Research Orchestrator

{
  "documents": [
    {
      "filename": "research_1.md",
      "sections": [{"heading": "...", "topic": "...", "claims": [...]}],
      "urls": [{"url": "...", "context": "...", "line": 42}],
      "unique_insights": ["..."]
    }
  ]
}

Phase 2: Cross-Compare

Build a comparison matrix showing where documents agree, disagree, or have unique content.

Steps

1. Agreement check: For each claim that appears in 2+ documents, note whether the facts match. Flag contradictions with both versions and source references.
2. Coverage matrix: Create a topic × document matrix showing which topics each doc covers and at what depth (none / brief / detailed).
3. Quality ranking: For each topic, identify which document has the best treatment (most detailed, best sourced, clearest explanation).
4. Contradiction log: List every factual disagreement with exact quotes from each source.

Save comparison to /home/claude/research-work/comparison.json.

Present a brief comparison summary to the user before proceeding — they may want to guide which document to prefer on contradictions.

Phase 3: Verify

This is the most critical phase. Three layers of verification:

Layer 1: Link Checking

Run the bundled scripts to extract and check every URL:

# Extract all URLs from source files
python /path/to/skill/scripts/extract_urls.py /home/claude/research-work/sources/* > /home/claude/research-work/urls.json

# Check all URLs
python /path/to/skill/scripts/check_links.py /home/claude/research-work/urls.json > /home/claude/research-work/link_results.json

Classify results:

• ✅ Working (HTTP 200): keep as-is
• ↗️ Redirected (3xx): update URL to final destination
• ❌ Broken (4xx/5xx/timeout): attempt to find replacement via web search, or remove
• ⚠️ Paywalled / Soft-blocked: note in final document

Layer 2: Cross-Reference Facts

For claims that appear in only ONE document (no corroboration from other inputs):

1. Use web_search to verify. Search for the specific claim (name + number + date).
2. If confirmed by a reputable source, keep and add the confirming source as a citation.
3. If contradicted, flag and use the correct version.
4. If unverifiable (no search results either way), mark with a [⚠️ Unverified] tag and include it in a separate "Unverified Claims" appendix rather than the main body.

For claims in 2+ documents that agree: mark as verified (corroborated). For claims in 2+ documents that contradict: use web search as tiebreaker.

Layer 3: Source Quality Assessment

Rate each source/URL on a simple scale:

• Tier 1: Official sources (gov sites, company IR pages, peer-reviewed journals, major news outlets)
• Tier 2: Reputable secondary sources (well-known blogs, industry reports, Wikipedia with citations)
• Tier 3: Low-reliability (forums, undated pages, personal blogs without sources)

Prefer Tier 1 citations in the final document. Note Tier 3 sources explicitly.

Save full verification results to /home/claude/research-work/verification.json.

Phase 4: Merge & Synthesize

Build the unified document by combining the best content from all sources.

Merge Strategy

1. Structure: Use the best section structure from the comparison phase. If documents have different structures, create a new one that is logically organized by topic.
2. Per section: Take the best version (from quality ranking), then enrich with unique insights from other documents.
3. Contradictions: Use the verified/correct version. Note the disagreement in a footnote if relevant.
4. Citations: Every factual claim in the final document must have at least one working source link. Use inline citations: [Source Name](URL).
5. Unverified section: Collect all unverifiable-but-potentially-useful claims in a clearly marked appendix.

Document Structure

# [Topic Title]

## Executive Summary
Brief synthesis of key findings across all sources.

## [Main Sections — organized by topic]
Content with inline citations.

## Source Comparison Notes
Brief notes on where sources agreed/disagreed, which was used and why.

## Verified Sources
Numbered list of all working URLs used, with Tier ratings.

## Appendix: Unverified Claims
Claims that could not be confirmed or denied, with original source noted.

## Verification Report
- Total links checked: N
- Working: N (X%)
- Broken (removed/replaced): N
- Facts cross-referenced: N
- Facts verified via web search: N
- Contradictions resolved: N

Phase 5: Generate DOCX Output

Use the docx skill (read /mnt/skills/public/docx/SKILL.md) to generate the final Word document.

The DOCX should include:

• Professional formatting with headings, table of contents
• Inline hyperlinks (only verified working URLs)
• Color-coded verification status where relevant (green = verified, yellow = single-source, red = unverified)
• Footer with generation date and source document list

Save final document to /mnt/user-data/outputs/ and present via present_files.

Communication with User

Throughout the process, keep the user informed:

1. After Phase 1: "I've parsed N documents. Here's what each covers: [brief summary]. Proceeding to compare."
2. After Phase 2: "Found X agreements, Y contradictions, Z unique insights. Here are the contradictions — which version do you prefer, or should I verify independently?" (Only ask if contradictions are significant.)
3. After Phase 3: "Verification complete: N/M links working, K facts confirmed via web search, J contradictions resolved. L claims unverifiable."
4. After Phase 5: Present the final DOCX.

If the user wants a quick result, compress phases 2-3 communication into a single status update.

Edge Cases

• Single document: Still useful — run link checking and fact verification, produce a "verified edition."
• Very large documents (>50 pages each): Process section-by-section rather than all at once. Prioritize executive summaries and key claims.
• Non-English content: Verify links and facts in the document's language. Use search queries in the appropriate language.
• Documents on completely different topics: Warn the user that merging may not make sense; offer to verify each independently instead.