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).

2. 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).

3. 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.