Agent skill

manuscript-ingest

Ingest a submitted manuscript into plain text (`output/PAPER.md`) so downstream review skills can extract claims with source pointers. **Trigger**: ingest paper, manuscript text, provide paper, paper.md, 输入论文, 导入稿件, 审稿输入. **Use when**: You are running the `peer-review` pipeline and need `output/PAPER.md` before `claims-extractor`. **Skip if**: `output/PAPER.md` already exists and looks like the full manuscript text. **Network**: none. **Guardrail**: Do not summarize or rewrite the paper; store the raw text (or a faithful extraction) so claims stay traceable.

View SKILL.md on GitHub Repository
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Install this agent skill to your Project

npx add-skill https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/manuscript-ingest

SKILL.md

Manuscript Ingest (paper -> text)

Goal: create output/PAPER.md as the single source of truth for the submitted manuscript text.

Downstream skills (e.g., claims-extractor) rely on this file to produce traceable claims (section/page/quote pointers).

Inputs

One of the following (choose the simplest):

  • The user pastes the manuscript text in chat (recommended).
  • A local PDF provided by the user (extract to text, then paste into output/PAPER.md).

Optional context:

  • GOAL.md (review focus / constraints)

Outputs

  • output/PAPER.md

Procedure

  1. Decide the input route
  • If GOAL.md exists, treat it as the review focus/constraints (but do not rewrite the paper to fit it).
  • If the user can paste text: use that.
  • If only PDF is available: extract text (any faithful extraction is OK; do not paraphrase).
  1. Write output/PAPER.md
  • Include the full text in order.
  • Preserve section headings if possible.
  • If page numbers are available, keep simple markers like \n\n[page 7]\n\n (helps traceability).
  1. Quick sanity check
  • Confirm output/PAPER.md contains the paper body (not just title/abstract).
  • Confirm key sections exist (Intro/Method/Experiments/Conclusion), if the paper has them.

Acceptance

  • output/PAPER.md exists.
  • The file contains the full manuscript text (or a faithful extraction), sufficient to quote with pointers.

Troubleshooting

I only have a PDF and the extracted text is messy

Fix:

  • Keep the messy text anyway, but preserve:
    • section headings
    • figure/table captions (if present)
    • page separators (if present)

The paper is very long

Fix:

  • Still ingest the full text.
  • If you must split, keep output/PAPER.md as the concatenated master file.

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