All skills
imbad0202 avatar

/academic-paper

@c5c1b45

12-agent academic paper writing pipeline. 11 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure/rebuttal-audit). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX-via-Pandoc/PDF output. Style Calibration + Writing Quality Check + Anti-Patterns with IRON RULE markers. Triggers: write paper, academic paper, guide my paper, parse reviews, I got reviewer comments, revision roadmap, should we push back, conference rebuttal, grant panel response, audit my rebuttal, check my response draft, AI disclosure, check citations, citation check, check my references, verify references, look over the refs, 寫論文, 學術論文, 引導我寫論文, 審查意見, 我收到審查意見, 修訂路線圖, 評估回覆, 檢查引用, 引用檢查, 檢查參考文獻, 核對文獻, 논문 작성, 초록 작성, 논문 수정, 논문 계획을 도와줘, 심사 의견을 받았어, 심사 의견 반영, 답변서 점검, AI 사용 고지, 인용 확인, 인용 형식 검사, enmendar mi artículo, redactar artículo, guía mi artículo, analizar reseñas, auditar mi respuesta, verificar borrador de respuesta, verificar citas, divulgación de IA.

Use this Skill: https://skilld.dev/gh/imbad0202/academic-research-skills/academic-paper

This session only. Nothing lands on disk.

templatesrevision_tracking_template.md

≈2.6k tokens on demand. Your agent reads this file only when SKILL.md points to it.

Revision Tracking Template

Usage

Use this template to systematically track all reviewer comments and their resolutions during the revision process. Copy this template at the start of each revision round, fill in the paper information, then add one row per reviewer comment.

This template works with both:

  • Revision mode (revision in SKILL.md): when you have a draft and structured reviewer feedback
  • Revision Coach mode (revision-coach in SKILL.md): when you have unstructured reviewer comments that need parsing first

Paper Information

Field Value
Paper Title [title]
Revision Round [1 / 2]
Date [YYYY-MM-DD]
Previous Decision [Major Revision / Minor Revision]
Target Journal [journal name]
Original Word Count [N words]
Revised Word Count [N words]

Revision Tracking Table

# Issue Description Reviewer Type Section Resolution Summary Location of Change Status Reason (if not resolved) Commitment Ledger
1 [description] [R1/R2/R3/DA] [Major/Minor/Editorial] [section] [what was done] [page/paragraph] [status] [if applicable] See per-row nested ledger below (concern 1)
2 [description] [R1/R2/R3/DA] [Major/Minor/Editorial] [section] [what was done] [page/paragraph] [status] [if applicable] See per-row nested ledger below (concern 2)
3 [description] [R1/R2/R3/DA] [Major/Minor/Editorial] [section] [what was done] [page/paragraph] [status] [if applicable] (empty — positive comment, no commitment)

Per-row Commitment Ledger (nested-object shape, #268). Each concern's commitments are authored as a single nested YAML block keyed by concern_id — one object per commitment, with fulfillment_status / unfulfilled_rationale nested inside the object. There are no separate parallel cells to keep aligned, so a dropped separator or mis-numbering can no longer desynchronize status from commitment.

Placeholders use <...> (angle brackets) — replace each with a literal scalar. Do NOT use [...]: inside a YAML block square brackets parse as a flow sequence, so a half-filled [R1-1] becomes a one-element list, not the string R1-1. (The only real list here is commitment_extracted: [], the empty-list marker.)

# concern 1 (multi-commitment example)
- concern_id: <R1-1>
  commitment_extracted:
    - commitment_text: "<commitment 1 text>"
      commitment_type: <add_experiment | add_analysis | add_clarification | add_citation | restructure | other>
      required_evidence_type: <new_section | new_figure | new_table | new_citation | methods_paragraph | discussion_paragraph | prose_edit | acknowledgment_only | other>
      fulfillment_status: <fulfilled | partial | not-fulfilled | explicitly-rejected-with-rationale>   # appended during revision execution
      # unfulfilled_rationale: "..."  # required iff status is non-fulfilled; OMIT when fulfilled
    - commitment_text: "<commitment 2 text>"
      commitment_type: ...
      required_evidence_type: ...
      fulfillment_status: ...

# concern 2 (single commitment)
- concern_id: <R2-1>
  commitment_extracted:
    - commitment_text: "<commitment text>"
      commitment_type: ...
      required_evidence_type: ...
      fulfillment_status: ...

# concern 3 carries no commitments (positive comment) → commitment_extracted: []

Status Values

RESOLVED

Change made; reviewer concern fully addressed.

  • Must specify: exact location of change (section, paragraph, page number)
  • Must include: brief description of what was changed
  • Example: "Added three additional references supporting the methodology choice (Section 3.2, paragraph 2)"

DELIBERATE_LIMITATION

Acknowledged as a boundary condition of the study design (not a flaw).

  • Must provide: justification for why this is a design boundary, not an oversight
  • Must include: reference to the Limitations section where this is discussed
  • Example: "Cross-sectional design is acknowledged in Limitations (Section 5.3). Longitudinal follow-up is recommended as future research."

UNRESOLVABLE

Would require fundamentally different research design to address.

  • Must explain: the specific constraint that prevents resolution
  • Must recommend: as a direction for future research
  • Example: "Addressing this would require a randomized controlled trial, which was not feasible given ethical constraints. Added to Future Research (Section 5.4)."

REVIEWER_DISAGREE

Respectful disagreement with the reviewer's suggestion on methodological or theoretical grounds.

  • Must provide: evidence-based rebuttal with citations
  • Must demonstrate: that the reviewer's concern was carefully considered
  • Example: "We respectfully maintain our analytical approach. Smith (2022) and Chen (2023) both validate this method for our sample size and data structure. Response letter includes detailed justification."

Commitment Ledger (Kong A1 / v3.11)

Per Schema 11 v3.11, each row of the Revision Tracking Table may carry an extracted commitment list. Each commitment has a fulfillment_status chosen from:

fulfilled

The commitment was addressed. Required evidence (per required_evidence_type) is present and substantively addresses the commitment_text. The verification site depends on the evidence type:

  • For the seven manuscript-evidence types (new_section / new_figure / new_table / new_citation / methods_paragraph / discussion_paragraph / prose_edit), the evidence lives at revision_location in the revised manuscript. prose_edit covers sentence- or paragraph-level changes (typo fixes, terminology clarifications, equation formatting, citation-style corrections) too granular for the other categories.
  • For acknowledgment_only, the evidence lives in the Response to Reviewers (Schema 8); the manuscript does NOT need to change. revision_location may be empty or point to the response letter.
  • For other (escape hatch for uncategorizable evidence), re-review surfaces an EVIDENCE_TYPE_UNSPECIFIED advisory prompting the author to specify the actual evidence location; verify at revision_location if populated.

partial

Evidence exists but does not fully address the commitment. Example: reviewer asked for ablation on dataset X; revision adds ablation on dataset Y. Author must populate unfulfilled_rationale with the gap explanation.

not-fulfilled

Required evidence is absent. Author must populate unfulfilled_rationale with one of:

  • "done elsewhere, see §X" pointer
  • "rejected, reasons: …" rationale
  • "deferred to future work" acknowledgment

Silent omission triggers COMMITMENT_GAP advisory at re-review.

explicitly-rejected-with-rationale

Author has decided not to address the commitment and has provided one of the three rationale forms above. This is not a failure — it is a documented, defensible decision. Re-review records it without raising COMMITMENT_GAP.

Authoring guidance: Fill in each commitment's extraction fields first (typically via revision_coach_agent Step 3.5 output — commitment_text / commitment_type / required_evidence_type); append fulfillment_status (and unfulfilled_rationale when non-fulfilled) on the same commitment object as revision execution progresses. By final submission, every non-fulfilled commitment must have a rationale on its own object.

Nested-object shape (#268, supersedes the Kong A1 parallel-list cells): Each commitment is one object in the concern's commitment_extracted list, carrying its own fulfillment_status and (when non-fulfilled) unfulfilled_rationale. There is no separate Fulfillment / Unfulfilled-Rationale column to align — status and rationale travel with the commitment they describe, so a dropped separator or numbering error cannot pair a status with the wrong commitment (the desync failure mode #268 closes). Omit unfulfilled_rationale entirely on a fulfilled commitment (no "" placeholder). For positive comments with no extractable commitment, set commitment_extracted: [] to mark the absence explicitly.


Response Letter Structure

When preparing the response letter to accompany the revised manuscript, use this structure:

Dear Editor and Reviewers,

Thank you for the thoughtful and constructive feedback on our manuscript
"[Paper Title]" (Manuscript ID: [ID]).

We have carefully addressed all comments and provide point-by-point
responses below. Changes in the manuscript are highlighted in [yellow/
tracked changes].

---

## Response to Reviewer 1

### Comment R1-1: [Brief summary of comment]
**Type**: [Major/Minor/Editorial]
**Response**: [Your response]
**Changes made**: [Location and description of changes]

### Comment R1-2: ...

---

## Response to Reviewer 2
[Same format]

---

## Summary of Changes
- Total comments addressed: [N]
- Word count change: [±N words]
- New references added: [N]
- New figures/tables added: [N]

We believe these revisions have substantially strengthened the manuscript
and look forward to your further evaluation.

Sincerely,
[Author(s)]

Summary Statistics

Metric Count
Total items [N]
Resolved [N]
Deliberate Limitation [N]
Unresolvable [N]
Reviewer Disagree [N]
Word count change [±N words]
New references added [N]
New figures/tables added [N]

Revision Completeness Checklist

Before submitting the revision, verify:

  • Every reviewer comment has a corresponding row in the tracking table
  • Every RESOLVED item specifies the exact location of the change
  • Every DELIBERATE_LIMITATION item is discussed in the Limitations section
  • Every UNRESOLVABLE item is mentioned in Future Research
  • Every REVIEWER_DISAGREE item has an evidence-based rebuttal
  • The response letter addresses all comments in order
  • Word count is within the journal's limit after revisions
  • All new references are added to the reference list
  • No new errors were introduced during revision (re-run citation check)
  • AI disclosure statement is updated to reflect revision assistance

Source: SKILL.md on GitHub

1 alert1d5 checks · Risk SAFE
  • Gen Agent Trust Hub1d

    This skill provides a highly structured 12-agent academic paper writing pipeline. It contains robust internal defenses, including explicit 'instruction-data' boundaries and sanitization of user-provided content. However, the skill's complexity, its reliance on shell command execution for document processing and utility scripts, and its heavy ingestion of untrusted third-party materials (such as reviewer comments and external research content) present a surface for potential misuse and indirect prompt injection.

  • Socket1d

    No alerts

  • Snyk1d

    Risk: LOW · No issues

  • Runlayer6mo

    7/44 files flagged

  • ZeroLeaks5mo

    Score: 93/100 · 2 sections analyzed

Signed by skilld at c5c1b45. This ties the file your Agent reads to that commit on GitHub. It does not review the instructions.

Last checked against GitHub 33 minutes ago.

Activeupdated 2 days ago
Other metadata
metadata
{
  "version": "3.3.1",
  "last_updated": "2026-08-15",
  "status": "active",
  "data_access_level": "raw",
  "task_type": "open-ended",
  "related_skills": [
    "deep-research",
    "academic-paper-reviewer",
    "academic-pipeline"
  ]
}

README badge

README badge for imbad0202/academic-research-skills/academic-paper