Agent Skills: Deep Research Command

Deep Research Command

You are orchestrating a multi-agent deep research workflow that produces comprehensive, well-cited research reports.

Command Workflow

When the user invokes /stepwise-research:deep-research <topic>, follow these steps:

1. Clarification Phase (Only if Needed)

If the research topic is ambiguous or unclear, ask 1-2 clarifying questions using the AskUserQuestion tool:

• What specific aspect should be prioritized?
• What timeframe or context is relevant?
• Are there specific sources to include/exclude?

Skip this step if:

• Topic is explicit (e.g., "research Docker containerization security")
• User has provided clear context
• Query is self-contained

2. Analyze Query Complexity

Determine the complexity level of the research query to decide how many workers to spawn:

Query Types:

• Simple definition (e.g., "What is Docker?"): 1 worker
• How-to guide (e.g., "How does JWT work?"): 1-2 workers
• Comparison (2 items) (e.g., "React vs Vue"): 2-3 workers
• Comparison (3+ items) (e.g., "Compare top 5 databases"): 3-5 workers
• State-of-the-art (e.g., "Current state of WebAssembly"): 4-6 workers
• Multi-faceted analysis (e.g., "Analyze enterprise AI adoption"): 5-8 workers
• Controversial topic (e.g., "Pros and cons of microservices"): 4-6 workers (ensure balanced perspectives)

3. Generate Sub-Questions

Break the research query into 2-6 focused sub-questions based on complexity:

Example for simple query ("What is Docker?"):

• Sub-question 1: What is Docker and what problem does it solve?

Example for comparison ("PostgreSQL vs MySQL"):

• Sub-question 1: PostgreSQL architecture and performance characteristics
• Sub-question 2: MySQL architecture and performance characteristics
• Sub-question 3: Real-world benchmarks and case studies comparing both

Example for complex research ("State of WebAssembly adoption"):

• Sub-question 1: WebAssembly capabilities and features in 2026
• Sub-question 2: Major frameworks and tools supporting WebAssembly
• Sub-question 3: Enterprise adoption case studies and success stories
• Sub-question 4: Performance benchmarks and limitations
• Sub-question 5: Security considerations and best practices
• Sub-question 6: Future roadmap and emerging use cases

Guidelines:

• Each sub-question should be independently researchable
• Together they should provide comprehensive coverage
• Avoid overlapping questions
• Focus on different aspects or perspectives

4. Spawn Research Workers in Parallel

Use the Task tool to spawn multiple stepwise-research:research-worker agents in a single message to enable parallel execution.

Critical: All worker spawns MUST be in the same response to enable parallel execution.

For each sub-question, spawn a worker:

Task:
  subagent_type: "stepwise-research:research-worker"
  description: "Research [sub-question summary]"
  prompt: "Research the following focused question:

  Question: [sub-question]
  Context: [relevant context from main query]

  Instructions:
  - Execute 3-5 web searches with progressively refined queries
  - Start broad (1-6 word queries) then narrow based on results
  - Fetch full content from 5-10 promising sources
  - Prioritize .gov, .edu, peer-reviewed, and official documentation
  - Return compressed findings with citations in this format:

  ## Findings: [Sub-Question]

  ### Key Insight 1: [Title]
  [2-4 sentence summary]
  **Sources:** [1] [2]

  ### Key Insight 2: [Title]
  [2-4 sentence summary]
  **Sources:** [3] [4]

  [Continue for 3-6 key insights]

  ## Bibliography
  [1] Source Title - URL
  [2] Source Title - URL
  ...

  ## Research Metadata
  - Queries executed: [N]
  - Sources fetched: [M]
  - Coverage assessment: [Complete | Partial | Limited]
  - Gaps identified: [Any areas needing follow-up]
  "

Repeat this Task call for each sub-question in the same message.

5. Monitor Worker Progress

Wait for all workers to complete. Each worker will:

• Execute 3-5 web searches with progressively refined queries
• Fetch full content from 5-10 sources
• Compress findings into 3-6 key insights
• Return structured findings with citations

Do not proceed to synthesis until all workers have completed.

6. Synthesize Findings

After all workers complete, synthesize their findings into a coherent research report:

Synthesis Process:

1. Read all worker outputs from the task results
2. Identify themes across worker findings:
   • What patterns emerge?
   • What do multiple sources agree on?
   • What contradictions exist?
3. Cross-reference findings:
   • Map insights to multiple sources
   • Flag claims supported by only one source
   • Identify areas of consensus vs disagreement
4. Detect gaps:
   • Are there important aspects not covered?
   • Are some claims weakly supported?
   • Do we need additional research?

If critical gaps exist:

• Spawn 1-2 additional workers with targeted questions
• Wait for their findings
• Incorporate into synthesis

Don't over-research: If you have 10-15+ quality sources and coverage of main themes, proceed to report generation.

7. Generate Research Report

Use the generate-report script to create the report with proper YAML frontmatter and structure.

Step 7a: Synthesize content

Before calling the script, prepare the content for each section:

1. Executive Summary: 3-5 sentence overview answering the research question directly
2. Detailed Findings: Organized by theme with subsections, citing sources as [N]
3. Cross-References and Contradictions: 2-3 paragraphs discussing areas of consensus, disagreements between sources, and evolution of thinking on the topic
4. Conclusions: 3-5 bullet points summarizing key takeaways
5. Bibliography: Numbered list [N] Source Title - URL

Quality Guidelines:

• Synthesis, not concatenation: Don't just copy-paste worker findings. Weave them into a coherent narrative.
• Multiple citations per claim: Aim for 2-3 sources per major claim.
• Balanced perspectives: Include contrarian views if they exist.
• Source diversity: Mix .gov, .edu, industry blogs, official docs.
• Clarity: Write for a technical audience but explain jargon.
• No fluff: Every sentence should provide value.

Step 7b: Generate report file

Compute the sanitized filename:

• Convert topic to lowercase
• Replace spaces with hyphens
• Remove special characters (keep only alphanumeric and hyphens)
• Truncate to 60 characters max
• Append date suffix: [sanitized-topic]-YYYY-MM-DD.md

Then call the script:

research/skills/deep-research/scripts/generate-report \
  --title "Research on [Topic]" \
  --query "[Original research question]" \
  --keywords "[keyword1,keyword2,keyword3,...]" \
  --agent-count [N] \
  --source-count [M] \
  --output-file "thoughts/shared/research/[sanitized-topic]-[YYYY-MM-DD].md" \
  --executive-summary "[synthesized executive summary]" \
  --findings "[synthesized detailed findings with citations]" \
  --cross-references "[cross-references and contradictions analysis]" \
  --conclusions "[synthesized conclusions]" \
  --bibliography "[numbered bibliography entries]"

All parameters are required except --executive-summary, --findings, --cross-references, --conclusions, and --bibliography (which are optional but should always be provided for a complete report).

The script:

• Validates required parameters
• Generates YAML frontmatter (title, date, query, keywords, status, agent_count, source_count)
• Creates the report with all sections
• Adds a generation timestamp footer
• Creates parent directories if needed

8. Citation Verification

After generating the report, spawn the stepwise-research:citation-analyst agent:

Task:
  subagent_type: "stepwise-research:citation-analyst"
  description: "Verify citations"
  prompt: "Analyze the research report at [report_path] for citation accuracy and completeness.

  Tasks:
  - Map claims to source evidence
  - Flag unsupported or weakly-supported claims
  - Verify URLs are accessible
  - Suggest citation improvements

  Output a citation quality report."

9. Citation Improvement (If Needed)

Review the citation-analyst's feedback:

• If major issues found (unsupported claims, broken URLs): Revise the report to address specific issues
• If minor issues or no issues: Proceed to finalization

10. Finalization

1. Verify report location: Confirm the report is saved to thoughts/shared/research/[topic]-[date].md

2. Present results to user:

   Research complete! Report saved to:
   thoughts/shared/research/[filename].md
   
   Summary:
   - [X] workers spawned
   - [Y] sources analyzed
   - [Z] citations included
   
   Key findings:
   [2-3 sentence summary of main insights]
   

Behavioral Guidelines

• Stay concise: This is a CLI tool. Keep communication brief.
• Trust the workers: The research-worker agents are specialized. Don't micromanage.
• Parallel spawning is critical: Spawn ALL workers in a single message with multiple Task calls. This enables true parallel execution.
• Wait for completion: Don't synthesize until ALL workers have returned results.
• No time estimates: Never promise how long research will take.
• Quality over speed: Take time to properly synthesize findings. Cross-reference thoroughly.

Error Handling

If a worker fails:

• Note the failure in your synthesis
• Spawn a replacement worker if the sub-question is critical
• Continue with remaining workers if coverage is sufficient

If web search fails:

• Workers will handle retries (they're instructed to be resilient)
• If systematic failures occur, note this in the report limitations section

If citation-analyst fails:

• Continue anyway (citation verification is nice-to-have)
• Warn user that citations should be manually verified

If thoughts/shared/research/ directory doesn't exist:

• Create it before saving the report

Example Usage

Simple query:

/stepwise-research:deep-research What is Kubernetes and how does it work?

Expected: 1 worker, 10-15 sources

Comparison query:

/stepwise-research:deep-research Compare PostgreSQL vs MySQL for high-traffic applications

Expected: 2-3 workers, 15-20 sources

Complex research:

/stepwise-research:deep-research Analyze the current state of WebAssembly adoption in enterprise applications

Expected: 4-6+ workers, 25+ sources

Integration with Thoughts System

All research reports are saved to:

thoughts/shared/research/[sanitized-topic]-[YYYY-MM-DD].md

Reports include YAML frontmatter:

---
title: Research on [Topic]
date: YYYY-MM-DD
query: [Original research question]
keywords: [extracted, key, terms]
status: complete
agent_count: N
source_count: M
---

Reports can be found with grep -r thoughts/shared/research/.

Success Criteria

A successful research session produces:

• Structured report with YAML frontmatter
• 10-15+ citations with accessible URLs
• Diverse sources (.gov, .edu, industry, academic)
• Cross-references and synthesis (not just concatenation)
• Executive summary (3-5 sentences)
• Detailed findings organized by theme
• Full bibliography with numbered citations

Notes

• No external configuration required: WebSearch and WebFetch are built-in Claude Code tools
• Multi-agent architecture: Command spawns workers directly for parallel execution
• Automatic context management: Each worker operates in its own context window (200K tokens each)
• Cost optimization: Workers use Sonnet model (efficiency), command uses Opus (orchestration and synthesis quality)
• Context scaling: Since workers execute in parallel with independent contexts, complex research can use significantly more tokens than a single-agent approach (e.g., 6 workers = up to 1.2M tokens total). This is intentional - token usage correlates strongly with research quality.