<required_reading> @~/.maestro/workflows/run-mode.md </required_reading>
Scholar WritingEnd-to-end workflow for writing publication-ready ML/AI papers from research repositories. Integrates paper writing craft, citation verification, and anti-AI polishing into a structured 6-phase pipeline.
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: "Write a paper from this repo"
|
v
┌──────────────────────────────────────────────────────────────────────┐
│ SKILL.md (Orchestrator) │
│ Collect preferences → Dispatch phases → Track progress │
└──────────┬───────────────────────────────────────────────────────────┘
|
┌───────┼───────┬───────────┬──────────┬──────────┬────────────┐
v v v v v v v
┌──────┐┌──────┐┌──────────┐┌──────────┐┌──────────┐┌──────────────┐
│ P1 ││ P2 ││ P3 ││ P4 ││ P5 ││ P6 │
│ Repo ││Struct││ Section ││ Citation ││ Anti-AI ││ Conference │
│ Under││Plan ││ Drafting ││ Manage ││ Polish ││ Formatting │
└──┬───┘└──┬───┘└────┬─────┘└────┬─────┘└────┬─────┘└──────┬───────┘
│ │ │ │ │ │
v v v v v v
repo outline full draft verified polished paper.tex
context + plan .bib file prose (camera-ready)
Key Design Principles
- Proactive drafting: Deliver complete drafts, then iterate on feedback. Do not block on every section.
- Never hallucinate citations: Every citation must be verified via WebSearch and Google Scholar. Mark unverifiable references as
[CITATION NEEDED]. - Narrative-first writing: A paper is a story with one clear contribution. Define the What/Why/So What before writing.
- Anti-AI polish is mandatory: All prose passes through pattern detection and humanization before final output.
- Conference-aware from start: Target venue influences page limits, required sections, and framing.
Interactive Preference Collection
Before dispatching to any phase, collect these preferences:
Questions to ask the user:
1. Research Repository
"Where is the research repo? (path or URL)"
→ repoPath
2. Target Conference
Options: NeurIPS | ICML | ICLR | ACL | AAAI | COLM | Other
→ targetConference
3. Paper Type
Options: Full Paper | Short Paper | Workshop Paper
→ paperType
4. Output Directory
"Where should the paper be written? (default: ./paper/)"
→ outputDir
5. Existing Materials
"Any existing drafts, notes, or outlines to build on? (path or 'none')"
→ existingMaterials
6. Writing Language
Options: English | Chinese | Bilingual
→ writingLanguage
Store responses as paperPreferences context for all phases.
Auto Mode Defaults
When workflowPreferences.autoYes === true:
- Use detected repo path from cwd
- Default to NeurIPS format, Full Paper, English
- Output to
./paper/ - Skip confirmation prompts within phases
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 Setup
Paper Writing Workflow:
- [ ] Phase 1: Repo Understanding — explore repo, identify contribution
- [ ] Phase 2: Structure Planning — plan outline, define narrative
- [ ] Phase 3: Section Drafting — write all sections
- [ ] Phase 4: Citation Management — find, verify, format citations
- [ ] Phase 5: Anti-AI Polish — remove AI patterns, humanize prose
- [ ] Phase 6: Conference Formatting — apply template, compile
Phase Sequence
Phase 1: Repo Understanding
└─ Ref: phases/01-repo-understanding.md
├─ Input: repoPath, existingMaterials
└─ Output: repoContext (contribution, results, existing citations)
Phase 2: Structure Planning
└─ Ref: phases/02-structure-planning.md
├─ Input: repoContext, targetConference, paperType
└─ Output: paperOutline (section plan, narrative arc, page budget)
Phase 3: Section Drafting
└─ Ref: phases/03-section-drafting.md
├─ Input: repoContext, paperOutline, writingLanguage
└─ Output: draftSections (all sections as LaTeX content)
Phase 4: Citation Management
└─ Ref: phases/04-citation-management.md
├─ Input: draftSections, repoContext.existingCitations
└─ Output: verifiedBib (references.bib), updatedDraft (citations resolved)
Phase 5: Anti-AI Polish
└─ Ref: phases/05-anti-ai-polish.md
├─ Input: updatedDraft
└─ Output: polishedDraft (humanized prose, AI patterns removed)
Phase 6: Conference Formatting
└─ Ref: phases/06-conference-formatting.md
├─ Input: polishedDraft, verifiedBib, targetConference
└─ Output: paper.tex (complete manuscript ready for compilation)
Phase Reference Documents (read on-demand when phase executes):
| Phase | Document | Purpose | Compact |
|---|---|---|---|
| 1 | phases/01-repo-understanding.md | Explore repo, identify contribution | TodoWrite driven |
| 2 | phases/02-structure-planning.md | Plan outline, define narrative | TodoWrite driven |
| 3 | phases/03-section-drafting.md | Write all paper sections | TodoWrite driven + sentinel |
| 4 | phases/04-citation-management.md | Find, verify, format citations | TodoWrite driven + sentinel |
| 5 | phases/05-anti-ai-polish.md | Remove AI patterns, humanize | TodoWrite driven + sentinel |
| 6 | phases/06-conference-formatting.md | Apply template, compile | TodoWrite driven |
Compact Rules:
- TodoWrite
in_progress→ preserve full content, do not compress - TodoWrite
completed→ may compress to summary - sentinel fallback → phases marked with sentinel contain compact sentinel; if only sentinel remains after compression, must immediately
Read()to recover before continuing
Core Rules
- Citation integrity: NEVER generate BibTeX from memory. Always verify via WebSearch + Google Scholar. Mark unverifiable as
[CITATION NEEDED]. - One contribution: The paper tells one story. Every section supports the central narrative.
- Proactive delivery: Write full drafts, flag uncertainties. Do not block waiting for per-section approval.
- Conference compliance: Respect page limits, required sections, and anonymization requirements.
- Anti-AI mandatory: All prose must pass anti-AI pattern detection before final output.
Input Processing
User input is parsed into paperPreferences:
REPO: [path to research repository]
CONFERENCE: [NeurIPS | ICML | ICLR | ACL | AAAI | COLM]
TYPE: [Full | Short | Workshop]
OUTPUT: [output directory path]
MATERIALS: [path to existing drafts or 'none']
LANGUAGE: [English | Chinese | Bilingual]
If user provides free text like "write a paper about my transformer project", extract:
- Repo path from context or ask
- Default conference to NeurIPS
- Default type to Full Paper
- Default language to English
Data Flow
Phase 1 ──repoContext──→ Phase 2
Phase 2 ──paperOutline──→ Phase 3
Phase 1 ──repoContext──→ Phase 3
Phase 3 ──draftSections──→ Phase 4
Phase 4 ──updatedDraft + verifiedBib──→ Phase 5
Phase 5 ──polishedDraft──→ Phase 6
Phase 4 ──verifiedBib──→ Phase 6
Data persistence: All intermediate outputs written to outputDir/
outputDir/.writing/
├── repo-context.md (Phase 1 output)
├── paper-outline.md (Phase 2 output)
├── drafts/ (Phase 3 output)
│ ├── abstract.tex
│ ├── introduction.tex
│ ├── methods.tex
│ ├── experiments.tex
│ ├── related-work.tex
│ ├── conclusion.tex
│ └── appendix.tex
├── references.bib (Phase 4 output)
├── polished/ (Phase 5 output)
│ └── (same structure as drafts/)
└── paper.tex (Phase 6 output)
TodoWrite Pattern
Phase Start (Attach)
When Phase N begins:
→ Mark Phase N as in_progress in TodoWrite
→ Add sub-tasks for Phase N steps
→ Execute sub-tasks sequentially
Phase End (Collapse)
When Phase N completes:
→ Mark all Phase N sub-tasks as completed
→ Collapse to summary: "Phase N complete: [key output]"
→ Mark Phase N+1 as in_progress
Post-Phase Updates
Between phases, update a running paper-notes document:
# Paper Writing Notes (accumulated)
## Contribution (Phase 1)
[One-sentence contribution statement]
## Outline (Phase 2)
[Section structure with page budgets]
## Draft Status (Phase 3)
[Section completion status]
## Citation Status (Phase 4)
[Verified count / placeholder count]
## Polish Status (Phase 5)
[Anti-AI score per section]
Written to: outputDir/.writing/paper-notes.md
Error Handling
| Error | Action |
|---|---|
| Repo path invalid | Ask user for correct path |
| Cannot identify contribution | Present top 3 candidates, ask user to choose |
| Citation not found | Mark [CITATION NEEDED], continue, report at end |
| LaTeX compilation fails | Fix common errors (missing packages, encoding), retry once |
| Anti-AI score below 35 | Re-polish section, flag for manual review |
| Page limit exceeded | Suggest specific cuts (move proofs to appendix, condense related work) |
Coordinator Checklist
Before Each Phase
- Previous phase output exists and is valid
- TodoWrite updated (current phase in_progress)
- Required inputs available
After Each Phase
- Output files written to outputDir/.writing/
- paper-notes.md updated
- TodoWrite collapsed (phase completed)
- User notified of phase completion and key decisions made
Final Checklist
- All 6 phases completed
- paper.tex compiles without errors
- All citations verified (no remaining
[CITATION NEEDED]) - Anti-AI score >= 35 for all sections
- Page limit respected
- Anonymization applied (for blind review)
- Conference checklist completed (if required)
Related Skills
- scholar-ideation: Use before this skill to develop research ideas
- scholar-experiment: Use before this skill to run experiments
- scholar-review: Use after this skill to review/revise the paper