conducting-deep-research

name	conducting-deep-research
description	Conducts comprehensive research on complex topics with technical rigor, synthesizing multiple sources including academic papers, technical documentation, industry reports, and practitioner insights. Use when the user needs structured, in-depth research with synthesis across diverse sources.

Conducting deep research

Follow the research process described below.

Phase 1: Initial Clarification

Use the AskUserQuestion tool to gather structured feedback on research parameters.

Ask the user to clarify:

1. Research purpose: What is the goal of this research/what angles should be explored? Suggest options contextually. (use AskUserQuestion with multiSelect: true)
2. Scope boundaries: What should be included/excluded? Any constraints? Suggest options contextually. (use AskUserQuestion with multiSelect: true)
3. Source preferences: Which types are most valuable? (use AskUserQuestion with multiSelect: true)
   • Academic papers and peer-reviewed research
   • Technical documentation / Industry whitepapers
   • Technical blogs from recognized experts
   • Practitioner discussions (Reddit, X, LinkedIn, HackerNews)
   • Company documentation and case studies
4. Research depth: How many sources? (use AskUserQuestion with options for Light: 6-8, Medium: 9-14, Deep: 15+)
5. Research mode: How should research be conducted? (use AskUserQuestion with single select)
   • Adaptive (sequential) - Each source informs the next. Better for exploratory research where you want to follow emerging threads and adapt strategy based on what you learn.
   • Parallel (fast) - All sources researched simultaneously. Faster execution but less adaptive. Best when research angles are well-defined upfront.

Phase 2: Planning & Approval

Brief preliminary investigation:

• Search for 2-3 representative sources
• Identify major themes, terminology, key authors/organizations
• Note unexpected angles or adjacent topics worth exploring

Create research plan:

1. Use template from ./templates/research-plan.md
2. Ask the user where they would like you to save your work or if you should create a new working directory
3. Create /[RESEARCH TOPIC] inside the working directory
4. Create and save your research plan to [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/plan.md

Plan structure:

• Research angles: 3-5 core sub-questions or perspectives
• Source strategy: Mix of source types with target quantities based on user preferences
• Analysis approach: Synthesis method (thematic, comparative, chronological)
• Expected deliverables: Final format and supporting documentation
• Potential challenges: Known gaps, access issues, complexity factors

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Research Execution: Choose Based on Mode

After completing Phase 2 (Planning & Approval), proceed based on the research mode selected in Phase 1:

• If Adaptive (sequential) mode selected: Proceed to Phase 3: Iterative Research & Progressive Synthesis (below)
• If Parallel (fast) mode selected: Proceed to Phase 3-Parallel: Parallel Research & Synthesis (see section after Phase 3)

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Phase 3: Iterative Research & Progressive Synthesis

Use this phase when: User selected Adaptive (sequential) research mode

IMPORTANT: Build synthesis progressively, rather than at the end. After every source, update synthesis and adapt approach.

Initial Setup

1. Create synthesis file from template: ./templates/research-synthesis.md
2. Save to: [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/synthesis.md
3. Initialize with research scope and empty theme sections
4. Create summaries directory: [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/summaries/

For Each Source (Sequential Loop)

Step 1: Identify Next Research Priority

Based on current synthesis state, determine:

• The highest-priority gap or angle to explore
• Specific search query to find a relevant source
• Which research angle from the plan this addresses
• Prioritize sources that:
  • Fill identified gaps in current synthesis
  • Validate or challenge emerging patterns
  • Provide missing perspectives from research angles

Step 2: Find and Validate URL

CRITICAL: You must identify a specific URL before spawning the researcher subagent.

1. Use WebSearch to find a relevant source for the identified research priority
2. Identify a specific URL from the search results
3. Use WebFetch with a simple prompt (e.g., "Extract the title and first paragraph") to verify the URL is accessible
4. If the URL is not accessible, find an alternative URL and validate it

Do not proceed to Step 3 until you have a verified, accessible URL.

Step 3: Spawn Research-Analyst Subagent

Use the Task tool to spawn a research-analyst subagent with the validated URL:

Task tool parameters:
- subagent_type: "general-purpose"
- description: "Research [brief topic description]"
- prompt: "You are executing the researcher subagent role defined in /agents/research-analyst.md.

Your assignment:
- Source URL: [VALIDATED_URL]
- Research focus: [specific research angle from plan]
- Research purpose: [overall research goal from Phase 1]
- Working directory: [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]

Follow the instructions in /agents/research-analyst.md to:
1. Fetch the source using WebFetch on the provided URL
2. Conduct deep analysis
3. Create comprehensive summary using analyzing-source/templates/article-summary.md
4. Save to: [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/summaries/[descriptive-filename].md

Provide a brief confirmation when complete with the key insights discovered."

Wait for the subagent to complete.

Step 4: Review Source Summary

Once the subagent completes:

1. Note the filename where the summary was saved
2. Read the summary file to understand the findings
3. Note key insights, themes, and gaps identified

Step 5: Update Synthesis Immediately (KEEP CONCISE)

CRITICAL: The synthesis document must remain concise and well-structured throughout. Add only essential insights.

Update [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/synthesis.md with findings from the summary:

• Add 1-3 key insights to relevant theme sections (not everything from the source)
• Update patterns/contradictions only if source significantly confirms or challenges findings
• Cite source summaries: [[filename]] (summaries include links to original source URLs)
• Refine gaps section (mark gaps filled, identify new gaps)
• Note important connections to previous sources (only significant ones)

Writing discipline:

• Extract the essence, not the details (details live in source summaries)
• Each insight should be 1-2 sentences maximum
• Combine overlapping insights from multiple sources rather than listing separately
• Remove or consolidate redundant information as you add new sources
• The synthesis should be increasingly refined, not increasingly bloated

Step 6: Evaluate & Adapt

After updating synthesis, explicitly evaluate:

What have we learned?

• What themes are emerging strongly?
• What contradictions or debates are appearing?
• What gaps remain most critical?

Should we adapt the approach?

• Are research angles still valid or should we pivot?
• Which source types are proving most valuable?
• Should we dig deeper on specific sub-topics vs broadening?
• Have we found enough evidence for key claims?

What to search for next?

• Determine next highest-priority angle/gap
• Adjust search strategy based on what's working
• Consider whether we're approaching target source count

Step 7: Continue or Conclude

• If more sources needed and target count not reached: return to Step 1
• If sufficient coverage achieved: proceed to Phase 4 (Packaging & Delivery)
• If unexpected angle discovered: use Progressive Clarification (see below)

Synthesis Principles

• Organize by themes, NOT by source
• Update progressively after each source, don't wait for the end
• Keep concise - synthesis should be information-dense and focus on key points
• Identify patterns as they emerge (2+ sources confirming)
• Track contradictions when sources disagree
• Note gaps in current understanding
• Draw evidence-based conclusions only when sufficient sources support them
• Citation format:
  • Source summaries: [[filename]]
  • With display text: [[filename|display text]]
  • External URLs: [display text](https://url.com)

Quality Checks During Research

• Synthesis remains concise and readable
• Contradictions identified and explained
• Synthesis references all key sources
• Conclusions are evidence-based
• Writing is clear, precise, information-dense
• All internal links work
• YAML frontmatter complete

Inform user: Share location, summarize findings, note limitations.

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Phase 3-Parallel: Parallel Research & Synthesis

Use this phase when: User selected Parallel (fast) research mode

Overview

In parallel mode, research is conducted by spawning multiple researcher subagents simultaneously—one for each source topic. Each researcher independently fetches, analyzes, and creates a comprehensive summary of their assigned source. After all researchers complete, you synthesize their findings into a unified research document.

Key differences from adaptive mode:

• All sources researched simultaneously (faster)
• No iterative adaptation based on findings from each source
• Commit to initial research plan without mid-research pivots
• More comprehensive individual summaries required (since main agent won't read original sources)
• Final synthesis happens after all research is complete

Step 1: Setup

1. Create synthesis file from template: ./templates/research-synthesis.md
2. Save to: [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/synthesis.md
3. Create summaries directory: [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/summaries/

Step 2: Identify Research Topics

From the approved research plan, identify specific search queries to research. Aim for target source count from Phase 1 (6-8 for Light, 9-14 for Medium, 15+ for Deep).

For each research angle in the plan, identify 2-4 specific search queries to investigate:

Example:

• Research Angle: "Performance patterns in distributed systems"
  • Query 1: "Kubernetes horizontal pod autoscaling best practices"
  • Query 2: "Netflix microservices scaling strategies"
  • Query 3: "Load balancing algorithms for distributed systems"

Create a list of N search queries to research (where N = target source count).

Step 3: Find and Validate URLs

CRITICAL: You must identify and validate specific URLs before spawning any researcher subagents.

For each search query from Step 2:

1. Use WebSearch to find relevant sources
2. Identify a specific URL from the search results that best addresses the query
3. Use WebFetch with a simple prompt (e.g., "Extract the title and first paragraph") to verify each URL is accessible
4. If a URL is not accessible, find an alternative URL for that query and validate it
5. Compile a list of N validated URLs (one per query)

Do not proceed to Step 4 until you have N validated, accessible URLs.

Document the validated URLs clearly, noting which research angle and query each URL addresses.

Step 4: Spawn Researcher Subagents in Parallel

CRITICAL: Use a single message with multiple Task tool calls to execute all researchers in parallel.

For each validated URL from Step 3, spawn a researcher subagent using the Task tool:

Task tool parameters for each researcher:
- subagent_type: "general-purpose"
- description: "Research [brief topic description]"
- prompt: "You are executing the researcher subagent role defined in /agents/research-analyst.md.

Your assignment:
- Source URL: [VALIDATED_URL]
- Research focus: [specific research angle from plan]
- Research purpose: [overall research goal from Phase 1]
- Working directory: [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]

Follow the instructions in /agents/research-analyst.md to:
1. Fetch the source using WebFetch on the provided URL
2. Conduct deep analysis
3. Create comprehensive summary using analyzing-source/templates/article-summary.md
4. Save to: [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/summaries/[descriptive-filename].md

Provide a brief confirmation when complete with the key insights discovered."

Execute all N researchers in parallel by including N Task tool calls in a single message.

Step 5: Wait for Completion

All researcher subagents will execute in parallel. Wait for all to complete before proceeding.

Step 6: Review Researcher Outputs

Once all researchers have completed:

1. List all summary files created in [YOUR WORKING DIRECTORY]/[RESEARCH TOPIC]/summaries/
2. Read each source summary file to understand what each researcher discovered
3. Note the range of perspectives, key themes, contradictions, and gaps

Step 7: Build Comprehensive Synthesis

Now synthesize all findings into the synthesis.md file:

Synthesis approach:

1. Identify major themes across all sources

   • Look for patterns that appear in multiple sources
   • Note areas of consensus and disagreement
   • Group related findings together

2. Organize synthesis by themes, not by source

   • Each theme section should integrate insights from multiple sources
   • Compare and contrast different perspectives
   • Build coherent narrative for each theme

3. For each theme, include:

   • Core insights and findings (citing source summaries using [[filename]])
   • Supporting evidence and examples from multiple sources
   • Areas of agreement across sources
   • Contradictions or debates (with citations)
   • Practical implications
   • Remaining gaps or open questions

4. Draw evidence-based conclusions

   • Only make claims supported by multiple sources
   • Note confidence level based on source quality and consensus
   • Identify areas requiring further research

5. Create executive summary

   • Synthesize key findings across all themes
   • Highlight most important insights
   • Note limitations of the research

Synthesis writing principles:

• Be comprehensive yet concise—capture all important insights without redundancy
• Cite liberally using [[source-filename]] format
• Make connections explicit between different sources and themes
• Distinguish between well-supported findings and tentative conclusions
• Note source quality in your assessments (per the "Evidence Quality Assessment" sections in summaries)

Step 8: Quality Review

Verify synthesis quality:

• All major themes from source summaries are represented
• Synthesis is organized thematically, not source-by-source
• Key findings are supported by citations to source summaries
• Contradictions and debates are identified and explained
• Conclusions are proportional to evidence strength
• Executive summary captures essential findings
• Writing is clear, precise, and information-dense
• All internal links work
• YAML frontmatter is complete

Step 9: Deliver Results

Inform user:

• Location of synthesis and all source summaries
• Summary of major findings and themes
• Note any limitations (inaccessible sources, areas with thin coverage, etc.)
• Highlight any unexpected or particularly significant discoveries

Notes on Parallel Mode

Advantages:

• Much faster execution (all sources researched simultaneously)
• Good for well-defined research questions with clear angles
• Efficient use of compute resources

Tradeoffs:

• Less adaptive—can't pivot based on what early sources reveal
• May miss emergent themes that would guide sequential search
• Requires well-defined source topics upfront
• No progressive clarification during research

Best suited for:

• Time-sensitive research needs
• Well-understood topics with clear structure
• Situations where research angles are predetermined
• Cases where breadth is more important than depth

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Progressive Clarification

Note: Progressive Clarification only applies to Adaptive (Phase 3) mode. In Parallel mode, commit to the initial plan.

If you discover important angles not in original plan:

1. Pause and inform user
2. Ask if scope should expand
3. Update plan if approved
4. Continue with revised plan

Source Quality Guidelines

Include if:

• Provides unique insights or data
• Represents authoritative voice
• Offers contrarian or edge perspectives
• Contains primary research or original analysis

Target Working Directory Structure

[YOUR WORKING DIRECTORY]/
└── [RESEARCH TOPIC]/
    ├── summaries/
    │   ├── example-source-1-summary.md
    │   └── example-source-2-summary.md
    ├── plan.md
    └── synthesis.md