paper-write-sci

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Original

English

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Chinese

Paper Write SCI

与 bensz-collect-bugs 的协作约定

Collaboration Agreement with bensz-collect-bugs

因本 skill 设计缺陷导致的 bug，先用
```
bensz-collect-bugs
```
规范记录到
```
~/.bensz-skills/bugs/
```
，不要直接修改用户本地已安装的 skill 源码；若有 workaround，先记 bug，再继续完成任务
只有用户明确要求“report bensz skills bugs”等公开上报时，才用本地
```
gh
```
上传新增 bug 到
```
huangwb8/bensz-bugs
```
；不要 pull 或 clone 整个仓库

用于根据 LaTeX 论文项目、Figure/Table 注释和用户补充要求，撰写或优化 SCI 期刊论文正文。

执行时优先把确定性步骤交给脚本，把启发式判断留给 AI：

初始化工作区、模式归一化、风格选择、计划文件命名：使用
```
config.yaml:scripts.prepare_workspace
```
长规则块按需从
```
references/
```
读取；不要把所有参考文档一次性塞进上下文

For bugs caused by design flaws of this skill, first use
```
bensz-collect-bugs
```
to record them in
```
~/.bensz-skills/bugs/
```
in a standardized manner; do not directly modify the locally installed skill source code of the user; if there is a workaround, record the bug first, then continue to complete the task
Only when the user explicitly requests actions like "report bensz skills bugs" for public submission, use the local
```
gh
```
to upload new bugs to
```
huangwb8/bensz-bugs
```
; do not pull or clone the entire repository

This skill is used to write or optimize the main text of SCI journal papers based on LaTeX paper projects, Figure/Table annotations, and user supplementary requirements.

During execution, prioritize assigning deterministic steps to scripts and leaving heuristic judgments to AI:

Initialize workspace, normalize mode, select style, name plan files: use
```
config.yaml:scripts.prepare_workspace
```
Read long rule blocks from
```
references/
```
as needed; do not load all reference documents into the context at once

目标

Objectives

写出更像作者本人、而不是通用 AI 模板的论文
在写作与修订过程中严格保护数字、逻辑和术语一致性
默认直接推进修改；当用户需要人机协作时，只输出计划，不直接改论文
除明确约定的对外交付物外，把所有中间文件收敛到
```
<paper_dir>/.paper-write-sci/run_{timestamp}/
```

Produce papers that are more like the author's own work rather than generic AI templates
Strictly protect consistency of numbers, logic, and terminology during writing and revision
Directly advance modifications by default; when the user requires human-machine collaboration, only output plans without directly modifying the paper
Converge all intermediate files into
```
<paper_dir>/.paper-write-sci/run_{timestamp}/
```
except for explicitly agreed external deliverables

输入

Inputs

输入项	是否必须	说明
论文源代码目录	必须	LaTeX 论文项目根目录
Figure/Table 注释	必须	解释每张图表支撑什么论点、有哪些关键数字
用户要求	可选	例如“只改 Results”“偏保守润色”“补强 Discussion”
参考论文/参考作者材料	可选	用于提炼额外风格信号，只学风格，不抄句子
运行模式	可选	默认值与别名以 `config.yaml:mode` 为准
风格	可选	默认值与可用列表以 `config.yaml:style` 为准

Input Item	Required	Description
Paper source code directory	Yes	Root directory of the LaTeX paper project
Figure/Table annotations	Yes	Explain what argument each chart supports and what key numbers it contains
User requirements	Optional	e.g., "Only modify Results", "Conservative polishing", "Strengthen Discussion"
Reference papers/author reference materials	Optional	Used to extract additional style signals; only learn the style, do not copy sentences
Running mode	Optional	Default values and aliases are based on `config.yaml:mode`
Style	Optional	Default values and available list are based on `config.yaml:style`

输出

Outputs

autonomous

autonomous

直接修改目标正文文件
将分析、审查、渲染日志写入当前运行目录
```
<paper_dir>/.paper-write-sci/run_{timestamp}/
```
若检测到可用构建链，尝试重新渲染 PDF 和 Word

Directly modify the target main text files
Write analysis, review, and rendering logs into the current running directory
```
<paper_dir>/.paper-write-sci/run_{timestamp}/
```
If an available build chain is detected, attempt to re-render PDF and Word

collaborative

collaborative

只输出计划文件，文件名模式以
```
config.yaml:runtime_outputs.collaborative_plan_pattern
```
为准，默认带上本轮
```
run_id
```
计划中总结论文缺陷、证据、建议修复方案、影响文件和风险
不直接修改论文内容
计划以外的中间文件仍写入当前运行目录
```
<paper_dir>/.paper-write-sci/run_{timestamp}/
```

Only output plan files, with the filename pattern based on
```
config.yaml:runtime_outputs.collaborative_plan_pattern
```
, which defaults to including the current
```
run_id
```
Summarize paper defects, evidence, recommended repair solutions, affected files, and risks in the plan
Do not directly modify the paper content
Intermediate files other than the plan are still written to the current running directory
```
<paper_dir>/.paper-write-sci/run_{timestamp}/
```

模式规则

Mode Rules

autonomous

（默认）

autonomous

(Default)

发现问题就直接修复
采用最小必要改动原则
在写入任何新数字前，必须先过数字审查
在结束前，必须通过章节职责终审、全文一致性终审和逻辑树终审

Fix problems directly when discovered
Adhere to the principle of minimal necessary changes
Must pass numerical review before writing any new numbers
Must pass final review of chapter responsibilities, full-text consistency, and logical tree before completion

collaborative

collaborative

先完整读论文，再归纳缺陷和修改路径
计划仅作为人类审查材料，不对正文落笔
计划文件名、主题 slug、
```
run_id
```
和输出目录都以
```
config.yaml:runtime_outputs
```
为准
计划内容至少包含：问题、证据、建议动作、影响章节、关联图表、风格锚点、章节分工风险、风险说明

Read the entire paper first, then summarize defects and modification paths
The plan is only used as human review material, no changes are made to the main text
Plan filename, topic slug,
```
run_id
```
, and output directory are all based on
```
config.yaml:runtime_outputs
```
The plan content must include at least: problems, evidence, recommended actions, affected chapters, associated charts, style anchors, chapter division risks, risk explanations

中间文件约束

Intermediate File Constraints

除下列“明确约定的对外交付物”外，其余中间文件都必须放在

<paper_dir>/.paper-write-sci/run_{timestamp}/

：

```
plans/{collaborative_plan_pattern}
```
论文最终构建产物，例如项目已有的 PDF 和 Word 输出

禁止再使用旧目录

.write-paper-sci/

与更早的

.write-paper/

。

Except for the following "explicitly agreed external deliverables", all other intermediate files must be placed in

<paper_dir>/.paper-write-sci/run_{timestamp}/

```
plans/{collaborative_plan_pattern}
```
Final paper build products, such as existing PDF and Word outputs of the project

Prohibit using the old directories

.write-paper-sci/

and the earlier

.write-paper/

风格系统

Style System

风格目录：
```
references/styles/
```
风格模板：
```
references/styles/style-template.md
```
默认风格以
```
config.yaml:style.default
```
为准

当前风格：

风格	领域	作用
`bensz-01`	生物医学	以作者风格为中心，强调问题导向、方法命名、强数字对比、详尽且对非领域读者友好的 figure legend，以及诚实局限
`general-01`	通用 SCI	综合官方 SCI 写作建议，提供未指定领域时的稳健默认风格

风格使用原则：

优先使用用户显式指定的风格
若用户提供了参考论文或作者材料，可在所选风格基础上提炼额外信号，保存到当前运行目录的
```
analysis/reference-style.md
```
若用户未指定，则使用
```
config.yaml:style.default
```
风格服务于“更像人”，不是为了堆砌花哨句子
风格只能改变表达方式，不能改变事实、数字和逻辑
当任务是“全面润色”“重写 Discussion”或任何明显涉及
```
Discussion
```
去结果化的请求时，先用
```
general-01
```
守住章节分工底线，再叠加
```
bensz-01
```
的作者感；不要让作者风格压过章节职责

Style directory:
```
references/styles/
```
Style template:
```
references/styles/style-template.md
```
Default style is based on
```
config.yaml:style.default
```

Current Styles:

Style	Field	Function
`bensz-01`	Biomedical	Author-style centered, emphasizing problem orientation, method naming, strong numerical comparison, detailed figure legends friendly to non-field readers, and honest limitations
`general-01`	General SCI	Integrate official SCI writing suggestions, provide a robust default style when no field is specified

Style Usage Principles:

Prioritize using the style explicitly specified by the user
If the user provides reference papers or author materials, additional signals can be refined based on the selected style and saved to
```
analysis/reference-style.md
```
in the current running directory
If the user does not specify, use
```
config.yaml:style.default
```
Style serves to "make the paper more human-like", not to pile up fancy sentences
Style can only change the way of expression, not facts, numbers, or logic
When the task is "full polishing", "rewrite Discussion" or any request obviously involving de-resulting of
```
Discussion
```
, first use
```
general-01
```
to hold the bottom line of chapter division, then overlay the author sense of
```
bensz-01
```
; do not let the author style override chapter responsibilities

按需读取的参考文件

On-Demand Reference Files

优先只读取当前任务所需的参考文件：

风格与章节写法：

references/writing-style-guide.md

、

references/styles/bensz-01.md

、

references/styles/general-01.md

执行护栏与通过标准：
```
references/execution-guards.md
```

协作计划模板：

references/collaborative-plan-template.md

数字审查模板：

references/templates/number-check-template.md

章节职责审查模板：

references/templates/section-role-check-template.md

Discussion audit

模板：

references/templates/discussion-role-check-template.md

逻辑树模板：

references/templates/logic-tree-template.md

逻辑审查模板：

references/templates/logic-check-template.md

读取建议：

涉及章节串位、
```
Discussion
```
重写或全文终审时，读取
```
references/execution-guards.md
```
只做风格化润色或图注润色时，优先读取
```
writing-style-guide.md
```
和目标风格文件
新增风格时，再读取
```
references/styles/style-template.md
```

Prioritize reading only the reference files required for the current task:

Style and chapter writing methods:

references/writing-style-guide.md

references/styles/bensz-01.md

references/styles/general-01.md

Execution guards and passing standards:
```
references/execution-guards.md
```

Collaborative plan template:

references/collaborative-plan-template.md

Numerical review template:

references/templates/number-check-template.md

Chapter responsibility review template:

references/templates/section-role-check-template.md

Discussion audit

template:

references/templates/discussion-role-check-template.md

Logical tree template:

references/templates/logic-tree-template.md

Logical review template:

references/templates/logic-check-template.md

Reading Recommendations:

Read
```
references/execution-guards.md
```
when involving chapter misplacement,
```
Discussion
```
rewriting, or full-text final review
Prioritize reading
```
writing-style-guide.md
```
and target style files when only doing stylized polishing or figure legend polishing
Read
```
references/styles/style-template.md
```
only when adding new styles

工作流程

Workflow

阶段 0：初始化

Phase 0: Initialization

确认论文目录、Figure/Table 注释存在且可读
定位主入口 tex，优先检查
```
main.tex
```
扫描
```
\input{}
```
和
```
\include{}
```
，建立章节路径映射
识别构建方式与受保护格式文件

运行

python3 scripts/prepare_workspace.py --paper-dir <paper_dir> [--mode ...] [--style ...] [--topic ...] [--reference-material ...]

根据脚本输出确认本轮
```
run_{timestamp}
```
目录、协作计划路径和隐藏工作区根目录
若有参考论文或参考作者材料，提炼补充风格信号
若任务涉及章节职责、数字、缩写或逻辑高风险问题，读取
```
references/execution-guards.md
```

Confirm that the paper directory and Figure/Table annotations exist and are readable
Locate the main entry tex, prioritize checking
```
main.tex
```
Scan
```
\input{}
```
and
```
\include{}
```
to establish chapter path mapping
Identify the build method and protected format files

Run

python3 scripts/prepare_workspace.py --paper-dir <paper_dir> [--mode ...] [--style ...] [--topic ...] [--reference-material ...]

Confirm the current
```
run_{timestamp}
```
directory, collaborative plan path, and hidden workspace root directory based on the script output
If there are reference papers or author reference materials, refine supplementary style signals
If the task involves high-risk issues such as chapter responsibilities, numbers, abbreviations, or logic, read
```
references/execution-guards.md
```

阶段 1：理解当前论文

Phase 1: Understand the Current Paper

读取全文正文与关键 front/back matter
对照 Figure/Table 注释，提取每张图表支撑的论点
识别已有优质段落、薄弱段落、事实风险、风格不一致位置
标记章节职责风险，特别是
```
Introduction
```
泄露结果、
```
Results
```
过度解释、
```
Discussion
```
复述结果的段落
初步构建逻辑树并写入当前运行目录的
```
analysis/logic-tree.md
```

若任务涉及全文缩写治理，按

references/execution-guards.md

建立

analysis/abbreviation-inventory.md

Read the full main text and key front/back matter
Extract the argument supported by each chart by comparing with Figure/Table annotations
Identify existing high-quality paragraphs, weak paragraphs, factual risks, and style inconsistencies
Mark chapter responsibility risks, especially paragraphs where
```
Introduction
```
reveals results,
```
Results
```
over-interprets, and
```
Discussion
```
repeats results
Initially build a logical tree and write it to
```
analysis/logic-tree.md
```
in the current running directory
If the task involves full-text abbreviation management, establish
```
analysis/abbreviation-inventory.md
```
according to
```
references/execution-guards.md
```

阶段 2：决定执行路径

Phase 2: Determine Execution Path

collaborative

collaborative

按

config.yaml:runtime_outputs.collaborative_plan_pattern

生成计划文件

计划应聚焦“缺陷与修复建议”，而不是直接给改后全文
计划必须显式写出
```
section-role risk
```
到此停止，不修改正文

Generate the plan file according to

config.yaml:runtime_outputs.collaborative_plan_pattern

The plan should focus on "defects and repair suggestions" rather than directly providing the revised full text
The plan must explicitly write out
```
section-role risk
```
Stop here, do not modify the main text

autonomous

autonomous

制定内部修订顺序
优先修正事实错误、数字风险和逻辑断裂
再做结构优化、语言润色和风格统一

Develop an internal revision order
Prioritize correcting factual errors, numerical risks, and logical breaks
Then perform structural optimization, language polishing, and style unification

阶段 3：逐节写作或修订

Phase 3: Section-by-Section Writing or Revision

默认顺序：

text

Introduction -> Methods -> Results -> Discussion -> Conclusion ->
Additional Information -> Figure Legends -> Supplementary Materials -> Abstract

每节处理时：

先读现有文本和对应图表证据
先判断该节的章节职责，再用所选风格判断“应该怎么写更像作者”
若涉及长规则判断，回到
```
references/execution-guards.md
```
若涉及新数字，先过数字审查
若命中
```
Discussion audit
```
触发条件，先完成专项审查，再动笔
若涉及新增、删除或改写缩写，先回查
```
analysis/abbreviation-inventory.md
```
在
```
autonomous
```
模式下对目标 tex 做最小必要修改，并遵守
```
config.yaml:tex_readability
```
更新逻辑树与必要的全文一致性记录，确保局部改动没有破坏全局

处理 Figure Legends 或 Supplementary Materials 时：

对每个 panel 解释读图所需的最小视觉语法
对首次出现且不够直观的术语或缩写，补全称并给一句短定义
只保留帮助读图的必要方法细节，避免把整段 Methods 重复进 legend

Default order:

text

Introduction -> Methods -> Results -> Discussion -> Conclusion ->
Additional Information -> Figure Legends -> Supplementary Materials -> Abstract

When processing each section:

First read the existing text and corresponding chart evidence
First judge the chapter responsibility of the section, then use the selected style to judge "how to write more like the author"
If long-rule judgment is involved, refer back to
```
references/execution-guards.md
```
If new numbers are involved, pass numerical review first
If the
```
Discussion audit
```
trigger condition is hit, complete the special review first, then start writing
If adding, deleting, or rewriting abbreviations is involved, check back
```
analysis/abbreviation-inventory.md
```
first
In
```
autonomous
```
mode, make minimal necessary modifications to the target tex and comply with
```
config.yaml:tex_readability
```
Update the logical tree and necessary full-text consistency records to ensure that local changes do not break the global consistency

When processing Figure Legends or Supplementary Materials:

Explain the minimal visual syntax required to read the figure for each panel
For terms or abbreviations that appear for the first time and are not intuitive enough, supplement the full name and a short definition
Only retain necessary method details that help read the figure, avoid repeating the entire Methods section into the legend

阶段 4：终审

Phase 4: Final Review

发起
```
section-role-check
```
完成全文一致性复核，包括数字、缩写、Figure/Table 引用与图注一致性
对最新文本重建逻辑树并发起逻辑审查
若有阻塞性问题，修复后再复审

Initiate
```
section-role-check
```
Complete full-text consistency review, including consistency of numbers, abbreviations, Figure/Table citations, and figure annotations
Rebuild the logical tree for the latest text and initiate logical review
If there are blocking issues, review again after fixing

阶段 5：渲染与交付

Phase 5: Rendering and Delivery

按以下优先级检测构建链：

项目内置一键构建或导出脚本
```
scripts/manuscript_tool.py
```
```
Makefile
```
```
latexmk
```
直接
```
xelatex
```

若存在 Word 导出链，也应尝试执行。构建日志放入当前运行目录的

render/

。

Detect the build chain in the following priority:

Project-built one-click build or export script
```
scripts/manuscript_tool.py
```
```
Makefile
```
```
latexmk
```
Direct
```
xelatex
```

If a Word export chain exists, attempt to execute it as well. Put the build logs into

render/

of the current running directory.

约束

Constraints

不修改

artifacts/

、

*.sty

、

*.cls

、

*.bst

、

*.bbx

、

*.cbx

、

latexmkrc

不改
```
main.tex
```
的结构，除非用户明确要求
不编造数字
不把缩写检查降级成“当前文件自洽”
不允许同一概念在不同 tex 中使用冲突缩写、冲突全称或忽有忽无的定义
不要为了局部简洁随意新造缩写；若新缩写不会在全文稳定复用，优先不用
不为“排版整齐”而重排无关段落或整节
```
.tex
```
用户要求“只改某节”时，严格限制改动范围
用户要求协作模式时，严格禁止直接修改论文

Do not modify

artifacts/

*.sty

*.cls

*.bst

*.bbx

*.cbx

latexmkrc

Do not modify the structure of
```
main.tex
```
unless explicitly requested by the user
Do not fabricate numbers
Do not downgrade abbreviation checks to "self-consistency in the current file"
Do not allow conflicting abbreviations, conflicting full names, or intermittent definitions of the same concept in different tex files
Do not arbitrarily create new abbreviations for local brevity; if the new abbreviation will not be stably reused in the full text, prefer not to use it
Do not rearrange irrelevant paragraphs or entire sections of
```
.tex
```
for "typesetting neatness"
Strictly limit the scope of changes when the user requests "only modify a certain section"
Strictly prohibit direct modification of the paper when the user requests collaborative mode

参考文件

Reference Files

运行准备脚本：
```
scripts/prepare_workspace.py
```
执行护栏：
```
references/execution-guards.md
```
风格模板：
```
references/styles/style-template.md
```
```
bensz-01
```
：
```
references/styles/bensz-01.md
```

general-01

：

references/styles/general-01.md

协作计划模板：

references/collaborative-plan-template.md

章节写作指南：
```
references/writing-style-guide.md
```

数字审查模板：

references/templates/number-check-template.md

章节职责审查模板：

references/templates/section-role-check-template.md

Discussion audit

模板：

references/templates/discussion-role-check-template.md

逻辑树模板：

references/templates/logic-tree-template.md

逻辑审查模板：

references/templates/logic-check-template.md

Workspace preparation script:
```
scripts/prepare_workspace.py
```
Execution guards:
```
references/execution-guards.md
```
Style template:
```
references/styles/style-template.md
```
```
bensz-01
```
:
```
references/styles/bensz-01.md
```

general-01

references/styles/general-01.md

Collaborative plan template:

references/collaborative-plan-template.md

Chapter writing guide:
```
references/writing-style-guide.md
```

Numerical review template:

references/templates/number-check-template.md

Chapter responsibility review template:

references/templates/section-role-check-template.md

Discussion audit

template:

references/templates/discussion-role-check-template.md

Logical tree template:

references/templates/logic-tree-template.md

Logical review template:

references/templates/logic-check-template.md

paper-write-sci

Original

Translation

Paper Write SCI

Paper Write SCI

与 bensz-collect-bugs 的协作约定

Collaboration Agreement with bensz-collect-bugs

目标

Objectives

输入

Inputs

输出

Outputs

autonomous

autonomous

collaborative

collaborative

模式规则

Mode Rules

autonomous（默认）

autonomous (Default)

collaborative

collaborative

中间文件约束

Intermediate File Constraints

风格系统

Style System

按需读取的参考文件

On-Demand Reference Files

工作流程

Workflow

阶段 0：初始化

Phase 0: Initialization

阶段 1：理解当前论文

Phase 1: Understand the Current Paper

阶段 2：决定执行路径

Phase 2: Determine Execution Path

collaborative

collaborative

autonomous

autonomous

阶段 3：逐节写作或修订

Phase 3: Section-by-Section Writing or Revision

阶段 4：终审

Phase 4: Final Review

阶段 5：渲染与交付

Phase 5: Rendering and Delivery

约束

Constraints

参考文件

Reference Files

`autonomous`

`autonomous`

`collaborative`

`collaborative`

`autonomous`
（默认）

`autonomous`
(Default)

`collaborative`

`collaborative`

`collaborative`

`collaborative`

`autonomous`

`autonomous`