papersmart-revision

name

papersmart-revision

description

Apply focused local revisions to an existing PaperSmart manuscript while preserving source integrity, evidence traceability, figure/table numbering, citations, and change logs. Use when the user asks for local edits, reviewer-style fixes, section polishing, targeted restructuring, citation cleanup, caption updates, inline AIGEN/AIPO markers, or specific changes after 03_output/manuscript/paper.md already exists.

PaperSmart-revision

Overview

Handle local manuscript changes after a draft exists. Keep the change scoped to the user's request, and synchronize any affected tables, figures, captions, citations, references, and logs.

Use PaperSmart-draft instead when the user asks for a full manuscript, a major rewrite of the argument, or new Results based on unaudited data.

Critical Rule: Review Advice Is Not Manuscript Text

Classify the task before editing:

• If the user asks for review, audit, reviewer-style critique, modification advice, method improvement suggestions, action steps, or operation steps, create a Markdown report under 03_output/revision or 03_output/supplement. Do not create or overwrite 03_output/manuscript/paper.md.
• If the user explicitly asks to implement already accepted changes into the manuscript, then edit paper.md and record the change in 03_output/revision/change_log.md.
• If the user asks for both advice and implementation, separate the artifacts: advice/report in 03_output/revision or 03_output/supplement, manuscript changes in 03_output/manuscript/paper.md.

Chinese triggers such as 审核, 审稿, 评审, 修改意见, 修改建议, 改进建议, 方法改进, 操作步骤, and 审核意见 are review/advice tasks by default, not manuscript-generation tasks. Match review/advice output language to the manuscript's primary language unless the user specifies otherwise.

Language And Path Mode

Before reading project files, read the PaperSmart profile:

• English mode: shared/memory/papersmart_profile.md
• Chinese mode: 共享/记忆/papersmart_profile.md

Use the configured path map. If language is zh, use Chinese folder names and answer in Chinese. If no profile exists, assume English mode.

Required Reading

Read from the active project:

1. 03_output/manuscript/paper.md
2. 03_output/revision/local_revision_tasks.md
3. config/project_config.md
4. 02_reference/style_notes.md
5. Any affected table, figure, caption, data, literature, or reference file

In Chinese mode, use the equivalent configured paths.

If the task references reviewer comments or an editor decision letter, read those files before editing. If the user only asks you to summarize, evaluate, or expand those comments, write a review/advice artifact outside paper.md.

Workflow

1. Identify whether this is implementation into the manuscript or advice/report generation. Stop before editing paper.md if the request is advice-only.
2. Identify the exact requested change and the affected manuscript sections.
3. Check whether the requested change requires evidence from 01_draft, 02_reference, 03_output/tables, 03_output/figures, or verified literature.
4. Treat user comments, reviewer comments, screenshots, and chat instructions as guidance, not manuscript prose. Extract the scientific change they imply; do not paste or paraphrase the conversational wrapper into the paper.
5. Apply only the requested local change. Do not opportunistically rewrite unrelated sections.
6. If the revision affects a table, figure, caption, in-text citation, reference entry, declaration, or numbering sequence, update the linked artifacts in the same pass.
7. Preserve all unsupported or missing information as precise TODO: [specific missing evidence or action] markers.
8. Keep citation numbers continuous and ordered by first appearance when using a numbered style.
9. Update 03_output/revision/change_log.md.
10. If the change is substantial, update logs/writing_log.md or logs/decision_log.md.

Revision Types

Use these patterns:

• Text polish: improve clarity, academic restraint, tense, transitions, and terminology without adding new claims.
• Local restructure: reorganize only the requested section and preserve claim support.
• Citation repair: add, remove, or renumber citations only when sources are verified.
• Figure/table sync: revise captions, in-text citations, numbering, or references to generated files.
• Reviewer response preparation: preserve a trace from each reviewer request to the manuscript change and change log.
• Journal adaptation: adjust headings, abstract shape, captions, or declarations only according to verified journal guidance.

Inline AI Marker Rules

Use these rules when editing Markdown manuscripts or local revision task files that contain inline markers in the form *content*AIGEN or *content*AIPO.

*content*AIGEN

Treat AIGEN as a request to regenerate the marked span from context.

• Read the surrounding paragraph, subsection, section thesis, nearby figure/table references, and claim-source map before rewriting.
• Replace the entire marked pattern, including the surrounding asterisks and AIGEN, with new manuscript-safe prose.
• Do not merely polish the marked words. Rebuild the content so it fits the argument, evidence boundary, terminology, tense, and paragraph flow.
• If the marker appears inside a paragraph, preserve the paragraph's single-message logic. If the marked span implies a second message, split or restructure only as much as needed.
• Do not add new claims, data, citations, author details, or methodology. Use TODO: when required evidence is missing.
• Example: *近期的讨论*AIGEN should become a context-specific phrase or sentence supported by the surrounding manuscript logic, not a generic replacement for "recent discussion".

*content*AIPO

Treat AIPO as a request to polish and repair the marked span from context.

• Keep the intended meaning unless the surrounding evidence shows the wording is inaccurate.
• Improve clarity, academic tone, terminology consistency, sentence rhythm, and logical fit with adjacent sentences.
• Repair repetition, semantic duplication, inconsistent keywords, vague nouns, tense mismatch, and weak transitions.
• Replace the entire marked pattern, including the surrounding asterisks and AIPO, with clean manuscript prose.
• Do not expand a local polishing marker into a new argument unless the user explicitly asks.

Marker Cleanup

• No AIGEN, AIPO, AIREF, or marker asterisks may remain in the final manuscript unless the user explicitly asks to keep them for review.
• When multiple markers appear close together, resolve them in reading order and then reread the whole paragraph for coherence.
• Log the marker pass in 03_output/revision/change_log.md, noting whether each marker was regenerated (AIGEN) or polished (AIPO) and whether any TODO remains.
• If a marker contains a claim whose evidence is not closed, do not write a workaround sentence. Replace it with TODO: [specific missing evidence or action] or move the unsupported material out of the manuscript.
• If a journal or institution requires AI-use disclosure, summarize resolved marker work in a formal disclosure statement rather than leaving AIGEN or AIPO labels in the article body.

Boundaries

• Do not invent data, results, citations, author details, ethics, funding, conflicts, acknowledgements, or journal requirements.
• Do not overwrite original files in 01_draft or 02_reference.
• Do not convert a local revision into a full rewrite unless the user asks.
• Do not convert review reports, audit findings, modification advice, action plans, or method-operation steps into manuscript prose unless the user explicitly asks to implement them and they are evidence-supported.
• Do not write advice-only artifacts to 03_output/manuscript/paper.md.
• Do not cite style-only target-journal samples as scholarly evidence.
• Do not insert conversation markers into manuscript prose, including 用户说, 用户提供, 根据用户意见, the user said, as requested, here I will, or screenshot provenance such as 用户提供的截图.
• Do not leave inline work markers such as AIGEN, AIPO, or AIREF in final manuscript prose unless the user explicitly requests a marked review copy.
• Do not turn unresolved evidence into manuscript commentary about why the gap is acceptable, cautious, temporary, or publishable. Keep the manuscript formal and place the decision rationale in revision notes, supplement files, or logs.
• Use humanizer only when the user asks to reduce AI-like prose; preserve scientific caution and citation precision.

Author Voice Preferences

• When a project contains author-specific style preferences, generalize them into manuscript-safe writing rules before applying them.
• Avoid disclaimer-like sentences that weaken the argument when the real task is to justify sample selection or comparison logic.
• When using comparisons across fields, state the positive selection logic directly: shared adoption intensity, responsibility intensity, evidence base, or argumentative role.
• Reserve limitation statements for real methodological constraints, and write them as method notes rather than defensive disclaimers.
• Avoid repeated negative parallelisms such as "not X but Y" unless the contrast is essential to the argument.

Change Log Entry

Append a concise entry like this:

| YYYY-MM-DD | Local revision: <short label> | <files changed> | <evidence or TODO notes> |

Final Check

Before finishing, report:

• Sections changed.
• Tables, figures, citations, or references updated.
• Any remaining TODO: or author-confirmation item.
• Whether any AIGEN or AIPO markers were resolved, and whether any markers remain intentionally.
• Whether user comments or chat instructions were converted into manuscript-safe scientific changes and logged outside the body text.
• Whether the task stayed local or should trigger a broader PaperSmart-draft pass later.