Research

Research Skill

Orchestrate parallel scientist agents for comprehensive research workflows with optional AUTO mode for fully autonomous execution.

Overview

Research is a multi-stage workflow that decomposes complex research goals into parallel investigations:

1. Decomposition - Break research goal into independent stages/hypotheses
2. Execution - Run parallel scientist agents on each stage
3. Verification - Cross-validate findings, check consistency
4. Synthesis - Aggregate results into comprehensive report

Usage Examples

/oh-my-codex:research <goal>                    # Standard research with user checkpoints
/oh-my-codex:research AUTO: <goal>              # Fully autonomous until complete
/oh-my-codex:research status                    # Check current research session status
/oh-my-codex:research resume                    # Resume interrupted research session
/oh-my-codex:research list                      # List all research sessions
/oh-my-codex:research report <session-id>       # Generate report for session

Quick Examples

/oh-my-codex:research What are the performance characteristics of different sorting algorithms?
/oh-my-codex:research AUTO: Analyze authentication patterns in this codebase
/oh-my-codex:research How does the error handling work across the API layer?

Research Protocol

Stage Decomposition Pattern

When given a research goal, decompose into 3-7 independent stages:

## Research Decomposition

**Goal:** <original research goal>

### Stage 1: <stage-name>
- **Focus:** What this stage investigates
- **Hypothesis:** Expected finding (if applicable)
- **Scope:** Files/areas to examine
- **Tier:** LOW | MEDIUM | HIGH

### Stage 2: <stage-name>
...

Parallel Scientist Invocation

Fire independent stages in parallel via Task tool:

// Stage 1 - Simple data gathering
Task(subagent_type="oh-my-codex:scientist", model="haiku", prompt="[RESEARCH_STAGE:1] Investigate...")

// Stage 2 - Standard analysis
Task(subagent_type="oh-my-codex:scientist", model="sonnet", prompt="[RESEARCH_STAGE:2] Analyze...")

// Stage 3 - Complex reasoning
Task(subagent_type="oh-my-codex:scientist-high", model="opus", prompt="[RESEARCH_STAGE:3] Deep analysis of...")

Smart Model Routing

CRITICAL: Always pass model parameter explicitly!

Routing Decision Guide

Verification Loop

After parallel execution completes, verify findings:

// Cross-validation stage
Task(subagent_type="oh-my-codex:scientist", model="sonnet", prompt="
[RESEARCH_VERIFICATION]
Cross-validate these findings for consistency:

Stage 1 findings: <summary>
Stage 2 findings: <summary>
Stage 3 findings: <summary>

Check for:
1. Contradictions between stages
2. Missing connections
3. Gaps in coverage
4. Evidence quality

Output: [VERIFIED] or [CONFLICTS:<list>]
")

AUTO Mode

AUTO mode runs the complete research workflow autonomously with loop control.

Loop Control Protocol

[RESEARCH + AUTO - ITERATION {{ITERATION}}/{{MAX}}]

Your previous attempt did not output the completion promise. Continue working.

Current state: {{STATE}}
Completed stages: {{COMPLETED_STAGES}}
Pending stages: {{PENDING_STAGES}}

Promise Tags

AUTO Mode Rules

1. Max Iterations: 10 (configurable)
2. Continue until: Promise tag emitted OR max iterations
3. State tracking: Persist after each stage completion
4. Cancellation: /oh-my-codex:cancel or "stop", "cancel"

AUTO Mode Example

/oh-my-codex:research AUTO: Comprehensive security analysis of the authentication system

[Decomposition]
- Stage 1 (LOW): Enumerate auth-related files
- Stage 2 (MEDIUM): Analyze token handling
- Stage 3 (MEDIUM): Review session management
- Stage 4 (HIGH): Identify vulnerability patterns
- Stage 5 (MEDIUM): Document security controls

[Execution - Parallel]
Firing stages 1-3 in parallel...
Firing stages 4-5 after dependencies complete...

[Verification]
Cross-validating findings...

[Synthesis]
Generating report...

[PROMISE:RESEARCH_COMPLETE]

Parallel Execution Patterns

Independent Dataset Analysis (Parallel)

When stages analyze different data sources:

// All fire simultaneously
Task(subagent_type="oh-my-codex:scientist", model="haiku", prompt="[STAGE:1] Analyze src/api/...")
Task(subagent_type="oh-my-codex:scientist", model="haiku", prompt="[STAGE:2] Analyze src/utils/...")
Task(subagent_type="oh-my-codex:scientist", model="haiku", prompt="[STAGE:3] Analyze src/components/...")

Hypothesis Battery (Parallel)

When testing multiple hypotheses:

// Test hypotheses simultaneously
Task(subagent_type="oh-my-codex:scientist", model="sonnet", prompt="[HYPOTHESIS:A] Test if caching improves...")
Task(subagent_type="oh-my-codex:scientist", model="sonnet", prompt="[HYPOTHESIS:B] Test if batching reduces...")
Task(subagent_type="oh-my-codex:scientist", model="sonnet", prompt="[HYPOTHESIS:C] Test if lazy loading helps...")

Cross-Validation (Sequential)

When verification depends on all findings:

// Wait for all parallel stages
[stages complete]

// Then sequential verification
Task(subagent_type="oh-my-codex:scientist-high", model="opus", prompt="
[CROSS_VALIDATION]
Validate consistency across all findings:
- Finding 1: ...
- Finding 2: ...
- Finding 3: ...
")

Concurrency Limit

Maximum 20 concurrent scientist agents to prevent resource exhaustion.

If more than 20 stages, batch them:

Batch 1: Stages 1-5 (parallel)
[wait for completion]
Batch 2: Stages 6-7 (parallel)

Session Management

Directory Structure

.omc/research/{session-id}/
  state.json              # Session state and progress
  stages/
    stage-1.md            # Stage 1 findings
    stage-2.md            # Stage 2 findings
    ...
  findings/
    raw/                  # Raw findings from scientists
    verified/             # Post-verification findings
  figures/
    figure-1.png          # Generated visualizations
    ...
  report.md               # Final synthesized report

State File Format

{
  "id": "research-20240115-abc123",
  "goal": "Original research goal",
  "status": "in_progress | complete | blocked | cancelled",
  "mode": "standard | auto",
  "iteration": 3,
  "maxIterations": 10,
  "stages": [
    {
      "id": 1,
      "name": "Stage name",
      "tier": "LOW | MEDIUM | HIGH",
      "status": "pending | running | complete | failed",
      "startedAt": "ISO timestamp",
      "completedAt": "ISO timestamp",
      "findingsFile": "stages/stage-1.md"
    }
  ],
  "verification": {
    "status": "pending | passed | failed",
    "conflicts": [],
    "completedAt": "ISO timestamp"
  },
  "createdAt": "ISO timestamp",
  "updatedAt": "ISO timestamp"
}

Session Commands

Tag Extraction

Scientists use structured tags for findings. Extract them with these patterns:

Finding Tags

[FINDING:<id>] <title>
<evidence and analysis>
[/FINDING]

[EVIDENCE:<finding-id>]
- File: <path>
- Lines: <range>
- Content: <relevant code/text>
[/EVIDENCE]

[CONFIDENCE:<level>] # HIGH | MEDIUM | LOW
<reasoning for confidence level>

Extraction Regex Patterns

// Finding extraction
const findingPattern = /\[FINDING:(\w+)\]\s*(.*?)\n([\s\S]*?)\[\/FINDING\]/g;

// Evidence extraction
const evidencePattern = /\[EVIDENCE:(\w+)\]([\s\S]*?)\[\/EVIDENCE\]/g;

// Confidence extraction
const confidencePattern = /\[CONFIDENCE:(HIGH|MEDIUM|LOW)\]\s*(.*)/g;

// Stage completion
const stageCompletePattern = /\[STAGE_COMPLETE:(\d+)\]/;

// Verification result
const verificationPattern = /\[(VERIFIED|CONFLICTS):?(.*?)\]/;

Evidence Window

When extracting evidence, include context window:

[EVIDENCE:F1]
- File: /src/auth/login.ts
- Lines: 45-52 (context: 40-57)
- Content:
  ```typescript
  // Lines 45-52 with 5 lines context above/below

[/EVIDENCE]

### Quality Validation

Findings must meet quality threshold:

| Quality Check | Requirement |
|---------------|-------------|
| Evidence present | At least 1 [EVIDENCE] per [FINDING] |
| Confidence stated | Each finding has [CONFIDENCE] |
| Source cited | File paths are absolute and valid |
| Reproducible | Another agent could verify |

## Report Generation

### Report Template

```markdown
# Research Report: {{GOAL}}

**Session ID:** {{SESSION_ID}}
**Date:** {{DATE}}
**Status:** {{STATUS}}

## Executive Summary

{{2-3 paragraph summary of key findings}}

## Methodology

### Research Stages

| Stage | Focus | Tier | Status |
|-------|-------|------|--------|
{{STAGES_TABLE}}

### Approach

{{Description of decomposition rationale and execution strategy}}

## Key Findings

### Finding 1: {{TITLE}}

**Confidence:** {{HIGH|MEDIUM|LOW}}

{{Detailed finding with evidence}}

#### Evidence

{{Embedded evidence blocks}}

### Finding 2: {{TITLE}}
...

## Visualizations

{{FIGURES}}

## Cross-Validation Results

{{Verification summary, any conflicts resolved}}

## Limitations

- {{Limitation 1}}
- {{Limitation 2}}
- {{Areas not covered and why}}

## Recommendations

1. {{Actionable recommendation}}
2. {{Actionable recommendation}}

## Appendix

### Raw Data

{{Links to raw findings files}}

### Session State

{{Link to state.json}}

Figure Embedding Protocol

Scientists generate visualizations using this marker:

[FIGURE:path/to/figure.png]
Caption: Description of what the figure shows
Alt: Accessibility description
[/FIGURE]

Report generator embeds figures:

## Visualizations

![Figure 1: Description](figures/figure-1.png)
*Caption: Description of what the figure shows*

![Figure 2: Description](figures/figure-2.png)
*Caption: Description of what the figure shows*

Figure Types

Configuration

Optional settings in .codex/settings.json:

{
  "omc": {
    "research": {
      "maxIterations": 10,
      "maxConcurrentScientists": 5,
      "defaultTier": "MEDIUM",
      "autoVerify": true,
      "generateFigures": true,
      "evidenceContextLines": 5
    }
  }
}

Cancellation

/oh-my-codex:cancel

Or say: "stop research", "cancel research", "abort"

Progress is preserved in .omc/research/{session-id}/ for resume.

Troubleshooting

Stuck in verification loop?

• Check for conflicting findings between stages
• Review state.json for specific conflicts
• May need to re-run specific stages with different approach

Scientists returning low-quality findings?

• Check tier assignment - complex analysis needs HIGH tier
• Ensure prompts include clear scope and expected output format
• Review if research goal is too broad

AUTO mode exhausted iterations?

• Review state to see where it's stuck
• Check if goal is achievable with available data
• Consider breaking into smaller research sessions

Missing figures in report?

• Verify figures/ directory exists
• Check [FIGURE:] tags in findings
• Ensure paths are relative to session directory

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