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	["Bash","Edit","Glob","Grep","Read","WebFetch","WebSearch","Write","request_user_input","update_plan"]
session-mode	none
version	0.5.55

Plan tracking: codex 无 TaskCreate/TaskUpdate/TodoWrite 任务板。进度清单用 update_plan({ explanation?, plan: [{ step, status }] }) 维护（整体提交步骤数组，status: pending | in_progress | completed），权威状态始终在 session 工件中；依赖/认领（addBlockedBy/owner）是工件字段，不是工具参数。

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:

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

request_user_input:
  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

request_user_input:
  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

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

request_user_input:
  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 update_plan phase status. The phase currently marked in_progress is the active execution phase — preserve its FULL content. Only compress phases marked completed or pending.

update_plan Initialization

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

Mark update_plan Phase 5 → completed

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

Phase	Document	Purpose	Compact
1	phases/01-literature-search.md	Search, discover, and organize literature	update_plan driven
2	phases/02-gap-analysis.md	Identify research gaps and opportunities	update_plan driven
3	phases/03-research-question.md	Formulate research questions and hypotheses	update_plan driven
4	phases/04-method-selection.md	Select and justify research methods	update_plan driven + sentinel
5	phases/05-research-planning.md	Create timeline, milestones, and final plan	update_plan driven + sentinel

Compact Rules:

1. update_plan in_progress — preserve full content, do not compress
2. update_plan 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 request_user_input.

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)

update_plan 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 update_plan status
• Read phase document (Read("phases/0N-xxx.md"))

Post-phase:

• Validate phase outputs (non-empty, well-structured)
• Update accumulated research notes
• Collapse update_plan 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