Deep Research
Core Purpose
Deliver citation-tracked research reports through a structured pipeline with evidence persistence, source identity management, claim-level verification, and progressive context management.
Autonomy Principle: Operate independently. Infer assumptions from context. Only stop for critical errors or incomprehensible queries. Surface high-materiality assumptions explicitly in the Introduction and Methodology rather than silently defaulting.
Decision Tree
Request Analysis
+-- Simple lookup? --> STOP: Use WebSearch
+-- Debugging? --> STOP: Use standard tools
+-- Complex analysis needed? --> CONTINUE
Mode Selection
+-- Initial exploration --> quick (3 phases, 2-5 min)
+-- Standard research --> standard (6 phases, 5-10 min) [DEFAULT]
+-- Critical decision --> deep (8 phases, 10-20 min)
+-- Comprehensive review --> ultradeep (8+ phases, 20-45 min)Default assumptions: Technical query = technical audience. Comparison = balanced perspective. Trend = recent 1-2 years.
Workflow Overview
| Phase | Name | Quick | Std | Deep | Ultra |
|---|---|---|---|---|---|
| 1 | SCOPE | Y | Y | Y | Y |
| 2 | PLAN | - | Y | Y | Y |
| 3 | RETRIEVE | Y | Y | Y | Y |
| 4 | TRIANGULATE | - | Y | Y | Y |
| 4.5 | OUTLINE REFINEMENT | - | Y | Y | Y |
| 5 | SYNTHESIZE | - | Y | Y | Y |
| 6 | CRITIQUE | - | - | Y | Y |
| 7 | REFINE | - | - | Y | Y |
| 8 | PACKAGE | Y | Y | Y | Y |
Note: Phases 3-5 operate as an evidence loop per section (retrieve → evidence store → refine outline → draft → verify claims → delta-retrieve if needed), not as strict sequential gates.
Execution
On invocation, load relevant reference files:
- Phase 1-7: Load methodology.md for detailed phase instructions
- Phase 8 (Report): Load report-assembly.md for progressive generation
- HTML/PDF output: Load html-generation.md
- Quality checks: Load quality-gates.md
- Long reports (>18K words): Load continuation.md
Templates:
- Report structure: report_template.md
- HTML styling: mckinsey_report_template.html
Scripts:
python scripts/validate_report.py --report [path]python scripts/verify_citations.py --report [path]python scripts/md_to_html.py [markdown_path]
Output Contract
Required sections:
- Executive Summary (200-400 words)
- Introduction (scope, methodology, assumptions)
- Main Analysis (4-8 findings, 600-2,000 words each, cited)
- Synthesis & Insights (patterns, implications)
- Limitations & Caveats
- Recommendations
- Bibliography (COMPLETE - every citation, no placeholders)
- Methodology Appendix
Output files (all to ~/Documents/[Topic]_Research_[YYYYMMDD]/):
- Markdown (primary source of truth)
sources.jsonl— stable source registry with canonical IDsevidence.jsonl— append-only evidence store with quotes and locatorsclaims.jsonl— atomic claim ledger with support statusrun_manifest.json— query, mode, assumptions, provider config- HTML (McKinsey style, auto-opened)
- PDF (professional print, auto-opened)
Quality standards:
- 10+ sources, 3+ per major claim (cluster-independent, not just count)
- All factual claims cited immediately [N] with evidence backing in
evidence.jsonl - Claim-support verification mandatory: no unsupported factual claims pass delivery
- No placeholders, no fabricated citations
- Prose-first (>=80%), bullets sparingly
When to Use / NOT Use
Use: Comprehensive analysis, technology comparisons, state-of-the-art reviews, multi-perspective investigation, market analysis.
Do NOT use: Simple lookups, debugging, 1-2 search answers, quick time-sensitive queries.