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)
- Codebase docs: If
.workflow/codebase/ARCHITECTURE.mdexists, read for project context - Specs:
maestro load --type spec --category coding— load coding conventions - Wiki knowledge:
maestro search "academic writing research paper" --json— top 5 entries as prior context - 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
- Progressive depth: Each phase builds on previous outputs — literature informs gaps, gaps inform questions, questions inform methods
- Interactive guidance: Collect user preferences and domain context before each major phase
- Zotero integration: Automatically organize discovered papers into Zotero collections when MCP tools are available
- Structured outputs: Each phase produces structured artifacts that feed into the final research plan
- 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_progressis the active execution phase — preserve its FULL content. Only compress phases markedcompletedorpending.
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):
| Phase | Document | Purpose | Compact |
|---|---|---|---|
| 1 | phases/01-literature-search.md | Search, discover, and organize literature | TodoWrite driven |
| 2 | phases/02-gap-analysis.md | Identify research gaps and opportunities | TodoWrite driven |
| 3 | phases/03-research-question.md | Formulate research questions and hypotheses | TodoWrite driven |
| 4 | phases/04-method-selection.md | Select and justify research methods | TodoWrite driven + sentinel |
| 5 | phases/05-research-planning.md | Create timeline, milestones, and final plan | TodoWrite driven + sentinel |
Compact Rules:
- TodoWrite
in_progress— preserve full content, do not compress - TodoWrite
completed— may compress to summary - sentinel fallback — phases marked with sentinel: if compact leaves only sentinel without full Step protocol, immediately
Read()to recover
Core Rules
- Literature first: Always complete literature search before gap analysis — gaps must be grounded in actual literature
- Evidence-based gaps: Every identified gap must reference specific papers or missing coverage areas
- SMART questions: Research questions must satisfy Specific, Measurable, Achievable, Relevant, Time-bound criteria
- Method-question alignment: Selected methods must directly address the formulated research questions
- Feasibility check: Research plan must account for available resources (compute, data, time, personnel)
- 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
- WebSearch fails: Retry with modified keywords; if persistent, ask user for alternative search terms
- No papers found: Broaden search scope, try synonyms and related terms, try different databases
- Zotero unavailable: Skip Zotero integration, continue with manual paper tracking in markdown
- Gap analysis inconclusive: Return to Phase 1 for additional targeted literature search
- 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 sectionsliterature-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