Comprehensive Research Skill

A systematic multi-phase research orchestration skill that coordinates specialized agents to conduct thorough investigations across codebases, documentation, and external sources. Based on proven patterns from codeflow research workflows with incentive-based prompting enhancements.

How It Works

This skill orchestrates a disciplined research workflow through three primary phases:

1. Discovery Phase (Parallel): Multiple locator agents scan simultaneously
2. Analysis Phase (Sequential): Deep analyzers process findings with evidence chains
3. Synthesis Phase: Consolidated insights with actionable recommendations

Research Methodology

Phase 1: Context & Scope Definition

Before spawning agents, establish:

## Research Scope Analysis
- **Primary Question**: [Core research objective]
- **Decomposed Sub-Questions**: [Derived investigation areas]
- **Scope Boundaries**: [What's in/out of scope]
- **Depth Level**: shallow | medium | deep
- **Expected Deliverables**: [Documentation, recommendations, code refs]

Critical Rule: Always read primary sources fully BEFORE spawning agents.

Phase 2: Parallel Discovery

Spawn these agents concurrently for comprehensive coverage:

Discovery Output Structure:

{
  "codebase_files": ["path/file.ext:lines"],
  "documentation": ["docs/path.md"],
  "patterns_identified": ["pattern-name"],
  "coverage_map": {"area": "percentage"}
}

Phase 3: Sequential Deep Analysis

After discovery completes, run analyzers sequentially:

For Complex Research, Add:

Phase 4: Synthesis & Documentation

Aggregate all findings into structured output:

---
date: YYYY-MM-DD
researcher: Assistant
topic: 'Research Topic'
tags: [research, relevant, tags]
status: complete
confidence: high|medium|low
---

## Synopsis
[1-2 sentence summary of research objective and outcome]

## Summary
[3-5 bullet points of high-level findings]

## Detailed Findings

### Component Analysis
- **Finding**: [Description]
- **Evidence**: `file.ext:line-range`
- **Implications**: [What this means]

### Documentation Insights
- **Decisions Made**: [Past architectural decisions]
- **Rationale**: [Why decisions were made]
- **Constraints**: [Technical/operational limits]

### Code References
- `path/file.ext:12-45` - Description of relevance
- `path/other.ext:78` - Key function location

## Architecture Insights
[Key patterns, design decisions, cross-component relationships]

## Historical Context
[Insights from existing documentation, evolution of the system]

## Recommendations
### Immediate Actions
1. [First priority action]
2. [Second priority action]

### Long-term Considerations
- [Strategic recommendation]

## Risks & Limitations
- [Identified risk with mitigation]
- [Research limitation]

## Open Questions
- [ ] [Unresolved question requiring further investigation]

Agent Coordination Best Practices

Execution Order Optimization

┌─────────────────────────────────────────────────────────────┐
│ Phase 1: Discovery (PARALLEL)                               │
│ ┌──────────────┐ ┌──────────────┐ ┌──────────────────────┐  │
│ │codebase-     │ │research-     │ │codebase-pattern-     │  │
│ │locator       │ │locator       │ │finder                │  │
│ └──────┬───────┘ └──────┬───────┘ └──────────┬───────────┘  │
│        │                │                     │              │
│        └────────────────┼─────────────────────┘              │
│                         ▼                                    │
├─────────────────────────────────────────────────────────────┤
│ Phase 2: Analysis (SEQUENTIAL)                              │
│ ┌──────────────┐       ┌──────────────┐                     │
│ │codebase-     │──────▶│research-     │                     │
│ │analyzer      │       │analyzer      │                     │
│ └──────────────┘       └──────────────┘                     │
│                                                              │
├─────────────────────────────────────────────────────────────┤
│ Phase 3: Domain Specialists (CONDITIONAL)                   │
│ ┌────────────┐ ┌────────────┐ ┌────────────┐               │
│ │web-search- │ │database-   │ │security-   │               │
│ │researcher  │ │expert      │ │scanner     │               │
│ └────────────┘ └────────────┘ └────────────┘               │
│                                                              │
├─────────────────────────────────────────────────────────────┤
│ Phase 4: Validation (PARALLEL)                              │
│ ┌──────────────┐       ┌──────────────┐                     │
│ │code-reviewer │       │architect-    │                     │
│ │              │       │review        │                     │
│ └──────────────┘       └──────────────┘                     │
└─────────────────────────────────────────────────────────────┘

Quality Indicators

• Comprehensive Coverage: Multiple agents provide overlapping validation
• Evidence-Based: All findings include specific file:line references
• Contextual Depth: Historical decisions and rationale included
• Actionable Insights: Clear next steps provided
• Risk Assessment: Potential issues identified

Caching Strategy

Cache Configuration

type: hierarchical
ttl: 3600  # 1 hour
invalidation: manual
scope: command

What to Cache

• Successful agent coordination strategies for similar topics
• Effective agent combinations
• Question decomposition patterns
• Pattern recognition results

Cache Performance Targets

• Hit rate: ≥60%
• Memory usage: <30MB
• Response time improvement: <150ms

Error Handling

Common Failure Modes

Escalation Triggers

• Multiple agent failures
• Scope exceeds single-session capacity
• Cross-repository research needed
• External API/service investigation required

Structured Output Format

{
  "status": "success|in_progress|error",
  "timestamp": "ISO-8601",
  "cache": {
    "hit": true,
    "key": "pattern:{hash}:{scope}",
    "ttl_remaining": 3600,
    "savings": 0.25
  },
  "research": {
    "question": "Primary research question",
    "scope": "codebase|documentation|external|all",
    "depth": "shallow|medium|deep"
  },
  "findings": {
    "total_files": 23,
    "codebase_refs": 18,
    "documentation_refs": 5,
    "insights_generated": 7,
    "patterns_identified": 3
  },
  "document": {
    "path": "docs/research/YYYY-MM-DD-topic.md",
    "sections": ["synopsis", "summary", "findings", "recommendations"],
    "code_references": 12,
    "historical_context": 3
  },
  "agents_used": [
    "codebase-locator",
    "research-locator",
    "codebase-analyzer",
    "research-analyzer"
  ],
  "metadata": {
    "processing_time_seconds": 180,
    "cache_savings_percent": 0.25,
    "agent_tasks_completed": 6,
    "follow_up_items": 2
  },
  "confidence": {
    "overall": 0.85,
    "codebase_coverage": 0.9,
    "documentation_coverage": 0.7,
    "external_coverage": 0.8
  }
}

Anti-Patterns to Avoid

1. Spawning agents before reading sources - Always understand context first
2. Running agents sequentially when parallelization is possible - Maximize concurrency
3. Relying solely on cached documentation - Prioritize current codebase state
4. Skipping cache checks - Always check for existing research
5. Ignoring historical context - Past decisions inform current understanding
6. Over-scoping initial research - Start focused, expand if needed

Integration with Incentive-Based Prompting

Apply these techniques when spawning research agents:

Expert Persona for Analyzers

You are a senior systems analyst with 12+ years of experience at companies like 
Google and Stripe. Your expertise is in extracting actionable insights from 
complex codebases and documentation.

Stakes Language for Discovery

This research is critical for the project's success. Missing relevant files 
or documentation will result in incomplete analysis.

Step-by-Step for Synthesis

Take a deep breath. Analyze findings systematically before synthesizing.
Cross-reference all claims with evidence. Identify gaps methodically.

Example Usage

Basic Research Request

/research "How does the authentication system work in this codebase?"

Advanced Research with Parameters

/research "Analyze payment processing implementation" --scope=codebase --depth=deep

Research from Ticket

/research --ticket="docs/tickets/AUTH-123.md" --scope=both

Follow-Up Commands

After research completes, typical next steps:

• /plan - Create implementation plan based on findings
• /review - Validate research conclusions
• /work - Begin implementation with full context

Research Quality Checklist

Before finalizing research output:

• All claims have file:line evidence
• Historical context included where relevant
• Open questions explicitly listed
• Recommendations are actionable
• Confidence levels assigned
• Cross-component relationships identified
• Potential risks documented

Research References

This skill incorporates methodologies from:

• Codeflow Research Patterns - Multi-agent orchestration
• Bsharat et al. (2023) - Principled prompting for quality
• Kong et al. (2023) - Expert persona effectiveness
• Yang et al. (2023) - Step-by-step reasoning optimization