alterlab-paper-writer

Academic Paper — Academic Paper Writing Agent Team

A general-purpose academic paper writing tool — 12-agent pipeline covering all disciplines, with higher education domain as the default reference. v2.4 hardens LaTeX output formatting: mandatory apa7 document class for APA 7.0, text justification override for man mode, table column width formula with \tabcolsep deduction, bilingual abstract centering, standardized font stack (Times New Roman + Source Han Serif TC VF + Courier New), and PDF compilation via tectonic.

Quick Start

Minimal command:

Write a paper on the impact of AI on higher education quality assurance

Write a paper on the impact of declining birth rates on private university management strategies

Execution flow:

1. Configuration interview — paper type, discipline, citation format, output format
2. Literature search — systematic search strategy, source screening
3. Architecture design — paper structure, outline, word count allocation
4. Argumentation construction — claim-evidence chains, logical flow
5. Full-text drafting — section-by-section draft, register adjustment
6. Citation compliance + bilingual abstract (parallel)
7. Peer review — five-dimension scoring, revision suggestions
8. Output formatting — LaTeX/DOCX/PDF/Markdown

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Trigger Conditions

Trigger Keywords

English: write paper, academic paper, paper outline, write abstract, revise paper, literature review paper, check citations, convert to LaTeX, convert format, format paper, conference paper, journal article, thesis chapter, research paper, guide my paper, help me plan my paper, step by step paper, draft manuscript, write methodology, write discussion, parse reviews, revision roadmap, help me with my revision, I got reviewer comments, convert citations

繁體中文: 寫論文, 學術論文, 論文大綱, 寫摘要, 修改論文, 文獻回顧論文, 檢查引用, 轉 LaTeX, 轉換格式, 研討會論文, 期刊文章, 學位論文, 研究論文, 引導我寫論文, 幫我規劃論文, 逐步寫論文, 寫方法論, 寫討論, 審查意見, 修訂路線圖, 幫我修改, 我收到審查意見, 轉換引用格式

Plan Mode Activation

Activate plan mode (Socratic chapter-by-chapter guidance) when the user's intent matches any of the following patterns, regardless of language. Detect meaning, not exact keywords.

Intent signals (any one is sufficient):

1. User wants to be guided or led through paper writing, not just given a finished paper
2. User asks for step-by-step or chapter-by-chapter planning
3. User expresses uncertainty about how to start or structure a paper
4. User is a first-time paper writer or explicitly says they are a beginner
5. User has research results but doesn't know how to turn them into a paper
6. User wants to think through each section before writing

Default rule: When intent is ambiguous between plan and full, prefer plan — it is safer to guide a user who needs help than to produce a paper they can't use. The user can always switch to full later.

Example triggers (illustrative, not exhaustive): "guide my paper", "help me plan my paper", "I don't know how to start", 「引導我寫論文」「幫我規劃論文」, or equivalent in any language

Does NOT Trigger

Scenario	Use Instead
Deep research / fact-checking (not paper writing)	alterlab-deep-research
Reviewing a paper (structured review)	alterlab-paper-reviewer
Full research-to-paper pipeline	alterlab-research-pipeline

Distinction from alterlab-deep-research

Feature	alterlab-paper-writer	alterlab-deep-research
Primary output	Publishable paper draft	Research report
Structure	Journal-ready (IMRaD, etc.)	APA 7.0 report
Citation	Multi-format (APA/Chicago/MLA/IEEE/Vancouver)	APA 7.0 only
Abstract	Bilingual (zh-TW + EN)	Single language
Peer review	Simulated 5-dimension review	Editorial review
Output format	LaTeX/DOCX/PDF/Markdown	Markdown only
Revision loop	Max 2 rounds with targeted feedback	Max 2 rounds

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Agent Team (12 Agents)

#	Agent	Role	Phase
1	intake_agent	Configuration interview: paper type, discipline, journal, citation format, output format, language, word count; Handoff detection; Plan mode simplified interview	Phase 0
2	literature_strategist_agent	Search strategy design, source screening, annotated bibliography, literature matrix	Phase 1
3	structure_architect_agent	Paper structure selection, detailed outline, word count allocation, evidence mapping	Phase 2
4	argument_builder_agent	Argument construction, claim-evidence chains, logical flow, counter-argument handling; Plan mode argument stress test	Phase 3 / Plan Step 3
5	draft_writer_agent	Section-by-section full draft writing, discipline register adjustment, word count tracking	Phase 4
6	citation_compliance_agent	Citation format verification, reference list completeness, DOI checking	Phase 5a
7	abstract_bilingual_agent	Bilingual abstract (zh-TW + EN), 5-7 keywords each	Phase 5b
8	peer_reviewer_agent	Simulated double-blind review, five-dimension scoring, revision suggestions (max 2 rounds)	Phase 6
9	formatter_agent	Convert to LaTeX/DOCX/PDF/Markdown, journal formatting, cover letter, citation format conversion (APA 7 / Chicago / MLA / IEEE / Vancouver)	Phase 7
10	socratic_mentor_agent	Plan mode Socratic mentor: chapter-by-chapter guidance, convergence criteria (4 signals), question taxonomy (4 types), INSIGHT extraction	Plan Step 0-3
11	visualization_agent	Parse paper data and generate publication-quality figure code (Python matplotlib / R ggplot2) with APA 7.0 formatting, colorblind-safe palettes, and LaTeX integration	Phase 4 / Phase 7
12	revision_coach_agent	Parse unstructured reviewer comments into structured Revision Roadmap; classify, map, and prioritize comments; works standalone without prior pipeline execution	Revision-Coach mode

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Output Formats

Text Formats

LaTeX (.tex + .bib), DOCX (via Pandoc), PDF (via LaTeX or Pandoc), Markdown.

Figures

When the paper contains quantitative results, the visualization_agent can generate publication-ready figures in Python (matplotlib/seaborn) or R (ggplot2) with APA 7.0 formatting and colorblind-safe palettes. Figures are delivered as runnable code + LaTeX \includegraphics integration code. See references/statistical_visualization_standards.md for chart type decision trees and code templates.

Citation Formats

APA 7.0 (default), Chicago (Author-Date or Notes-Bibliography), MLA 9, IEEE, Vancouver. The formatter_agent supports late-stage citation format conversion between any two supported formats via "Convert citations to [format]".

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Orchestration Workflow (8 Phases)

User: "Write a paper on [topic]"
     |
=== Phase 0: CONFIG (Interactive) ===
     |
     +-> [intake_agent] -> Paper Configuration Record
         - Paper type (IMRaD / Lit Review / Theoretical / Case Study / Policy Brief / Conference)
         - Discipline and sub-field
         - Target journal (optional)
         - Citation format (APA 7 / Chicago / MLA / IEEE / Vancouver)
         - Output format (LaTeX / DOCX / PDF / Markdown / Combined)
         - Language (EN / zh-TW / bilingual sections)
         - Bilingual abstract (Yes / EN-only / zh-TW-only)
         - Word count target
         - Existing materials (RQ, data, drafts, lit)
     |
     ** User confirms configuration **
     |
=== Phase 1: RESEARCH ===
     |
     +-> [literature_strategist_agent] -> Search Strategy + Source Corpus
         - Database selection + search strings
         - Inclusion/exclusion criteria
         - Source screening + annotated bibliography
         - Literature matrix (Source x Theme)
         - Research gap mapping
     |
     ** User reviews sources (optional add/remove) **
     |
=== Phase 2: ARCHITECTURE ===
     |
     +-> [structure_architect_agent] -> Paper Outline + Evidence Map
         - Structure pattern selection (from paper_structure_patterns.md)
         - Section-by-section outline with word count allocation
         - Evidence-to-section assignment
         - Transition logic between sections
     |
     ** User approves outline **
     |
=== Phase 3: ARGUMENTATION ===
     |
     +-> [argument_builder_agent] -> Argument Blueprint
         - Central thesis + sub-arguments
         - Claim-Evidence-Reasoning chains per section
         - Counter-argument identification + rebuttal strategy
         - Logical flow diagram
     |
=== Phase 4: DRAFTING ===
     |
     +-> [draft_writer_agent] -> Complete Draft
         - Section-by-section writing following outline
         - Register adjustment for discipline
         - In-text citations integrated
         - Word count tracking per section
         - Transition paragraphs between sections
     |
=== Phase 5a & 5b: CITATIONS + ABSTRACT (Parallel) ===
     |
     |-> [citation_compliance_agent] -> Citation Audit Report
     |   - In-text <-> reference list cross-check (zero orphans)
     |   - Format compliance (per selected style)
     |   - DOI/URL verification
     |   - Self-citation ratio check
     |   - Auto-correction of detected errors
     |
     +-> [abstract_bilingual_agent] -> Bilingual Abstract + Keywords
         - English abstract (150-300 words, structured)
         - Traditional Chinese abstract (300-500 characters, structured)
         - EN keywords (5-7)
         - zh-TW keywords (5-7)
         - Independent writing (not mechanical translation)
     |
=== Phase 6: PEER REVIEW ===
     |
     +-> [peer_reviewer_agent] -> Review Report + Revision Instructions
         - 5-dimension scoring:
           Originality (20%) | Methodological Rigor (25%) | Evidence Sufficiency (25%)
           Argument Coherence (15%) | Writing Quality (15%)
         - Verdict: Accept / Minor Revision / Major Revision / Reject
         - Line-level feedback with suggested fixes
         - Max 2 revision loops -> back to Phase 4 [draft_writer_agent] (limited to 1 round in alterlab-research-pipeline)
     |
=== Phase 7: FORMAT ===
     |
     +-> [formatter_agent] -> Final Output Package
         - Target format conversion (LaTeX + .bib / DOCX / PDF / Markdown)
         - Journal-specific formatting (if target journal specified)
         - Cover letter (if journal submission)
         - AI disclosure statement
         - Final quality checklist

Checkpoint Rules

1. Phase 0 -> 1: User must confirm Paper Configuration Record
2. Phase 2 -> 3: User must approve outline (can request restructuring)
3. Phase 6: Max 2 revision loops; unresolved items -> "Acknowledged Limitations"
4. Peer Review Critical-severity issues block progression to Phase 7
5. User can skip Phase 1 (literature) if providing own sources

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Operational Modes (9 Modes)

See references/mode_selection_guide.md for details.

Mode	Trigger	Agents	Output
full	"Write a paper"	All 9 (+ 11 if quantitative)	Complete paper draft (with figures if applicable)
outline-only	"Paper outline"	1->2->3	Detailed outline + evidence map
revision	"Revise paper"	8->5->6	Revised draft with tracked changes (uses templates/revision_tracking_template.md)
abstract-only	"Write abstract"	1->7	Bilingual abstract + keywords
lit-review	"Literature review"	1->2	Annotated bibliography + synthesis
format-convert	"Convert to LaTeX" / "Convert citations to [format]"	9 only	Formatted document; includes citation format conversion (APA 7 / Chicago / MLA / IEEE / Vancouver)
citation-check	"Check citations"	6 only	Citation error report
plan	"guide my paper" / "help me plan my paper"	1->10->3->4	Chapter Plan + INSIGHT Collection
revision-coach	"parse reviews" / "revision roadmap" / "I got reviewer comments"	12 only	Revision Roadmap + optional Tracking Template + Response Letter Skeleton

Quick Mode Selection Guide

Your Situation	Recommended Mode
Starting from scratch with a clear RQ	full
Need help planning before writing	plan
Just need an outline	outline-only
Have a draft, received review feedback	revision
Have unstructured reviewer comments	revision-coach
Just need an abstract	abstract-only
Need to check/fix citations	citation-check
Need to convert format (LaTeX, DOCX) or citation style	format-convert
Want a systematic literature review paper	lit-review

Not sure? Start with plan — it will guide you step by step.

Mode Selection Logic

"Write a paper on SDGs in HEI"           -> full
"Give me a paper outline for..."         -> outline-only
"Revise this paper based on feedback"    -> revision
"Write an abstract for this paper"       -> abstract-only
"Do a literature review on..."           -> lit-review
"Convert this paper to LaTeX"            -> format-convert
"Convert citations to IEEE"              -> format-convert
"Check the citations in this paper"      -> citation-check
"guide my paper"                         -> plan
"help me plan my paper"                  -> plan
"I got reviewer comments"               -> revision-coach
"parse these reviews"                    -> revision-coach
"help me with my revision"              -> revision-coach

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Plan Mode: CHAPTER-BY-CHAPTER GUIDED PLANNING

Core principle: From the perspective of a senior doctoral advisor and disciplinary methodology expert, guide users to think through every part of their paper chapter by chapter. Instead of writing directly, use Socratic dialogue to help users clarify what they want to write.

User: "guide my paper" / "help me plan my paper"
     |
=== Step 0: RESEARCH READINESS CHECK ===
     |
     +-> [socratic_mentor_agent] -> Confirm what materials the user already has
         - "What research materials do you currently have? (literature, data, analysis results)"
         - "Is your research question finalized? Can you state it in one sentence?"
         -> If research foundation is lacking, recommend running alterlab-deep-research (socratic mode) first
     |
=== Step 1: THESIS CRYSTALLIZATION ===
     |
     +-> [socratic_mentor_agent] -> Probe the core thesis
         - "What is your paper arguing?"
         - "How would someone who disagrees with you respond?"
         - "After reading your paper, what should the reader think differently about?"
         Extract [INSIGHT: thesis_statement]
     |
=== Step 2: CHAPTER-BY-CHAPTER NEGOTIATION ===
     |
     For each chapter (Introduction -> Literature -> Method -> Results -> Discussion -> Conclusion):
     |
     +-> [socratic_mentor_agent] -> Probe the purpose and content of each chapter
     |
     |   Introduction:
     |   - "What sense of urgency should the reader feel by the end of this chapter?"
     |   - "After reading the Introduction, what should the reader expect to see next?"
     |   - "What is your research gap? State it in one sentence."
     |
     |   Literature Review:
     |   - "How many stories are you telling? What is the relationship between them?"
     |   - "What conclusion should your literature review ultimately lead to?"
     |   - "Is there an important work you disagree with? Why?"
     |
     |   Methodology:
     |   - "If someone challenges your method, how would you respond?"
     |   - "Is there a simpler method that could also answer your question? Why didn't you choose it?"
     |   - "What is the biggest limitation of your method? How do you handle it?"
     |
     |   Results:
     |   - "What is your most important finding? State it in one sentence."
     |   - "Were there any unexpected results? How do you explain them?"
     |   - "Is there any evidence in your data that does not support your hypothesis?"
     |
     |   Discussion:
     |   - "How do your results dialogue with existing literature?"
     |   - "What is the one thing you most want the reader to remember?"
     |   - "What recommendations does your research have for practice/policy?"
     |
     |   Conclusion:
     |   - "If you could only leave one paragraph, what would you say?"
     |   - "What future research directions does your study open up?"
     |
     At least 2 rounds of dialogue per chapter
     After each chapter concludes, [socratic_mentor_agent] extracts a Chapter Summary
     |
     +-> [structure_architect_agent] -> Produce complete outline based on all Chapter Summaries
     |
=== Step 3: ARGUMENT STRESS TEST ===
     |
     +-> [socratic_mentor_agent + argument_builder_agent]
         -> Probe evidence and logic for each sub-argument
         -> "Where is the weakest point in this argument?"
         -> "If you reverse your argument, does it still hold?"
         -> Final output: Chapter Plan (with core argument, supporting evidence, expected word count per chapter)
     |
Output: Chapter Plan + INSIGHT Collection
-> User can then use full mode to produce the complete paper
-> Or use alterlab-paper-reviewer to review the Chapter Plan

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Handoff Protocol: alterlab-deep-research -> alterlab-paper-writer

intake_agent automatically detects alterlab-deep-research materials (RQ Brief / Bibliography / Synthesis / INSIGHT Collection) and skips redundant steps. See alterlab-deep-research/SKILL.md Handoff Protocol for the complete handoff material format.

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Failure Paths

See references/failure_paths.md for details. Quick reference:

Failure Scenario	Handling Strategy
Insufficient research foundation	Recommend running alterlab-deep-research first
Wrong paper structure selected	Return to Phase 2, suggest alternative structure
Word count significantly over/under target	Identify problematic chapters, suggest trimming/expansion
Citation format entirely wrong	Re-run the entire citation phase
Peer review rejection	Analyze rejection reasons, suggest major revision or restructuring
Plan mode not converging	Suggest switching to outline-only mode
Incomplete handoff materials	List missing items, suggest supplementing or re-running
User abandons midway	Save completed Chapter Plan

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Full Academic Pipeline

See alterlab-research-pipeline/SKILL.md for the complete workflow.

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Phase 0: Configuration Interview

See agents/intake_agent.md for the complete field definitions of the Phase 0 configuration interview. The interview covers 9 items: paper type, discipline, target journal, citation format, output format, language, abstract, word count, and existing materials. Outputs a Paper Configuration Record, awaiting user confirmation.

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Agent File References

Agent	Definition File
intake_agent	agents/intake_agent.md
literature_strategist_agent	agents/literature_strategist_agent.md
structure_architect_agent	agents/structure_architect_agent.md
argument_builder_agent	agents/argument_builder_agent.md
draft_writer_agent	agents/draft_writer_agent.md
citation_compliance_agent	agents/citation_compliance_agent.md
abstract_bilingual_agent	agents/abstract_bilingual_agent.md
peer_reviewer_agent	agents/peer_reviewer_agent.md
formatter_agent	agents/formatter_agent.md
socratic_mentor_agent	agents/socratic_mentor_agent.md
visualization_agent	agents/visualization_agent.md
revision_coach_agent	agents/revision_coach_agent.md

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Reference Files

Reference	Purpose	Used By
references/apa7_extended_guide.md	APA 7th extended guide (extends alterlab-deep-research version)	citation_compliance, draft_writer, formatter
references/apa7_chinese_citation_guide.md	APA 7.0 Chinese citation complete specification (Taiwan academic conventions)	citation_compliance, draft_writer, formatter
references/citation_format_switcher.md	Multi-citation format switching rules (including Chinese formats)	citation_compliance, formatter
references/paper_structure_patterns.md	6 paper structure patterns	structure_architect, intake
references/academic_writing_style.md	Academic writing style guide	draft_writer, peer_reviewer
references/hei_domain_glossary.md	Higher education terminology bilingual glossary	all agents (domain context)
references/journal_submission_guide.md	Journal submission guide	formatter, intake
references/abstract_writing_guide.md	Abstract writing guide	abstract_bilingual
references/latex_template_reference.md	LaTeX template reference	formatter
references/failure_paths.md	Failure path map (12 scenarios + handling strategies)	all agents
references/mode_selection_guide.md	8 mode selection guide + transition paths	intake
references/credit_authorship_guide.md	CRediT 14 roles + ICMJE + AI policy + contribution matrix	intake, formatter, draft_writer
references/funding_statement_guide.md	Taiwan/international funding formats + statement templates	intake, formatter, draft_writer
references/statistical_visualization_standards.md	APA 7.0 figure guidelines, accessible color palettes, chart type decision tree, matplotlib/ggplot2 code templates	visualization

Also references from alterlab-deep-research:

• alterlab-deep-research/references/apa7_style_guide.md — base APA 7 reference (this skill extends, not duplicates)

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Templates

Template	Purpose
templates/imrad_template.md	IMRaD structure template
templates/literature_review_template.md	Literature review template
templates/case_study_template.md	Case study template
templates/theoretical_paper_template.md	Theoretical paper template
templates/policy_brief_template.md	Policy brief template
templates/conference_paper_template.md	Conference paper template
templates/latex_article_template.tex	LaTeX starter template
templates/bilingual_abstract_template.md	Bilingual abstract template
templates/credit_statement_template.md	Author x Role contribution matrix + CRediT statement output
templates/funding_statement_template.md	Funding source registration + statement output
templates/revision_tracking_template.md	Systematic tracker for reviewer comments and resolutions during revision (4 status types: RESOLVED, DELIBERATE_LIMITATION, UNRESOLVABLE, REVIEWER_DISAGREE)

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Examples

Example	Demonstrates
examples/imrad_hei_example.md	Complete IMRaD paper example (higher education domain, English)
examples/literature_review_example.md	Literature review paper example
examples/plan_mode_guided_writing.md	Plan mode chapter-by-chapter guided dialogue example (blended learning topic)
examples/chinese_paper_example.md	Complete Chinese academic paper example (IMRaD, Chinese APA 7.0 citations)
examples/revision_mode_example.md	Revision mode complete workflow: peer review response + revision comparison table

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Quality Standards

Writing Quality

1. Every claim must have a citation or be supported by the paper's own data
2. Zero citation orphans — in-text citations <-> reference list must perfectly match
3. Consistent register — academic tone appropriate for the discipline
4. Logical flow — clear transitions between paragraphs and sections
5. Word count compliance — within +/-10% of target

Bilingual Abstract Quality

6. Independent writing — zh-TW and EN abstracts are independently composed, NOT mechanical translations
7. Structural alignment — both abstracts cover the same key points in the same order
8. Keywords — 5-7 per language, reflecting the paper's core concepts
9. Word count — EN: 150-300 words; zh-TW: 300-500 characters

Citation Quality

10. Format compliance — 100% adherence to selected citation style
11. DOI inclusion — every source with a DOI must include it
12. Currency — flag sources older than 10 years (unless seminal works)
13. Self-citation ratio — flag if >15%

Peer Review

14. Five dimensions — Originality (20%), Methodological Rigor (25%), Evidence Sufficiency (25%), Argument Coherence (15%), Writing Quality (15%)
15. Actionable feedback — every criticism must include a specific suggestion
16. Max 2 revision rounds — unresolved items become Acknowledged Limitations

Mandatory Inclusions

17. AI disclosure statement — every paper must include a statement on AI tool usage
18. Limitations section — explicitly discuss study limitations
19. Ethics statement — when applicable (human subjects, sensitive data)

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Output Language

Follows the user's language. Academic terminology is kept in English. Bilingual abstracts are always provided regardless of the main text language.

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Integration with Other Skills

alterlab-paper-writer + tw-hei-intelligence  -> Evidence-based HEI paper with real MOE data
alterlab-paper-writer + alterlab-deep-research        -> Deep research phase -> paper writing phase (auto-handoff)
alterlab-paper-writer + report-to-website    -> Interactive web version of the paper
alterlab-paper-writer + notebooklm-slides-generator -> Presentation slides from paper
alterlab-paper-writer + alterlab-paper-reviewer -> Peer review -> revision loop

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Version History

Version	Date	Changes
2.4	2026-03-08	LaTeX output formatting hardening: mandatory apa7 document class for APA 7.0 output; text justification fix (ragged2e + etoolbox to override apa7 man mode \raggedright); table column width formula ((\linewidth - N\tabcolsep) * \real{proportion} — prevents overflow); bilingual abstract centering (\begin{center}\textbf{...}\end{center}); font stack standardized (Times New Roman + Source Han Serif TC VF + Courier New); xurl for URL line breaking; fancyvrb Verbatim with fontsize for wide content; PDF must compile from LaTeX via tectonic (no HTML-to-PDF)
2.3	2026-03-08	NEW visualization_agent (11th: publication-quality figures with matplotlib/ggplot2, APA 7.0, colorblind-safe); NEW revision_coach_agent (12th: standalone reviewer comment parser → Revision Roadmap); Socratic convergence criteria (4 signals: thesis clarity, chapter coherence, evidence mapping, limitation honesty) + question taxonomy (clarifying, probing, structuring, challenging); revision tracking template (4 status types); citation format conversion in formatter_agent (APA 7 ↔ Chicago ↔ MLA ↔ IEEE ↔ Vancouver); Quick Mode Selection Guide; 9th mode: revision-coach
2.2	2025-03-05	4-level argument strength scoring with quantified thresholds; plagiarism & retraction screening protocol; F11 Desk-Reject Recovery + F12 Conference-to-Journal Conversion failure paths; Plan -> Full mode conversion protocol; cross-skill reference to shared/handoff_schemas.md
2.1	2026-03	Added CRediT authorship guide, funding statement guide, 2 new templates (credit_statement_template, funding_statement_template); enhanced intake_agent with co-author + funding questions (Step 9-10); enhanced formatter_agent with CRediT + funding quality checks
2.0	2026-02	NEW plan mode (Socratic guided chapter-by-chapter planning), alterlab-deep-research handoff protocol, Chinese APA 7.0 citation guide, failure path handling, mode selection guide
1.0	2026-01	Initial release: 9-agent pipeline, 6 paper types, 5 citation formats, bilingual abstracts, multi-format output