1---
2name: deep-research
3description: Use when the user needs multi-source research with citation tracking, evidence persistence, and structured report generation. Triggers on "deep research", "comprehensive analysis", "research report", "compare X vs Y", "analyze trends", or "state of the art". Not for simple lookups, debugging, or questions answerable with 1-2 searches.
4---
5 
6# Deep Research
7 
8## Core Purpose
9 
10Deliver citation-tracked research reports through a structured pipeline with evidence persistence, source identity management, claim-level verification, and progressive context management.
11 
12**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.
13 
14---
15 
16## Decision Tree
17 
18```
19Request Analysis
20+-- Simple lookup? --> STOP: Use WebSearch
21+-- Debugging? --> STOP: Use standard tools
22+-- Complex analysis needed? --> CONTINUE
23 
24Mode Selection
25+-- Initial exploration --> quick (3 phases, 2-5 min)
26+-- Standard research --> standard (6 phases, 5-10 min) [DEFAULT]
27+-- Critical decision --> deep (8 phases, 10-20 min)
28+-- Comprehensive review --> ultradeep (8+ phases, 20-45 min)
29```
30 
31**Default assumptions:** Technical query = technical audience. Comparison = balanced perspective. Trend = recent 1-2 years.
32 
33---
34 
35## Workflow Overview
36 
37| Phase | Name | Quick | Std | Deep | Ultra |
38|-------|------|-------|-----|------|-------|
39| 1 | SCOPE | Y | Y | Y | Y |
40| 2 | PLAN | - | Y | Y | Y |
41| 3 | RETRIEVE | Y | Y | Y | Y |
42| 4 | TRIANGULATE | - | Y | Y | Y |
43| 4.5 | OUTLINE REFINEMENT | - | Y | Y | Y |
44| 5 | SYNTHESIZE | - | Y | Y | Y |
45| 6 | CRITIQUE | - | - | Y | Y |
46| 7 | REFINE | - | - | Y | Y |
47| 8 | PACKAGE | Y | Y | Y | Y |
48 
49**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.
50 
51---
52 
53## Execution
54 
55**On invocation, load relevant reference files:**
56 
571. **Phase 1-7:** Load [methodology.md](./reference/methodology.md) for detailed phase instructions
582. **Phase 8 (Report):** Load [report-assembly.md](./reference/report-assembly.md) for progressive generation
593. **HTML/PDF output:** Load [html-generation.md](./reference/html-generation.md)
604. **Quality checks:** Load [quality-gates.md](./reference/quality-gates.md)
615. **Long reports (>18K words):** Load [continuation.md](./reference/continuation.md)
62 
63**Templates:**
64- Report structure: [report_template.md](./templates/report_template.md)
65- HTML styling: [mckinsey_report_template.html](./templates/mckinsey_report_template.html)
66 
67**Scripts:**
68- `python scripts/validate_report.py --report [path]`
69- `python scripts/verify_citations.py --report [path]`
70- `python scripts/md_to_html.py [markdown_path]`
71 
72---
73 
74## Output Contract
75 
76**Required sections:**
77- Executive Summary (200-400 words)
78- Introduction (scope, methodology, assumptions)
79- Main Analysis (4-8 findings, 600-2,000 words each, cited)
80- Synthesis & Insights (patterns, implications)
81- Limitations & Caveats
82- Recommendations
83- Bibliography (COMPLETE - every citation, no placeholders)
84- Methodology Appendix
85 
86**Output files (all to `~/Documents/[Topic]_Research_[YYYYMMDD]/`):**
87- Markdown (primary source of truth)
88- `sources.jsonl` — stable source registry with canonical IDs
89- `evidence.jsonl` — append-only evidence store with quotes and locators
90- `claims.jsonl` — atomic claim ledger with support status
91- `run_manifest.json` — query, mode, assumptions, provider config
92- HTML (McKinsey style, auto-opened)
93- PDF (professional print, auto-opened)
94 
95**Quality standards:**
96- 10+ sources, 3+ per major claim (cluster-independent, not just count)
97- All factual claims cited immediately [N] with evidence backing in `evidence.jsonl`
98- Claim-support verification mandatory: no unsupported factual claims pass delivery
99- No placeholders, no fabricated citations
100- Prose-first (>=80%), bullets sparingly
101 
102---
103 
104## When to Use / NOT Use
105 
106**Use:** Comprehensive analysis, technology comparisons, state-of-the-art reviews, multi-perspective investigation, market analysis.
107 
108**Do NOT use:** Simple lookups, debugging, 1-2 search answers, quick time-sensitive queries.
109