/文献/预算等全局项）也 fail（无法按 unit 局部化）。注：即便保留续跑，若原稿段落发生插入/删除导致全局段落索引漂移，最终 in-place 导出仍会在身份校验处硬停（见 export_docx P1），属预期 fail-safe。--resume must also fail fast when the stored skill signature differs from the current script tree signature.--resume-from <step> must clear the selected step and all downstream generated artifacts, then rebuild only from that step onward under the same verified input fingerprint.--force-rebuild clears generated project artifacts, including data/ and citation intermediate files, and reruns the pipeline from scratch inside the same project_root.state_manager.py refresh must materialize state/section_digests.json and state/comment_registry.json before revise_units.py starts.revise_units.py must write state/comment_windows/<comment_id>.json and state/write_cycle_reports/<comment_id>.json for every comment unit, then append state/comment_cycle_log.json.--live-citation-verify enables online title/identifier verification when paper-search results are provided; pipeline mode should be recorded in preflight output.final_consistency_report.md should list each needs_author_confirmation item with a blocker type and the exact stored reason.final_consistency_report.md should also summarize reference coverage status, including detected numeric citations, reference entry count, and missing reference numbers when present.final_consistency_report.md should also report whether reference_search_required=true and the current reference_search_decision.final_consistency_report.md should also summarize intake mode, expected mode, state-window budget, section digest counts, and comment-window counts.- Word export should render common markdown emphasis and list markers as real Word formatting instead of leaving raw
**...** and list prefixes in the document body.
response_to_reviewers.docx should include a visible heading hierarchy plus a TOC field, centered header text, and footer page-number field so the exported package is review-ready rather than plain-text only.export_docx.py should support profile-based manuscript export via --journal-style, with distinct body/title/heading/reference/table styles for at least journal-manuscript, nature-review, cell-press, and lancet-review.- Markdown pipe tables in manuscript or response markdown should be rendered as actual Word tables rather than plain paragraphs.
- Response block labels such as
Text / Image / Table should be rendered with a dedicated Word paragraph style so exported reviewer-response documents keep a consistent block structure.
- If
reference_search_decision=approved and --auto-run-reference-search is enabled, the pipeline should invoke a local runner hook via execute_reference_search.py; this runner must still obey review-writing governance and may only emit paper-search rows.
- If approved auto-run is requested but no local runner is configured, the pipeline must fail explicitly and write
reference_search_execution_request.md instead of pretending that search has already been executed.
- The local runner contract must remain machine-checkable:
--rounds-json <path> --output <path> --project-root <path>, with output saved to project_root/paper_search_results.json.
- Approved search auto-execution must rerun
citation_guard.py, revise_units.py, literature-index/matrix steps, reference_sync.py, and build_reference_registry.py before export and gate.
- If no explicit local runner is provided but
opencode is available, the workflow may fall back to an internal opencode run driver that still writes the same paper_search_results.json schema under review-writing governance.
- The
opencode fallback must write a preserved prompt file (reference_search_opencode_prompt.md) and an execution report (reference_search_execution.json) so the retrieval path remains auditable.
strict_gate.py and final_consistency_report.md should surface reference_search_execution.json state instead of hiding the actual execution mode.- Query hints for approved search should come not only from missing reference coverage but also from pending citation-oriented review comments that still point to
paper-search as a required evidence source.
- Lexical paragraph localization should use structured fields with low-signal-token filtering and heading-weighted scoring; if the best lexical candidate is still low-confidence, keep the item in
needs_author_confirmation.
- Reviewer-response Word export should use dedicated body, reviewer-heading, label, and comment-heading styles, with improved spacing and Word-native table header shading, rather than leaving all blocks as generic paragraphs.
- Automatic manuscript rewriting must stay at the changed-fragment level.
revise_units.py should replace only the targeted sentence, or append only the new limitation sentence, rather than rewriting the entire paragraph.
- A dedicated
polish stage must run after revise and before literature/reference merge. This stage consumes only revision_plan.raw_fragment, never untouched original sentences.
- The polishing stage must follow
article-writing, review-writing, and humanizer-zh constraints together: direct evidence-bounded wording, no invented claims, no new citations, no banned AI phrases, no decorative transitions, and no paragraph-wide rewrite unless the new content is itself a new paragraph.
- The polishing stage must emit
revision_polish_manifest.json, revision_polish_prompt.md, and revision_polish_execution.json so the anti-AI prompt, driver mode, and candidate coverage remain auditable.
strict_gate.py must verify that completed revised fragments with a non-empty revision_plan.scope have polish state, a valid polish_driver_mode, and no residual banned AI-style markers.- The polishing prompt must be layered, not flat. It must include: role definition, non-negotiable edit/evidence/citation/length constraints, deep anti-AI rewriting protocol, and a JSON-only output contract.
- Polish anti-AI 去AI五项（适用于中英文改稿正文）。硬/软分层：写作时五项都要守；门禁对「主干」硬失败，套话禁词、scare quotes、解释性冒号、-ing 假分析从句、装饰性破折号这类真正的 AI 味硬拦（fail-close）；只把「句长 >30 词」降为软提示（
strict_gate.py 响亮上报、不 fail-close）。装饰性破折号禁止使用，命中即 FAIL。
- 禁装饰性破折号（🔴 硬门禁，禁止使用，命中即 FAIL）：禁用 —/——/em-dash 充当停顿、补充或强调（如"该结果——尽管样本量小——表明…"）；改用逗号、句号或拆为两句。连字符（"dose-response"）与数值范围不受限。中英文均适用。
strict_gate.py/polish_guard 对破折号 fail-close，不放行。
- 禁 scare quotes：禁用双引号包裹自造词或普通短语以暗示"新概念/反讽"；保留：术语首次定义、原始审稿人评论直接引用、已固化的术语隐喻。
- 禁解释性冒号：禁用"概念: 解释"或"Concept: explanation"格式的装饰句式；合法冒号包括比例、时间、列表引导、标题、图表标签。
- 英文单句 ≤30 词（🟡 软提示，不阻断）：polished 片段中任何独立英文句子（以
.!/? 分界）词数应 ≤30 词；超限建议拆句、不要用分号逃避拆句。句长超限只在 strict_gate.py 软提示 banner 上报，不 fail-close（sentence >30 words 已归入 SOFT_STYLE_MARKERS）。禁止 -ing 分词从句作假分析：形如 , reflecting … / , ensuring … / , highlighting … / , suggesting … 的尾置 -ing 从句禁止用于添加未经数据支撑的推断；已有明确证据锚点的 participial phrase 不受此限。find_ai_style_markers 中 "trailing -ing clause" 检测已覆盖以 ,\s*(thus|thereby|therefore)\s+[a-z-]+ing 模式；追加覆盖 , (reflecting|ensuring|highlighting|suggesting|demonstrating|indicating|revealing)\b 模式。
- 中文单句 ≤50 字、从句 ≤2 层（如正文含中文）：任何中文句子（句号/问号/感叹号分界）字数不得超过 50 字；嵌套从句层数不超过 2 层（如"A（B（C））"为第 3 层，须拆分）。连续 3 句字数差异 <5 字时应主动变换句长。
- 硬/软实现：
common.hard_ai_style_markers() 返回会 fail-close 的主干标志（套话/scare quotes/解释性冒号/-ing 假分析/not only…but also/反问/em dash 破折号等）；common.soft_ai_style_markers() 只返回软项（sentence >30 words，即 SOFT_STYLE_MARKERS）。polish_revisions.py 的 polish_guard_ok 与 strict_gate.py 的 polished-fragment 校验都对 hard 子集 fail（破折号在内）；soft 项由 strict_gate.py 汇总为「去AI软提示」banner 逐条列出、并写入 unit 的 polish_soft_style_flags，不阻断。中文句长/从句层数为软警告，记录于 notes。
revision_plan should carry locked_prefix, locked_suffix, evidence_boundary_note, and citation_strings so the polishing step can preserve untouched context explicitly rather than infer it.- The polishing output schema should include
edit_decision, meaning_changed, scope_respected, ai_style_flags_removed, and notes.
strict_gate.py must fail if a polished revision reports meaning_changed=true, scope_respected=false, or if reconstructed paragraph text no longer preserves the locked prefix/suffix context.- Polish 片段级守卫（A/B/C/MID，仅比对锁定的
raw_fragment 与 polished_fragment 两个字符串，不破坏 scope-lock）：
- A 数值守卫：
common.numeric_tokens_preserved(raw, polished) 抽取数字 token（整数/小数/百分比/p 值如 p=0.03/CI/n=N）并比对集合。polished 引入原片段没有的新数值，或丢失原有数值，视为 numeric drift。polish_revisions.py 写入 polish_numbers_ok，strict_gate.py 不通过则 fail。
- B 不确定性动词校准：
common.detect_certainty_upgrade(raw, polished) 只拦截证据强度被升高的方向。谨慎动词（may/might/could/suggests/indicates/is associated with/appears/is consistent with）被升级为强断言（demonstrates/proves/establishes/confirms/shows definitively）即判越权加强，符合保守哲学。写入 polish_certainty_ok，strict_gate.py 不通过则 fail。
- C Risk Flags：上述拦截在 fail 之外额外输出结构化清单
polish_risk_flags: [{type: numeric_drift|certainty_upgrade|overstatement|invented_claim, fragment_id, detail}]，写入每个 unit、revision_polish_execution.json 与对应 comment_records/<id>.md。fail 行为保留，不放行。
- MID 禁词表：
common.AI_CLICHE_TERMS_EN（与 general-sci-writing/scripts/style_checker.py 的 FORBIDDEN_EXACT 对齐：moreover/delve into/it is worth noting 等）+ AI_CLICHE_TERMS_ZH（值得注意的是/综上所述等），由 find_ai_style_markers 在 polished 片段上检测套话词，命中归入 overstatement 风险并阻断门禁。
strict_gate.py must also fail if comments_input_mode is unsupported, expected_comments_mode and detected mode diverge, or the required state-window artifacts are missing.
Character-level typography contract（字符级排版契约）
Applies to all newly written or rewritten content (revised fragments, new sentences, response-letter prose). These inline markers are rendered into real Word character formatting by scripts/export_docx.py (bold/italic/superscript/subscript runs). This contract governs the markers you emit when authoring new text. Reading the original docx now preserves run-level formatting too: read_docx_paragraphs(..., inline_format=True)（仅 atomize_manuscript.py 开启）把原稿 run 的 italic/bold/sup/sub 序列化成同一套行内标记进 section text/current_text，所以未改片段的原格式经 revise→export 往返不丢；被改片段也按同一套标记在 in-place 写出时重建 run。默认读取器仍为纯文本（inline_format=False），数值/引用/AI 风格红线比对不受标记污染。
- Italic via
*...* for: species Latin names (*E. coli*, *Staphylococcus aureus*), gene names (*TP53*, *BRCA1*), single-letter statistical symbols (*p*, *t*, *n*, *F*, *r*), and Latin abbreviations (*in vitro*, *in vivo*, *et al.*, *e.g.*, *i.e.*).
- Superscript via
<sup>...</sup>: exponents and powers (10<sup>6</sup>, cm<sup>2</sup>, mg·kg<sup>-1</sup>). Subscript via <sub>...</sub>: chemical subscripts and indexed terms (H<sub>2</sub>O, CO<sub>2</sub>, IC<sub>50</sub>, T<sub>max</sub>). Never emit bare H2O / CO2 / IC50.
- Bold via
**...** only for headings and inline labels (e.g. **Limitations.**), never for emphasis inside running scientific prose.
- 中文回复部分：句内标点全角（，。：；），英文与数字保持半角，中英文之间不强制空格但须一致。
These inline markers are load-bearing and carry the same status as citation markers [n]: when rewriting a locked fragment, do not add, drop, or mis-pair them. Adding */<sup>/<sub> where the source had none, or stripping existing ones, is a meaning/format drift and is subject to the same fragment-only and scope-lock rules as [n].
❌ 反例黑名单（Anti-Patterns）
- ❌ 跳过
intake_router.py 直接跑 run_pipeline.py，或输入源未分类／不支持仍硬跑（preflight 须 fail-fast，不得猜分支）。
- ❌ 重写整段而非只改目标句或只追加新句（fragment-only，
revise_units.py 只动 revision_plan 锁定的片段）。
- ❌ 把全文加全部意见塞进一个上下文窗，违反防遗忘 token 预算，须用 comment-scoped state window 逐条加载。
- ❌ 虚构实验、数据、统计或引用来回应意见；缺信息须写
Not provided by user 或 需作者确认。
- ❌ 用 websearch／tavily／openalex 补文献；只允许 paper-search，且新引用须过
citation_guard 双向核验。
- ❌ 段落定位模糊却硬选一个段落；多候选评分相近时须落
needs_author_confirmation，不得激进选段。
- ❌ 把实质性请求（新机制／新证据／新图／未匹配章节）当
completed 自动收口；只有保守的纯文本澄清或限制句可 auto-complete。
- ❌ Patch 修订哈希不符仍强行套用或自动重定位（fail-closed，整批拒绝、写空、退非零，不静默部分应用）。
- ❌ 去 AI 主干未过（硬）：scare quotes、解释性冒号、套话禁词、-ing 假分析从句、装饰性破折号（🔴 硬门禁，禁止使用，命中即 FAIL）。（仅英文 >30 词为软提示：上报不阻断，但仍应改。）
- ❌ 主 agent 自评 DoD 当通过；
strict_gate.py 前须委托独立subagent盲检，verify 未 exit 0 不得声明改稿完成；盲检过后仍须摆逐项结论 + HALT 等用户确认才收口。
- ❌ 把「有意驳回不改（
push_back）」误判成「漏改」，或反过来把真漏改的意见混进 push_back 蒙混；驳回必须在回复信据理反驳，正文不动但回应不能缺。
- ❌ 退稿信漏回某条意见，或某
completed comment_id 在 manuscript_edit_plan.md 中无 revised_excerpt 落点（push_back/需作者确认 不要求 revised_excerpt）。
- ❌ 补新文献只验真实性（DOI/PMID）就下笔，跳过「引文↔论点」核证；或用
--offline 跑 citation_guard 就交付（承重句须过 citation_claim_check.py，guard 须 --live）。
- ❌ 引文
[n] 与参考列表不对应、缺号或编号不连续就交付（reference_coverage_audit.json 须 ok=true）。
- ❌
--resume 时输入指纹或脚本签名已变仍信任旧产物，而非 fail-fast 重建。
- ❌ 改稿删/换句子时丢失某缩写的唯一首展、在首展前裸用 ABBR、新增术语不首展，或 Title 出现缩写（
abbreviation_index.json 的 undefined_use / duplicate_definition / title_abbreviation 硬错须清零）。
- ❌ 改写锁定片段时增删或错配行内排版标记（
*italic* / <sup> / <sub> / **bold**），等同于篡改引文标记 [n]；裸写 H2O/CO2/IC50 或漏给物种名、基因名、统计符号加斜体。
Definition-of-Done (DoD) 自检清单（改稿收口）
位置：polish 完成后、strict_gate.py 运行前。硬规则：清单未逐项确认通过，不得向用户声明"改稿完成"。
🔴 委托盲检（不得主 agent 自评）：改稿完成后自评容易默认通过且漏项。strict_gate.py 运行前必须把 DoD 清单委托给独立上下文的subagent盲检，不得自己直接打勾：
- 生成任务包：
python scripts/delegate_review.py pack --checklist references/dod_checklist.json --gate revision-dod --files <改稿相关文件> --comments <comments_path>（--comments 传本次审稿信原文，盲检子代理据原信逐条点名核对漏回/答非所问；同一 comments_path 与 run_pipeline.py --comments 一致）
- 派一个独立subagent（Claude Code 用
academic-blind-reviewer；其他平台派通用subagent），把任务包原样给它、不要给它本次改稿的写作上下文，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 revision-dod --return <subagent返回.json>；退出码非 0（任一缺项/fail/无证据）= fail-closed，据subagent证据修复后重跑，未过不得声明改稿完成。
⚠️ 盲检降级告警：若当前环境派不出真正独立的subagent（非 Claude Code 客户端、provider 不支持 Task/子会话），绝不能用同一个 AI 自问自答冒充盲检（那就是自证）。此时明确告诉用户：「本环境盲检不可靠，请你亲自复核这几点：（列出该盲检本应查的关键点，如 RV-G1 引文↔参考一一对应、RV-G3 改动是否跑题、RV-G5 去AI五项、RV-G7 缩略语首展、RV-G8 常识/事实错误等）」，把判断权交回用户，不得伪造一份"通过"的盲检返回。
下列清单与 references/dod_checklist.json 逐项对应（改清单先改 JSON，再同步此处散文）；能脚本核的项subagent会先跑脚本：
通用 8 项（id: RV-G1 ~ RV-G8）
| id | 项目 | 核验方式 |
|---|
| RV-G1 | 引文 [n] ↔ 参考列表一一对应，无孤儿引用、无缺号，编号连续 | python scripts/build_reference_registry.py → data/reference_coverage_audit.json ok=true |
| RV-G2 | 本轮新增引用已过 citation_guard 双重核验 | python scripts/citation_guard.py → ok=true，无 manual_review 条目 |
| RV-G3 | 改动符合原文 storyline / 主线（不跑题，不与原文主线矛盾） | 人工对照 issue_matrix.md 逐段核查（无脚本可自动核验） |
| RV-G4 | 占位符清零：无 CITE_PENDING / DATA_PENDING / 【待AI】 / {{ 残留 | grep -r "CITE_PENDING|DATA_PENDING|待AI|{{" <project_root>/ 零命中 |
| RV-G5 | 去 AI 五项（破折号/scare quotes/解释性冒号/英文≤30词/-ing从句/中文≤50字≤2层从句）通过 | python scripts/strict_gate.py --project-root <project_root> → ai_style_flags_removed 无残留；句长警告记录于 notes |
| RV-G6 | 字数达标（改动前后正文字数在期刊要求范围内） | 人工或期刊要求核对 |
| RV-G7 | 缩略语首展一致：abbreviation_index.json 无 undefined_use / duplicate_definition / title_abbreviation 硬错；改稿未破坏既有首展，Title 不含缩写（defined_unused 为软警告可人工豁免） | python scripts/manuscript_index.py --manuscript <output_md> --project-root <project_root> 后读 abbreviation_index.json，硬错 orphan 零命中（启发式索引，可疑项人工复核） |
| RV-G8 | Commonsense sanity (🟡 soft report, non-blocking): the blind-review subagent also scans rewritten fragments for obvious commonsense/factual errors (absurd unit magnitudes, physiology/mechanism mistakes, internal numeric contradictions) introduced by the rewrite. Report only, never block delivery, never auto-edit content. Distinct from the citation/reference verification gates (RV-G1/RV-G2) and from reviewer-simulator's full scientific audit. | 盲检subagent LLM 判断（复用现有 delegate_review 盲检机制，无新脚本）；命中只在subagent返回 notes 报告，软项不进 strict_gate.py 硬失败、不计入 delegate_review verify 的阻断退出码（与 references/dod_checklist.json 硬门禁互不冲突） |
🔴 收口前置闸口：delegate_review verify 必须 exit 0（含 RV-R8 结构完整性），否则不得声明改稿完成。任一项 fail 均为阻断。
🛑 DoD 停·摆结论等确认（strict_gate 前的最后一道人工闸）：盲检 delegate_review verify exit 0 之后、strict_gate.py 之前，不得直接收口。先把逐项结论摆给用户，每条 DoD（RV-G1G8 / RV-R1R12）是 pass / na / 🟡soft-report，软项（RV-G8 常识、RV-R12 拉丁斜体、去AI软提示、句长）列出但标明不阻断；同时给「意见 × 是否回复 × 是否改稿 × 结局（completed/push_back/需作者确认）」对照表。打印后 HALT，等用户明确说「可以收口」再跑 strict_gate.py 并交付。用户没确认就继续 = 违规。这与开场监工卡、清单核对是三道不同的人工闸：开场提醒 → 拆完核对 → 收口前摆结论。
Revise-Sci 特有项（id: RV-R1 ~ RV-R12）
| id | 项目 | 核验方式 |
|---|
| RV-R1 | strict_gate.py 通过（exit code 0） | python scripts/strict_gate.py --project-root <project_root> → STRICT_GATE: PASS |
| RV-R2 | Reference coverage 无缺口：data/reference_coverage_audit.json ok=true，无 unresolved numeric/author-year gap | python scripts/build_reference_registry.py → coverage_audit 直接读；或 RV-R1 覆盖 |
| RV-R3 | Patch 修订哈希一致（如使用 Patch 修订协议）：apply_revision_patch.py 未报告任何 hash mismatch，所有未触及 block 字节不变（fail-closed，哈希不符则整批拒绝，不得静默部分应用）；未使用则标 na 并注明 | python scripts/apply_revision_patch.py --manifest <block_manifest.json> --patch <patch.json> --output <revised.md> exit code 0 |
| RV-R4 | 退稿信每条意见有落点：issue_matrix.md 每个 comment_id 在 manuscript_edit_plan.md 中有 revised_excerpt | python scripts/strict_gate.py --project-root <project_root>（strict_gate 内含此检查，RV-R1 通过则本项通过） |
| RV-R5 | 审稿意见已原子化：atomize_comments.py 在 pipeline 中已运行，每条意见有 severity 字段，comment_id 唯一，无混合意见跨意见合并改动 | 人工确认 state/comment_registry.json 已生成且 comment_id 唯一（atomize_comments.py 无 --dry-run flag，须通过 pipeline 正式运行核验） |
| RV-R6 | polish 状态完整：所有含非空 revision_plan.scope 的片段已有 polish state，无 meaning_changed=true 或 scope_respected=false | python scripts/strict_gate.py --project-root <project_root>（strict_gate 内含此检查，RV-R1 通过则本项通过） |
| RV-R9 | polish 片段级守卫通过：每个 polished 片段 polish_numbers_ok=true（无数值漂移/丢失）、polish_certainty_ok=true（谨慎动词未被升级为强断言）、无套话禁词残留；polish_risk_flags 已落盘到 unit / revision_polish_execution.json / comment_records/<id>.md | python scripts/strict_gate.py --project-root <project_root>（strict_gate 内含 A/B/MID 三项检查，RV-R1 通过则本项通过） |
| RV-R7 | response_to_reviewers.docx 结构完整：每个 comment block 都有 comment heading / response-section heading / evidence-section heading | python scripts/strict_gate.py --project-root <project_root>（strict_gate 解析 docx 核验结构，RV-R1 通过则本项通过） |
| RV-R8 | 结构完整性：改后稿件结构完整（原结构无破坏、参考文献编号连续、response 各 unit 三要素齐全）；退稿信每条意见在 edit_plan 中有落点无遗漏 | python scripts/strict_gate.py --project-root <project_root>（RV-R1 通过则本项通过）；或人工逐段核查 |
| RV-R10 | 跨节一致性盲检（全局层，超出片段级 RV-R9）：改稿后关键数值/样本量/效应量/主要结论在摘要-正文-图表-结论间仍一一对应、无新引入矛盾；改动未把原谨慎表述升级为新过度声称（因果化/普适化/夸大疗效）。跨节不一致或新增过度声称=fail，列冲突两处原文为证 | python scripts/cross_section_consistency.py --project-root .（客观信号）+ 盲检subagent据此判定 |
| RV-R11 | 语法拼写与字符级格式：对原子化正文 manuscript_sections/ 跑字符级体检。高置信类别 misspelling（英文常见错拼）/ chinese_punct（中文标点漏入英文句）/ subsup_bare（H2O、IC50、cm² 等应上下标却裸写，含 CJK 安全边界）零容忍：命中任一即 fail_on_hits 非空、ok=false、退出码非 0；其余类别（学术错拼/中文错字/单位/英美混用/数字格式/术语不一致/Methods 时态/断链）仅报告不阻断。只报告供用户决断，绝不自动改正文（fragment-only 保真），命中后由用户决定是否回片段修订 | python scripts/proofread.py --manuscript-dir manuscript_sections --report proofread_report.json --fail-on misspelling,chinese_punct,subsup_bare → ok=true 且 fail_on_hits 为空 |
| RV-R12 | 拉丁短语斜体软提醒（🟡软/人工确认，不阻断）：proofread.py 的 latin_italic_missing 类别，正文里 in vitro/in vivo/ex vivo/in situ/de novo/post hoc/per se 等公认须斜体的拉丁短语若裸写（未被 *...* 斜体标记包裹）则报告。仅提示，不阻断、不进 --fail-on、不扣分，由人工确认是否补斜体（et al./e.g./vs. 等正体惯例不在词表内） | 同 RV-R11 脚本，读 proofread_report.json 中 latin_italic_missing 计数供人工决断，不影响 ok/退出码 |
RV-R3 仅在使用 Patch 修订协议时适用，跳过需在 notes 中注明原因。RV-R4/R6/R7/R8/R9 已由 strict_gate 覆盖，RV-R1 通过即视为通过；RV-R5 须确认 pipeline 正式运行产出 comment_registry.json。RV-R10 为跨节一致性全局盲检（独立脚本 cross_section_consistency.py + subagent判定），不由 strict_gate 覆盖，须单独核。
投稿前作者自检（🟡 soft 提醒，不阻断交付）
终稿交付前，对照 references/presubmission_checklist.md 过一遍（数字一致性、英美拼写统一、图像无不当处理、Source Data、查重、临床注册号、报告规范附件、投稿材料齐全等）。这些项多需作者掌握原始数据/图像/外部工具，机器无法可靠裁决，故只提醒、不阻断；与本技能既有 hard 门禁（引用一一对应、去AI、跨节一致、字符级体检 RV-R11 等）不重复。
发现 AI 跳步/漏做了怎么办（用户自救）
如果你怀疑 AI 拆意见拆漏了、改稿改跑了、或直接把半成品当成品交付，下面几句话可直接复制发给它，逼它回到正轨：
- 「审稿信里 Reviewer X 第 N 点你没拆出来，回去把它作为独立 comment 加进
units/，重新原子化再重跑 revise_units.py。」
- 「把第 X 条对应的原句和你改后的句子并排贴给我，我要确认意思没变、没夹带我没同意的新结论。」
- 「给我一张表：每条审稿意见 × 有没有回复 × 正文改了哪句（引用
manuscript_edit_plan.md 的 revised_excerpt）。哪条空着就是漏了，当场补。」
- 「先别跑完整 pipeline，先只跑到
atomize_comments.py 把意见清单给我看，我对照原始审稿信确认条数无误了再往下。」
- 「你这环境派不出独立subagent就别假装盲检通过了。把这轮该盲检的关键点列给我，我自己核。」
