deep-research

Deep Research Command

Conduct systematic, multi-source research on specified topics using AI-powered analysis and cross-referenced insights.

🎯 Purpose & Scope

What this command does NOT do:

• Generate research without source attribution
• Create content without verification

When to REJECT:

• Topic is better suited for simple web search

🔄 Workflow

ultrathink: you'd perform the following steps

Step 1: Planning

1. Analyze Requirements

   • Parse research topic from $ARGUMENTS
   • Identify optional focus areas
   • Determine research scope and boundaries
   • Select Research Strategy based on topic type:
     • Technical/Scientific: Prioritize academic papers, documentation, code repos
     • Historical: Focus on primary sources, archives, temporal progression
     • Current Events: Emphasize recent sources, news, real-time updates
     • Theoretical/Conceptual: Balance foundational texts with recent developments
     • Product/Market: Industry reports, user feedback, competitive analysis
   • Plan source discovery strategy aligned with selected approach

2. Initialize Research Infrastructure

   • Create research workspace: research_$ARGUMENTS_$(date +%Y%m%d)
   • Initialize source tracker: source_tracker.md
   • Set up finding templates for cross-source insights
   • Check for existing research sessions: Look for source_tracker.md in workspace
     • If exists: Resume from last state (check status fields)
     • Auto-save progress to tracker after each source analysis
     • Tracker serves as both documentation and checkpoint
     • Resume capability: Continue from any 'pending' or 'analyzing' sources

3. Identify Applicable Workflows & Standards

   • Identify any relevant workflows for research processes
   • Identify any related documentation standards
   • Note: MUST follow any matching workflows and standards

4. Delegation Decision

   • Plan parallel source analysis tasks
   • Identify specialized research agents needed
   • Define synthesis coordination points

5. Risk Assessment

   • Identify potential source reliability issues
   • Plan verification strategies
   • Note information gaps

Step 2: Execution

1. Workflow Compliance

   • MUST follow workflows identified in Phase 1
   • Apply research methodology standards
   • Reference specific workflow files when applicable

2. Primary Implementation

   • Dispatch subagents for iterative source analysis
   • Each agent analyzes assigned sources for:
     • Key information relevant to topic
     • Cross-source patterns and themes
     • Contradictions and debates
     • NEW INSIGHTS requiring further research
   • Update source tracker with analysis status
   • CRITICAL: When finding new insights, discover additional sources

3. Cross-Source Finding Format

   • Pattern/Theme identification
   • Evidence compilation from multiple sources
   • Implication analysis for research topic
   • Source attribution with locations

4. Iterative Deep Research Strategy

   • Discovery Triggers: When subagents identify:
     • Unfamiliar concepts or terminology
     • References to related work
     • Gaps in understanding
     • Contradictory information requiring more context
   • Action Protocol:
     1. Add discovered sources to tracker immediately
     2. Spawn new research tasks for high-relevance discoveries
     3. Update finding files with connection chains
     4. Document research depth (initial → level 2 → level 3)
   • Depth Limits: Maximum 3 levels of iterative discovery
   • Priority Management: High-relevance discoveries analyzed first

5. Edge Case Handling

   • No sources found: Expand search parameters
   • Duplicate sources: Check content similarity before analysis
   • Conflicting information: Document all perspectives
   • Subagent timeout: Mark as failed, continue with available data
   • Discovery overflow: Prioritize by relevance + credibility
   • Circular references: Document but don't re-analyze
   • Early termination: If high-confidence convergent evidence achieved

Step 3: Verification

1. Quality Assurance

   • Verify all sources marked as analyzed have summaries
   • Confirm discovered sources are tracked and processed
   • Cross-reference findings across multiple sources
   • Identify contradictions between sources
   • Flag gaps in research coverage
   • Validate discovery chains (source → insight → new source)

2. Consolidation Tasks

   • Merge similar findings from different subagents
   • Resolve conflicting information with source priority
   • Apply Synthesis Framework:
     • Convergent Evidence: Multiple sources supporting same conclusion
     • Divergent Perspectives: Document contrasting viewpoints with context
     • Confidence Scoring: Weight findings by source credibility + convergence
     • Knowledge Gaps: Explicitly mark where evidence is insufficient
   • Create synthesis notes for complex topics with confidence levels

3. Source Validation

   • Confirm source reliability and credibility
   • Check for citation accuracy
   • Verify quotes and references

4. Side Effect Validation

   • Clean temporary sketchpad files
   • Ensure all findings traceable to sources
   • Verify workspace organization

Step 4: Reporting

Output Format:

[✅/❌] Research: $ARGUMENTS

## Summary
- Initial sources: [count]
- **Discovered sources: [count] (across [N] levels)**
- Total sources analyzed: [count]
- **Duplicates detected: [count]**
- Key findings: [count]
- Research gaps: [count]
- **Overall confidence**: [High/Medium/Low]
- **Discovery depth reached: [1-3 levels]**
- **Credibility distribution**: Academic:[N] | Official:[N] | Industry:[N] | Community:[N]

## Executive Summary
[3-5 sentence overview of key discoveries]

## Key Findings
### Finding 1: [Title] (Confidence: High/Medium/Low)
- **Evidence**: [Sources and quotes with credibility indicators]
- **Convergence**: [N sources agree] | [M sources disagree]
- **Significance**: [Why this matters]

### Finding 2: [Title] (Confidence: High/Medium/Low)
[Continue pattern...]

## Thematic Analysis
### Theme A: [Emergent Pattern]
[Synthesis across multiple findings]

## Debates and Contradictions
[Areas where sources disagree]

## Discovery Chains
### Chain 1: [Initial Topic → Discovery]
- Started with: [initial source]
- Led to discovery of: [concept/source]
- Further revealed: [deeper insight]

### Chain 2: [Another Discovery Path]
[Continue pattern...]

## Research Gaps
[What wasn't found or needs further investigation]

## References
[Complete source list with access information, grouped by discovery level]
### Level 1 (Initial Sources)
- [Source 1]
- [Source 2]

### Level 2 (Discovered from initial research)
- [Source A] ← discovered from [Source 1]
- [Source B] ← discovered from [Source 2]

### Level 3 (Deep discoveries)
- [Source X] ← discovered from [Source A]

📝 Examples

Basic Research

/deep-research "quantum computing applications"
# Conducts comprehensive research on quantum computing uses

Focused Research

/deep-research "machine learning" "healthcare applications"
# Researches ML specifically in healthcare context

Complex Multi-Domain Research

/deep-research "climate change impact on global supply chains"
# Analyzes intersection of climate and supply chain topics

Iterative Discovery Research

/deep-research "emerging AI safety frameworks"
# Initial search finds 3 sources
# Agent A discovers reference to "constitutional AI" → adds 2 new sources
# Agent B finds mention of "RLHF techniques" → triggers deep dive with 4 sources
# Agent C identifies "red teaming methodologies" → spawns specialized search
# Result: 15 total sources analyzed across 3 discovery levels

Parallel Source Analysis

/deep-research "blockchain scalability solutions"
# Automatically delegates to:
#   - Agent A: Academic papers analysis
#   - Agent B: Industry reports (parallel)
#   - Agent C: Technical documentation (parallel)
#   - Agent D: Synthesis and consolidation

Error Case Handling

/deep-research "classified-information"
# Error: Topic requires restricted access
# Suggestion: Refine to publicly available information
# Alternative: Focus on general concepts instead