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commands/brainstorm.md

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+Use the @research-strategist agent to deeply investigate and reflect on the following aspect: $ARGUMENTS

commands/ideate.md

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+## Brainstorm Research Idea
+
+You are helping to brainstorm and iteratively refine a research idea through critical assessment, related work analysis, and focused questioning. This command orchestrates a multi-phase workflow that:
+
+- **Assesses the Idea**: Analyzes the initial idea with extensive related work research
+- **Refines the Assessment**: Critically evaluates and improves the assessment to focus on key concerns
+- **Engages the User**: Presents clarifying questions and incorporates responses
+- **Updates the Idea**: Rewrites idea.md with improvements based on user feedback
+
+This iterative process can be repeated multiple times to progressively refine the research concept.
+
+### PHASE 1: Initial Idea Assessment
+
+Use the **idea-assessment** agent to analyze the idea in `research-os/project/idea.md` and create a comprehensive assessment.
+
+The idea-assessment agent will:
+- Read the initial idea from `research-os/project/idea.md`
+- Perform extensive related work searches
+- Create `research-os/project/research-journal.md` documenting the exploration
+- Create `research-os/project/assessment.md` with detailed critique and questions
+
+**Important**: Ensure `research-os/project/idea.md` exists before starting. If it doesn't exist, inform the user:
+```
+Please create research-os/project/idea.md with your research idea first, then run /brainstorm again.
+```
+
+### PHASE 2: Assessment Refinement
+
+Use the **assessment-refiner** agent to critically evaluate and improve the assessment.
+
+The assessment-refiner agent will:
+- Read `research-os/project/assessment.md`
+- Verify claims and assertions through additional research
+- Identify which concerns are substantive vs. minor distractions
+- Rewrite `research-os/project/assessment.md` with a refined, focused assessment
+- Prioritize the most critical questions and recommendations
+
+### PHASE 3: Extract and Present Top Questions to User
+
+After the refined assessment is complete:
+
+1. Read `research-os/project/assessment.md`
+2. Provide a short overall assessment (2-3 sentences)
+2. Identify the **three most pressing and crucial questions** from the assessment that would have the greatest impact on improving and clarifying the research project
+3. For each of the three questions, provide:
+   - The question itself
+   - Context explaining why this question is critical
+   - A potential solution or answer based on the assessment and related work
+
+4. Present these to the user in a clear, organized format:
+
+```
+## Assessment summary
+[A short 2-3 sentence summary of the overall assessment. Be constructive but also very clear about potential shortcomings or unclear design decisions]
+
+Based on the assessment, here are the three most crucial questions to refine your research idea:
+
+## Question 1: [Question text]
+
+**Why this matters:**
+[Context explaining the importance and impact of this question - 2-3 sentences]
+
+**Potential approach:**
+[A concrete, actionable suggestion or potential answer based on the assessment and related work - 2-3 sentences]
+
+## Question 2: [Question text]
+
+**Why this matters:**
+[Context explaining the importance and impact of this question]
+
+**Potential approach:**
+[A concrete, actionable suggestion or potential answer]
+
+## Question 3: [Question text]
+
+**Why this matters:**
+[Context explaining the importance and impact of this question]
+
+**Potential approach:**
+[A concrete, actionable suggestion or potential answer]
+
+---
+
+Please provide your thoughts on these questions and the proposed approaches. Your responses will guide the refinement of your research idea.
+```
+
+5. Wait for the user to provide their responses to the questions.
+
+### PHASE 4: Update research-os/project/idea.md with Refined Vision
+
+Once the user provides their responses:
+
+1. Read the current `research-os/project/idea.md`
+2. Read the refined `research-os/project/assessment.md`
+3. Incorporate the user's responses to the clarifying questions
+4. Write an updated, more focused version of `research-os/project/idea.md` that:
+   - Maintains the core vision but with greater clarity
+   - Addresses the key concerns raised in the assessment
+   - Integrates insights from the user's responses
+   - Reflects a more refined understanding of positioning in the field
+   - Includes specific improvements based on recommendations
+   - Is focused and concise
+
+The updated `research-os/project/idea.md` should be substantially improved while staying true to the original intent.
+
+### PHASE 5: Completion Message
+
+Display to the user:
+
+```
+Your idea has been refined based on the assessment and your responses!
+
+The following files have been updated:
+✓ research-os/project/idea.md (refined research idea)
+✓ research-os/project/assessment.md (critical assessment)
+✓ research-os/project/research-journal.md (related work exploration)
+
+You can now:
+1. Review the updated research-os/project/idea.md to see the refined version
+2. Run /brainstorm again for another iteration of refinement
+3. When satisfied with the idea, run /plan-research to create a full research plan
+
+Each iteration of /brainstorm will deepen the analysis and sharpen the focus.
+```
+
+## Output
+
+Upon completion of one brainstorm iteration, the following files should have been created/updated:
+
+- `research-os/project/idea.md` - Refined research idea incorporating feedback and user responses
+- `research-os/project/assessment.md` - Refined critical assessment with prioritized concerns
+- `research-os/project/research-journal.md` - Documentation of related work exploration
+
+The user can then iterate by running `/brainstorm` again, which will reassess the refined idea and continue the improvement cycle.

commands/plan-research.md

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+## Research Planning Process
+
+You are helping to plan and document a research project with a mission, experiment roadmap, and technical requirements. This will include:
+
+- **Iterative Refinement**: Through intelligent questioning and related work discovery, refine the research vision
+- **Related Work Discovery**: Find and document relevant prior work to position the research
+- **Mission Document**: Create a professional research mission with hypothetical results
+- **Experiment Roadmap**: Create a dependency-based experimental plan with minimum triage experiment
+- **Tech Stack**: Document technical requirements, datasets, and evaluation metrics
+
+This process will create these files in `research-os/project/` directory.
+
+### PHASE 1: Iterative Research Refinement & Related Work Discovery
+
+Use the **gather-research-info** subagent to iteratively refine the research idea and create comprehensive documentation.
+
+IF the user has provided any initial details about their research idea, hypothesis, methodology, or target venue, provide those to the **gather-research-info** subagent.
+
+The gather-research-info agent will:
+- Iteratively refine the research idea through multiple rounds of intelligent questioning
+- Search for and document related work throughout the refinement process
+- Create `research-os/project/research-journal.md` capturing the complete refinement journey
+- Create `research-os/project/related-work.md` consolidating all discovered literature
+
+### PHASE 2: Create Research Mission
+
+Use the **create-research-mission** agent to turn the research idea into a compelling mission statement for a top-tier venue.
+
+The create-research-mission agent will:
+- Create `research-os/project/mission.md` with positioned mission and hypothetical results
+
+### PHASE 3: Create Experiment Roadmap
+
+The create-experiment-roadmap agent will:
+- Create `research-os/project/roadmap.md` with experiment dependencies and minimum triage experiment
+
+### PHASE 4: Document Technical Stack
+
+The document-tech-stack agent will:
+- Create `research-os/project/tech-stack.md` documenting frameworks, datasets, and metrics
+
+### PHASE 5: Final Validation
+
+Verify all files created successfully:
+
+```bash
+# Validate all research planning files exist
+for file in research-journal.md related-work.md mission.md roadmap.md tech-stack.md; do
+    if [ ! -f "research-os/project/$file" ]; then
+        echo "Error: Missing $file"
+    else
+        echo "✓ Created research-os/project/$file"
+    fi
+done
+
+echo "Research planning complete! Review your research documentation in research-os/project/"
+```
+
+### PHASE 6: Display Results
+
+Display to the user:
+- Confirmation of files created
+- Summary of the research vision and differentiation
+- Overview of experiment phases with minimum triage experiment
+- Key related work identified
+
+Output to user:
+
+"Review these files to ensure they accurately capture your research vision, position it properly in the field, and provide a realistic experimental path forward."
+
+## Output
+
+Upon completion, the following files should have been created and delivered to the user:
+
+- `research-os/project/research-journal.md` - Complete iterative refinement history with Q&A
+- `research-os/project/related-work.md` - Consolidated literature review from searches
+- `research-os/project/mission.md` - Research mission with hypothetical results
+- `research-os/project/roadmap.md` - Experiment roadmap with dependencies and triage
+- `research-os/project/tech-stack.md` - Technical requirements and evaluation protocols