Paper Distill

Input Sources

The user must provide at least ONE of:

• Paper title — Claude uses training knowledge + web search
• Uploaded PDF — read from /mnt/user-data/uploads/
• URL — link to paper (arXiv, ACM, IEEE, etc.)

Optional:

• GitHub repo URL — for code cross-referencing

If none are provided, ask the user to specify the paper.

Phase 1: Distill and Write

Step 1: First Read Wiki (read-wiki)

Execute read-wiki to:

1. Check if this paper already has a wiki entry — avoid duplication
2. Find related wiki pages for context and cross-referencing
3. Understand existing knowledge landscape on this topic

If an entry already exists:

Wiki entry for "{paper title}" already exists (last updated {date}).
Update the existing entry, or skip?

Step 2: Read the Paper

Based on the input source:

• Uploaded PDF: read from /mnt/user-data/uploads/
• URL: use web_fetch to retrieve
• Title only: use training knowledge + web search, flag as "unverified source"

Extract all content needed for the six-section format.

Step 3: Cross-Reference with Code (conditional — clone-codebase)

Only if the user provides a repo URL.

Execute clone-codebase with the provided URL. After cloning, search the codebase for:

• Algorithm implementations mentioned in the paper
• Parameter names and default values
• Discrepancies between paper description and actual implementation

Add findings to the Method section as implementation notes.

If no repo URL is provided, skip this step entirely.

Step 4: Draft Six-Section Entry (HARD STOP)

Generate the wiki entry in mandatory format:

## Goal
{What problem does this paper solve? Core motivation.}

## Background
{Prerequisites, assumptions, target domain.
 Link to related wiki entries found in Step 1.}

## Related Works
{Papers compared against. How this work differs.
 Cross-reference existing wiki entries:
 - "See also: [Wiki: {related paper}] — {relationship}"}

## Method
{Core algorithm and data flow.
 Processing model (parallelism, dataflow pattern).
 Architecture design (hardware/software structure).
 [If code cross-referenced]: Implementation notes from {repo}.}

## Evaluation
{Benchmark setup: datasets, platforms, baselines.
 Experimental methodology.}

## Results
{Key metrics and numbers — exact values, not paraphrased.
 Limitations and applicability scope.
 Claims that could NOT be verified from the paper alone.}

Present the draft to the user. Do NOT write to Notion until approved.

Step 5: Write to Wiki (write-wiki-page)

After user approval:

Target folder: "Knowledge Base"
Page title: "{Paper title} ({year})"
Content: {approved six-section entry}

Phase 2: Cross-Reference Propagation

Step 6: Second Read Wiki (read-wiki)

Execute read-wiki again — this time scanning ALL pages to find:

A. Pages that should link to the new entry:

• Other wiki pages that mention this paper by name or cite its authors
• Pages whose Related Works section covers the same topic area
• Pages whose Method section uses similar algorithms or architectures

B. Pages whose claims contradict the new entry:

• Conflicting performance numbers for the same benchmark
• Opposite conclusions about trade-offs
• Incompatible architectural assumptions

Step 7: Generate Changelist (HARD STOP)

Present the changelist to the user:

[CROSS-REFERENCE CHANGELIST]

--- Direct Updates (will apply automatically if approved) ---

1. "{page title}" — Related Works section
   Add: "See also: [{new paper title}] — {relationship description}"

2. "{page title}" — Related Works section
   Add: "See also: [{new paper title}] — {relationship description}"

--- Contradictions (will post as inline comments) ---

3. "{page title}" — {section}
   Content: "{existing claim}"
   Contradicts: "{new paper's finding}"
   Comment to post: "[CONTRADICTION from {new paper}] {explanation}"

4. ...

Type "confirm" to apply all changes, or specify which to skip.

Step 8: Apply Changes

After user approval:

For direct updates (Related Works links): Execute write-wiki-page for each affected page, updating only the Related Works section to add a cross-reference link and short description. Do NOT modify any other section of the affected page.

For contradictions: Execute write-comments to post inline comments on the affected pages:

page_id: {affected page id}