This guide helps users and the intake_agent select the most appropriate operational mode.
User Input →
│
├── Already have complete research?
│ ├── Yes → Want a full paper?
│ │ ├── Yes ─────────────────────────→ full mode
│ │ └── No → Just need an outline?
│ │ ├── Yes ─────────────────────→ outline-only mode
│ │ └── No → Just need an abstract?
│ │ ├── Yes ──────────────────→ abstract-only mode
│ │ └── No → Just need a literature review?
│ │ ├── Yes ─────────────→ lit-review mode
│ │ └── No ──────────────→ full mode
│ │
│ └── No → Want guided thinking?
│ ├── Yes ─────────────────────────→ plan mode ★ NEW
│ └── No ──────────────────────────→ full mode (Phase 0 will conduct an interview)
│
├── Have an existing paper to revise? ──────────────────────→ revision mode
├── Have reviewer comments to handle?
│ ├── Comments only, no response written yet ──────────→ revision-coach mode
│ └── Comments + an existing rebuttal/response draft ──→ rebuttal-audit mode
├── Need an AI-usage disclosure statement? ─────────────────→ disclosure mode
├── Just need format conversion? ────────────────────────→ format-convert mode
└── Just need a citation check? ────────────────────────→ citation-check mode
Applicable Scenarios: - User has a clear research question and (partial) materials - Needs to produce a complete paper from start to finish - Includes all phases: Interview → Literature → Structure → Argumentation → Writing → Citation → Review → Formatting
Not Applicable When:
- User has no idea about research direction (→ use deep-research first)
- Only need a specific section (→ use another specialized mode)
Expected Output: Complete paper draft + references + bilingual abstract + review report Expected Duration: Long (all 8 Phases fully executed) Agents Used: All 9 + socratic_mentor (if needed)
Applicable Scenarios: - Only need the paper structure and outline - A proposal to submit to an advisor for review - Need to quickly plan the paper structure
Not Applicable When: - Need complete paper content (→ full mode) - Need guided thinking (→ plan mode)
Expected Output: Detailed outline + evidence allocation + word count distribution Expected Duration: Short (Phase 0-2) Agents Used: intake → literature_strategist → structure_architect
Applicable Scenarios: - User has ideas but they are not yet clear enough - Wants guided thinking for each chapter's content - First-time academic paper writer - Wants to think through every section before writing - Just received materials from deep-research and needs to transform them into a paper plan
Not Applicable When: - Already knows exactly what to write (→ full mode is faster) - Only needs an outline without deep thinking (→ outline-only mode) - Time-pressured and needs rapid output (→ full mode)
Expected Output: Chapter Plan + INSIGHT Collection Expected Duration: Medium (Step 0-3, approximately 20-30 rounds of conversation) Agents Used: intake → socratic_mentor → structure_architect → argument_builder
Subsequent Connections: - Chapter Plan → full mode (produce complete paper) - Chapter Plan → academic-paper-reviewer (review the plan)
Applicable Scenarios: - Already have a completed paper draft - Received reviewer comments requiring revision - Feel certain sections need improvement
Not Applicable When: - No existing paper draft (→ full mode) - Only need to check citation format (→ citation-check mode)
Expected Output: Revised paper + revision notes (tracked changes) Expected Duration: Medium Agents Used: peer_reviewer → draft_writer → citation_compliance
Prerequisite: User must provide existing paper content
Applicable Scenarios: - Paper is already complete, only need an abstract - Need to submit a conference abstract - Need a bilingual abstract
Not Applicable When: - No paper content to summarize (→ full mode or plan mode)
Expected Output: Bilingual abstract (zh-TW + EN) + keywords Expected Duration: Short Agents Used: intake → abstract_bilingual
Applicable Scenarios: - Need a literature review on a specific topic - Preparing the Literature Review chapter of a paper - Need a systematic search strategy and literature matrix
Not Applicable When: - Need a complete paper (→ full mode) - Need an in-depth research investigation (→ deep-research)
Expected Output: Annotated bibliography + literature matrix + synthesis analysis Expected Duration: Medium Agents Used: intake → literature_strategist
Applicable Scenarios: - Already have paper content, need format conversion - Markdown → LaTeX / DOCX / PDF - Need to comply with a specific journal's formatting requirements
Not Applicable When: - No existing content (→ full mode) - Need content modifications (→ revision mode)
Expected Output: Document in target format Expected Duration: Short Agents Used: formatter used standalone
Applicable Scenarios: - Already have a paper, only need to check citation format - Final check before submission - Switching citation format (e.g., APA → IEEE)
Not Applicable When: - No existing citation list (→ full mode) - Need to modify paper content (→ revision mode)
Expected Output: Citation error report + automatic correction suggestions Expected Duration: Short Agents Used: citation_compliance used standalone
Applicable Scenarios: - Received reviewer comments / a decision letter and need them parsed into a structured plan - Want a Revision Roadmap that classifies, maps, and prioritizes each comment - Need a Response Letter Skeleton to start drafting replies - Deciding whether to address or push back on a comment (disagreement posture) - Non-journal scopes: conference rebuttal, grant-panel response, transfer-after-review
Not Applicable When: - Already have a written rebuttal/response draft you want QA'd (→ rebuttal-audit mode) - The paper itself needs rewriting based on the comments (→ revision mode)
Expected Output: Revision Roadmap + optional Tracking Template + Response Letter Skeleton Expected Duration: Short-Medium Agents Used: revision_coach_agent used standalone (no prior pipeline execution required)
Applicable Scenarios: - Paper is drafted and you need a venue-specific AI-usage disclosure paragraph - Submitting to a venue with a defined AI-disclosure policy (ICLR, NeurIPS, Nature, Science, ACL, EMNLP) - Need placement guidance for where the statement goes in the manuscript
Not Applicable When: - No paper drafted yet — disclosure is a finishing step (→ full mode first) - The venue is not in the policy database (confirm the venue's current policy manually)
Expected Output: Venue-specific AI-usage disclosure paragraph(s) + placement instructions Expected Duration: Short Agents Used: disclosure protocol used standalone (venue policy database lookup)
Applicable Scenarios: - You already wrote a rebuttal/response-to-reviewers draft and want it checked before sending - Need a per-comment coverage table (which reviewer concerns the draft addresses, partially addresses, or misses) - Want risk flags for tone (too combative), unsupported claims, or a response that misreads the reviewer's point
Not Applicable When: - You have reviewer comments but have not written a response yet (→ revision-coach mode, which generates a skeleton) - The manuscript itself needs revising (→ revision mode)
Input gate: requires BOTH (a) the reviewer comments / decision letter AND (b) an existing rebuttal draft. Comments only → route to revision-coach. If intent is ambiguous, clarify rather than guess.
Expected Output: Advisory QA report — per-comment coverage + gap list + risk flags. Generates no new response. Expected Duration: Short Agents Used: revision_coach_agent's comment-parsing capability, run standalone (advisory)
Integrity boundary: a standalone invocation runs outside the pipeline, so rebuttal-audit does not emit a Schema 11 ledger, does not write the Material Passport, and does not mark anything ready_to_submit or verified. The output is advisory QA only.
deep-research completed
│
├── deep-research (full mode) outputs:
│ RQ Brief + Methodology Blueprint + Annotated Bibliography + Synthesis Report
│ │
│ ├── Want to write the paper directly ──→ academic-paper (full mode)
│ │ intake_agent auto-detects materials, skips redundant questions
│ │
│ └── Want to plan before writing ──→ academic-paper (plan mode)
│ socratic_mentor leverages existing materials to accelerate guidance
│
└── deep-research (socratic mode) outputs:
INSIGHT Collection + Synthesis Report
│
├── INSIGHTs are sufficiently clear ──→ academic-paper (full mode)
│
└── Need more guidance ──→ academic-paper (plan mode)
socratic_mentor continues deepening from INSIGHTs
academic-paper completed
│
├── full mode produces complete paper ──→ academic-paper-reviewer (full / guided)
│ Complete peer review + revision suggestions
│
├── plan mode produces Chapter Plan ──→ academic-paper-reviewer (guided)
│ Review the plan's feasibility and completeness
│
└── reviewer feedback ──→ academic-paper (revision mode)
Revise paper based on review comments
| User Says | Easily Misselected | Correct Choice | Reason |
|---|---|---|---|
| "Help me write an outline" / 「幫我寫大綱」 | outline-only | First confirm: Do they want a simple outline or deep planning? | May need plan mode |
| "I want to write a paper but don't know how to start" / 「想寫論文但不知道怎麼開始」 | full | plan mode | Needs guided thinking |
| "Help me revise my paper" / 「幫我修改論文」 | revision | First confirm: Are there reviewer comments? | May need full mode rewrite |
| "Help me search for literature" / 「幫我找文獻」 | lit-review | First confirm: Is it a literature review for a paper or a research investigation? | May need deep-research |
| "I have deep-research results, help me write a paper" / 「我有研究結果，幫我寫成論文」 | full (skip Phase 0 directly) | full (but intake needs to detect handoff) | Materials need to be properly imported |
| "I want to plan my paper step by step" / 「我想逐步規劃論文」 | outline-only | plan mode | Needs interactive guidance |
| "The paper format is wrong" / 「論文格式不對」 | revision | citation-check or format-convert | May only need format correction |
| 「帶我寫論文」/「引導我寫論文」 | full | plan mode | 使用者需要互動式引導，不是直接產出 |
| 「第一次寫論文」/「論文新手」 | full | plan mode | 新手需要蘇格拉底式逐章引導 |
| What Do You Have? | What Do You Want? | Choose This Mode |
|---|---|---|
| Nothing | Complete paper | plan mode → full mode |
| Research question + literature | Complete paper | full mode |
| Research question + literature | Outline | outline-only mode |
| Vague idea | Paper plan | plan mode |
| deep-research results | Complete paper | full mode (auto-handoff) |
| deep-research results | Guided planning | plan mode |
| Completed paper | Revision | revision mode |
| Completed paper | Abstract | abstract-only mode |
| Completed paper | Format conversion | format-convert mode |
| Completed paper | Citation check | citation-check mode |
| Reviewer comments (no response yet) | Parse + roadmap + reply skeleton | revision-coach mode |
| Reviewer comments + a written rebuttal draft | QA the draft before sending | rebuttal-audit mode |
| Drafted paper + target venue | AI-usage disclosure statement | disclosure mode |
When a user completes plan mode and wants to proceed to full mode for actual paper writing:
| Plan Mode Output | Full Mode Input | Conversion Action |
|---|---|---|
| Chapter Plan (structure outline) | structure_architect agent |
Map chapters → formal sections with heading levels; validate against paper_structure_patterns.md |
| Socratic Responses (Q&A transcripts) | argument_builder agent |
Extract claims + evidence + warrants from dialogue; discard conversational scaffolding |
| Literature Notes (if any) | literature_strategist agent |
Independent execution — plan mode notes serve as seed keywords only; full systematic search required |
| Argument Sketches | argument_builder agent |
Evaluate each sketch against 4-level scoring; only adequate or above proceed |
Before conversion, ALL of the following must be true:
- [ ] Every chapter in the Chapter Plan has at least 1 argument sketch rated adequate or above
- [ ] The overall paper structure maps to a recognized pattern in paper_structure_patterns.md
- [ ] At least 5 potential references have been identified (seeds for literature_strategist)
- [ ] The research question is finalized (not still evolving from Socratic dialogue)
"Write a paper on SDGs in HEI" -> full
"Give me a paper outline for..." -> outline-only
"Revise this paper based on feedback" -> revision
"Write an abstract for this paper" -> abstract-only
"Do a literature review on..." -> lit-review
"Convert this paper to LaTeX" -> format-convert
"Convert citations to IEEE" -> format-convert
"Check the citations in this paper" -> citation-check
"guide my paper" -> plan
"help me plan my paper" -> plan
"I got reviewer comments" -> revision-coach
"parse these reviews" -> revision-coach
"help me with my revision" -> revision-coach
"should we push back on reviewer 2" -> revision-coach
"conference rebuttal" / "grant response" -> revision-coach
"audit my rebuttal draft" -> rebuttal-audit (needs comments + an existing draft)
"did I miss any reviewer comment" -> rebuttal-audit
"AI disclosure for Nature" -> disclosure
"generate an AI usage statement" -> disclosure