Scholar Ideation

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 TodoWrite Phase 5 → completed

Phase Reference Documents (read on-demand when phase executes):

Compact Rules:

1. TodoWrite in_progress — preserve full content, do not compress
2. TodoWrite completed — may compress to summary
3. sentinel fallback — phases marked with sentinel: if compact leaves only sentinel without full Step protocol, immediately Read() to recover

Core Rules

1. Literature first: Always complete literature search before gap analysis — gaps must be grounded in actual literature
2. Evidence-based gaps: Every identified gap must reference specific papers or missing coverage areas
3. SMART questions: Research questions must satisfy Specific, Measurable, Achievable, Relevant, Time-bound criteria
4. Method-question alignment: Selected methods must directly address the formulated research questions
5. Feasibility check: Research plan must account for available resources (compute, data, time, personnel)
6. No hallucinated papers: Only reference papers actually found via WebSearch — never fabricate citations

Input Processing

User input (free text or structured) is converted to:

TOPIC: [research topic or interest]
SCOPE: [broad | focused | applied]
TIMELINE: [short | medium | long]
CONTEXT: [additional constraints, domain, background]

If user provides a simple topic string, derive scope and timeline from the topic description or ask via AskUserQuestion.

Data Flow

workflowPreferences
    ├─→ Phase 1: topic, scope, useZotero
    │       └─→ literatureResults {papers[], trends[], keyFindings[], zoteroCollection?}
    │
    ├─→ Phase 2: literatureResults
    │       └─→ gapAnalysis {gaps[], opportunities[], prioritizedGaps[]}
    │
    ├─→ Phase 3: gapAnalysis + literatureResults
    │       └─→ researchQuestions {questions[], hypotheses[], objectives[]}
    │
    ├─→ Phase 4: researchQuestions + gapAnalysis
    │       └─→ selectedMethods {methods[], justification, resources[]}
    │
    └─→ Phase 5: ALL outputs
            └─→ research-plan.md (final structured document)

TodoWrite Pattern

Phase start — Attach sub-tasks:

Mark Phase N → in_progress
Add sub-tasks:
  - "Step N.1: ..." (in_progress)
  - "Step N.2: ..." (pending)
  - "Step N.3: ..." (pending)

Phase end — Collapse:

Mark all Phase N sub-tasks → completed
Mark Phase N → completed
Mark Phase N+1 → in_progress

Post-Phase Updates

After each phase completes, update an accumulated research notes document:

## Research Notes (accumulated)

### After Phase 1 (Literature Search)
- Papers found: [count]
- Key trends: [list]
- Zotero collection: [name, if applicable]

### After Phase 2 (Gap Analysis)
- Gaps identified: [count]
- Top priorities: [list]

### After Phase 3 (Research Questions)
- Primary RQ: [question]
- Sub-questions: [count]

### After Phase 4 (Method Selection)
- Selected approach: [method]
- Required resources: [list]

Error Handling

1. WebSearch fails: Retry with modified keywords; if persistent, ask user for alternative search terms
2. No papers found: Broaden search scope, try synonyms and related terms, try different databases
3. Zotero unavailable: Skip Zotero integration, continue with manual paper tracking in markdown
4. Gap analysis inconclusive: Return to Phase 1 for additional targeted literature search
5. Infeasible plan: Adjust scope, timeline, or methods; consult user for trade-off decisions

Coordinator Checklist

Pre-phase:

• Verify previous phase outputs are available
• Update TodoWrite status
• Read phase document (Read("phases/0N-xxx.md"))

Post-phase:

• Validate phase outputs (non-empty, well-structured)
• Update accumulated research notes
• Collapse TodoWrite sub-tasks
• If not autoYes, confirm with user before proceeding

Output Files

The workflow produces:

• research-plan.md — Final structured research proposal with all sections
• literature-review.md — Structured literature review with categorized papers
• Zotero collection — Organized papers with PDFs (if Zotero enabled)

Related Skills

• scholar-experiment — Experiment execution and tracking (follows this skill)
• scholar-writing — Paper writing workflow (uses outputs from experiment)
• scholar-review — Paper review and revision workflow