add-paper

name	Add-Paper
description	Add a paper to the research collection — download PDF, extract text, add to PAPER_INDEX.md and PAPER_SUMMARIES.md. Ensures every paper is fully integrated with text extraction and indexed summaries.

*CRITICAL* Add the following steps to your Todo list using TodoWrite:

1. Obtain the PDF
2. Extract text
3. Add entry to PAPER_INDEX.md
4. Read the paper and add entry to PAPER_SUMMARIES.md
5. Stage all new files

Adding a Paper

Announce at start: "I'm using the Add Paper skill to integrate this paper into the collection."

Step 1: Obtain the PDF

• If the user provides a URL: download to papers/ using curl -L -o papers/<filename>.pdf <url>
• If the user provides a local file path: copy to papers/
• If the user just names a paper: search for it and confirm the URL before downloading

Filename convention: AuthorLast_Year__short_description.pdf

• Double underscore separates author/year from description
• Use snake_case for the description
• Examples: Acemoglu_2024__simple_macroeconomics_AI.pdf, Eloundou_2023__gpts_are_gpts.pdf

If the paper already exists in papers/, skip to Step 2.

Step 2: Extract text

Extract the PDF text to papers/text/ with the same base filename and .txt extension:

# Using pdftotext if available
pdftotext papers/<filename>.pdf papers/text/<filename>.txt

# If pdftotext is not available, use Python
python3 -c "
import subprocess
result = subprocess.run(['python3', '-m', 'pymupdf', 'convert', '-output', 'papers/text/<filename>.txt', 'papers/<filename>.pdf'])
"

If neither tool works, read the PDF directly using the Read tool and write the extracted content to papers/text/<filename>.txt. This is the fallback — it works but may lose some formatting.

Verify the extraction is reasonable: check the first ~20 lines to confirm it's not garbled.

Step 3: Add to PAPER_INDEX.md

Add a one-line entry in the appropriate section (or create a section if needed):

| Author (Year) | One-sentence description of what the paper contributes | `filename.pdf` |

Keep entries sorted by author within each section. If PAPER_INDEX.md doesn't exist yet, create it:

# Paper Index

| Paper | Description | File |
|-------|-------------|------|
| Author (Year) | One-sentence description | `filename.pdf` |

Step 4: Add to PAPER_SUMMARIES.md

Read the paper (use the extracted text from papers/text/). Write a summary entry:

### Paper Title

- Authors: Names (Affiliations)
- Date: Month Year
- File: `filename.pdf`
- Source: [URL or DOI if available]

Summary: [2-3 sentences on core contribution and approach]

Key findings:
- [Finding with numerical result and context — not raw numbers, always include what was measured and the baseline]
- [Finding with range estimate if available]
- [Comparison to baseline/prior work]

Relevance: [1-2 sentences on why this paper matters for this research collection]

Important:

• Read the actual results tables and figures, not just the abstract. Key findings are often buried in the results.
• Always include numerical results with context (e.g., "67% accuracy on X, compared to 52% baseline" not just "67%")
• If the paper is long, focus on the sections most relevant to the research collection's focus

Step 5: Stage files

git add papers/<filename>.pdf papers/text/<filename>.txt PAPER_INDEX.md PAPER_SUMMARIES.md

Do NOT commit — the user may be adding multiple papers or may want to review first.

Adding Multiple Papers

If the user asks to add several papers at once:

• Process each paper through all 5 steps before moving to the next
• This ensures each paper is fully integrated before context moves on
• For bulk additions (5+), consider using subagents in parallel for text extraction and summary writing

Common Mistakes

Skipping text extraction

• Problem: Future sessions can't search or discuss the paper's details without re-parsing the PDF
• Fix: Always extract, even if the current task doesn't need the text

Writing summaries from the abstract only

• Problem: Abstracts omit key numerical findings, edge cases, and limitations
• Fix: Read the results/discussion sections; check tables and figures

Adding numbers without context

• Problem: "The model achieved 0.73" means nothing without knowing what was measured, on what data, and what the baseline was
• Fix: Always include metric name, dataset, and comparison point

Forgetting to update PAPER_INDEX when updating PAPER_SUMMARIES

• Problem: Index and summaries get out of sync
• Fix: Always update both in the same operation