Research Brainstorm Skill

Description

Generates and cross-validates research ideas using Gemini and Codex in parallel, then synthesizes results with Claude.

Usage

/research-brainstorm "research topic" [--domain physics|ai_ml|statistics|mathematics|paper] [--weights '{"novelty":0.4,...}'|adaptive] [--depth low|medium|high|max|auto] [--personas N] [--claude-only] [--substitute "Gemini -> Opus"]

Arguments

• $ARGUMENTS — The research topic and optional flags:
  • --domain — Research domain (physics, ai_ml, statistics, mathematics, paper). Auto-inferred if omitted.
  • --weights — Scoring mode for finding ranking:
    • Omitted (default — holistic mode): Claude ranks findings based on its own expert judgment, with detailed rationale for each ranking position. No numeric dimension weights are used.
    • JSON object (e.g., '{"novelty":0.4,"feasibility":0.2,"impact":0.2,"rigor":0.1,"scalability":0.1}'): Weighted scoring — dimensions novelty, feasibility, impact, rigor, scalability with values summing to 1.0.
    • adaptive: Claude analyzes the prompt, adjusts domain defaults, and asks for user confirmation before scoring (see Step 0c).
  • --depth — Controls review depth (default: medium):
    • low — Skip cross-review, go directly to synthesis
    • medium — Standard one-shot cross-review (current behavior)
    • high — Cross-review + evidence anchoring + adversarial debate round
    • max — Hierarchical MAGI-in-MAGI: N persona subagents run parallel mini-MAGI pipelines, then meta-review + evidence anchoring + adversarial debate across all perspectives
    • auto — Adaptive depth: starts as medium, auto-escalates to high or deep based on cross-review disagreement signals (see T12)
  • --personas N|auto — Number of domain-specialist subagents for --depth max (default: auto, range: 2-4). When auto, Claude analyzes the topic to determine the optimal persona count. Ignored for other depth levels.
  • --claude-only — Replace all Gemini/Codex MCP calls with Claude Agent subagents. Use when external model endpoints are unavailable or for a Claude-only workflow. Two subagents with distinct cognitive styles (Creative-Divergent and Analytical-Convergent) ensure perspective diversity.
  • --substitute "Agent -> Opus" — Replace a specific MAGI agent with a Claude (Opus) subagent. Accepted forms: "Gemini -> Opus", "Codex -> Opus". Can be specified multiple times. Use when a specific model hits rate limits but other models are still available. The substituted agent uses the same cognitive style mapping as --claude-only mode. If both agents are substituted, functionally equivalent to --claude-only. Mutually exclusive with --claude-only (if both provided, --claude-only takes precedence).

Instructions

MCP Tool Rules

• Gemini: Use the following model fallback chain. Try each model in order; if a call fails (error, timeout, or model-not-found), retry with the next model:
  1. model: "gemini-3.1-pro-preview" (preferred)
  2. model: "gemini-2.5-pro" (fallback)
  3. Claude Opus subagent (last resort — skip Gemini MCP tool, spawn an Agent subagent with T1-CD cognitive style, same as --substitute "Gemini -> Opus")
• Codex: Use model: "gpt-5.4" for all Codex MCP calls. Use mcp__codex-cli__brainstorm for ideation, mcp__codex-cli__ask-codex for analysis/review. If Codex fails 2+ times, fall back to a Claude Opus subagent with T1-AC cognitive style (same as --substitute "Codex -> Opus").
• File References: Use @filepath in the prompt parameter to pass saved artifacts (e.g., @brainstorm/codex_ideas.md) instead of pasting file content inline. The CLI tools read files directly, preventing context truncation.
• Web Search: Use web search freely whenever factual verification, recent developments, or literature context would strengthen the discussion:
  • Claude: Use the WebSearch tool directly
  • Gemini: Add search: true to mcp__gemini-cli__ask-gemini or mcp__gemini-cli__brainstorm calls
  • Codex: Add search: true to mcp__codex-cli__ask-codex or mcp__codex-cli__brainstorm calls
  • When to search: prior work verification, methodological precedents, dataset/library availability, related approaches, fact-checking quantitative claims
  • Claude-only mode: Claude Agent subagents cannot use WebSearch. The main Claude agent should search beforehand and include findings in the subagent prompt.

Claude-Only Mode

When --claude-only is active, all Gemini/Codex MCP tool calls are replaced with Claude Agent subagents (subagent_type: general-purpose). The table below maps each original call to its replacement:

Key rules for claude-only mode:

1. File access: Subagents use the Read tool to access files (no @filepath syntax).
2. Output filenames: Keep original names (gemini_ideas.md, codex_ideas.md, etc.) — add a header > Source: Claude Agent subagent (claude-only mode, {style}) to each output file.
3. Independence: Both subagents are spawned simultaneously so neither can see the other's output.
4. --depth max internal subagents: Within each persona's mini-MAGI pipeline, use Expansive Explorer (replaces Gemini) and Grounded Builder (replaces Codex) cognitive styles to maintain internal diversity.

Agent Substitution (--substitute)

When --substitute is used, only the specified agent's MCP calls are replaced with Claude Agent subagents. The replacement uses the same cognitive style and prompt structure as --claude-only mode:

Key differences from --claude-only:

• Only the substituted agent's calls change; the other agent continues using its MCP tool normally.
• Both substituted (Claude subagent) and non-substituted (MCP) calls can still execute in parallel.
• File naming is unchanged (gemini_ideas.md, codex_ideas.md, etc.). Add header > Source: Claude Agent subagent (substituted for {Agent}, {CognitiveStyle}) to files written by substituted agents.
• For --depth max internal subagents: the substituted agent uses Expansive Explorer (if Gemini) or Grounded Builder (if Codex).

Substitution shorthand: Throughout this document, every > **If \--claude-only`**:block also applies when the relevant agent is substituted via--substitute`. When only one agent is substituted, apply the replacement only to that agent's call — the other agent's call remains unchanged as an MCP tool call. Both can still execute in parallel.

Reusable Templates

Templates T1–T13 are defined in references/templates.md. Read that file when you need template definitions. Quick reference: