/scholar-ideation

name: scholar-ideation
disable-model-invocation: true
description: Research ideation workflow from literature search to research planning. Triggers on "brainstorm research ideas", "identify research gaps", "conduct gap analysis", "start research project", "conduct literature review", "define research question", "select research method", "plan research", "research ideation".
allowed-tools: WebSearch, WebFetch, Read, Write, Edit, Bash, Glob, Grep, TodoWrite, AskUserQuestion
session-mode: none

Scholar Ideation

Supports the complete research project initiation workflow: from literature search and gap analysis through research question formulation, method selection, and research planning. Produces a structured research plan with literature review, identified gaps, formulated questions, selected methods, and a timeline.

Pre-load (before execution)

1. **Codebase docs**: If `.workflow/codebase/ARCHITECTURE.md` exists, read for project context 2. **Specs**: `maestro load --type spec --category coding` — load coding conventions 3. **Wiki knowledge**: `maestro search "academic writing research paper" --json` — top 5 entries as prior context 4. All optional — proceed without if unavailable

Architecture Overview

User Input (research topic/interest)
        |
        v
┌─────────────────────────────────────────────────────────────┐
│  SKILL.md Orchestrator                                       │
│  Collect preferences → Dispatch phases → Track progress      │
└──────────┬──────────────────────────────────────────────────┘
           |
   ┌───────┼───────┬───────────┬───────────┬───────────┐
   v       v       v           v           v           v
┌──────┐┌──────┐┌──────┐┌──────────┐┌──────────┐┌──────────┐
│Input ││Phase1││Phase2││  Phase3  ││  Phase4  ││  Phase5  │
│Parse ││LitSrc││GapAnl││  RQ Form ││  Method  ││  Plan    │
└──────┘└──────┘└──────┘└──────────┘└──────────┘└──────────┘
   |       |       |         |           |           |
 topic   papers   gaps    questions    methods    plan
 scope   trends   opps    hypotheses   justify    timeline

Key Design Principles

1. **Progressive depth**: Each phase builds on previous outputs — literature informs gaps, gaps inform questions, questions inform methods 2. **Interactive guidance**: Collect user preferences and domain context before each major phase 3. **Zotero integration**: Automatically organize discovered papers into Zotero collections when MCP tools are available 4. **Structured outputs**: Each phase produces structured artifacts that feed into the final research plan 5. **5W1H grounding**: Use the 5W1H framework to ensure comprehensive research scoping

Interactive Preference Collection

Before dispatching to phases, collect research context and workflow preferences:

AskUserQuestion:
  question: "Please describe your research topic or interest area."
  → Store as: researchTopic

AskUserQuestion:
  question: "What is the scope and context of your research?"
  options:
    - "Broad exploration (survey a field)"
    - "Focused investigation (specific problem)"
    - "Applied research (practical application)"
  → Store as: researchScope

AskUserQuestion:
  question: "What is your target research timeline?"
  options:
    - "Short-term (3-6 months)"
    - "Medium-term (6-12 months)"
    - "Long-term (1-2 years)"
  → Store as: researchTimeline

AskUserQuestion:
  question: "Do you have access to Zotero for literature management?"
  options:
    - "Yes (auto-import papers to Zotero)"
    - "No (skip Zotero integration)"
  → Store as: useZotero

AskUserQuestion:
  question: "Workflow mode?"
  options:
    - "Interactive (confirm at each phase)"
    - "Auto (run all phases continuously)"
  → Store as: workflowMode

Derived preferences:

workflowPreferences = {
  topic: researchTopic,
  scope: researchScope,
  timeline: researchTimeline,
  useZotero: useZotero === "Yes",
  autoYes: workflowMode === "Auto"
}

Auto Mode Defaults

When `workflowPreferences.autoYes === true`: Execute all 5 phases sequentially without confirmation prompts between phases. Still pause for user input when phase-specific questions arise (e.g., confirming search keywords, selecting papers for deep reading).

Execution Flow

> **COMPACT DIRECTIVE**: Context compression MUST check TodoWrite phase status. > The phase currently marked `in_progress` is the active execution phase — preserve its FULL content. > Only compress phases marked `completed` or `pending`.

TodoWrite Initialization

TodoWrite:
  - "Phase 1: Literature Search" (pending)
  - "Phase 2: Gap Analysis" (pending)
  - "Phase 3: Research Question Formulation" (pending)
  - "Phase 4: Method Selection" (pending)
  - "Phase 5: Research Planning" (pending)

Phase Dispatch

Phase 1: Literature Search
   Mark TodoWrite Phase 1 → in_progress
   └─ Ref: phases/01-literature-search.md
      ├─ Input: workflowPreferences (topic, scope, useZotero)
      └─ Output: literatureResults (papers, trends, keyFindings)

Phase 2: Gap Analysis
   Mark TodoWrite Phase 1 → completed, Phase 2 → in_progress
   └─ Ref: phases/02-gap-analysis.md
      ├─ Input: literatureResults
      └─ Output: gapAnalysis (gaps, opportunities, priorities)

Phase 3: Research Question Formulation
   Mark TodoWrite Phase 2 → completed, Phase 3 → in_progress
   └─ Ref: phases/03-research-question.md
      ├─ Input: gapAnalysis + literatureResults
      └─ Output: researchQuestions (questions, hypotheses, objectives)

Phase 4: Method Selection
   Mark TodoWrite Phase 3 → completed, Phase 4 → in_progress
   └─ Ref: phases/04-method-selection.md
      ├─ Input: researchQuestions + gapAnalysis
      └─ Output: selectedMethods (methods, justification, resources)

Phase 5: Research Planning
   Mark TodoWrite Phase 4 → completed, Phase 5 → in_progress
   └─ Ref: phases/05-research-planning.md
      ├─ Input: ALL previous outputs
      └─ Output: research-plan.md (final deliverable)

Mark Tod