@research-copilot/plugin 1.1.17 → 1.1.18

package/dist/skills/medical-imaging-review/references/TEMPLATES.md

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+# Project File Templates
+
+Templates for `CLAUDE.md`, `IMPLEMENTATION_PLAN.md`, and the 3 standard tables. v3 updates: Stage 4 (Methods) uses **3-axis structure**, not flat 10-subsection list. Bibliography target removed.
+
+---
+
+## CLAUDE.md Template
+
+```markdown
+# [Topic] Literature Review Writing Guidelines
+
+## Project info
+- **Topic**: [specific topic]
+- **Target journals**: [Tier 1: e.g., Nat Rev Cardiol] / [Tier 2: e.g., JACC Cardiovasc Imaging] / [Tier 3: e.g., Eur Radiol]
+- **Paradigm spec**: see PARADIGM.md (Phase 0 output)
+- **Citation integrity**: see references/CITATION_INTEGRITY.md
+- **Hallucination self-check**: see references/HALLUCINATION_PATTERNS.md
+
+## Terminology Standardization
+
+| Unified Term | Avoid Using |
+|---|---|
+| coronary CT angiography (CCTA) | cardiac CT, CT angio, CTA (ambiguous) |
+| centerline (anatomical structure) | midline, vessel line |
+| [add domain-specific terms] | [variants to avoid] |
+
+## Canonical Paper / Dataset Descriptions
+
+To prevent internal inconsistency (HALLUCINATION_PATTERNS.md ▸ Pattern 9), lock in canonical descriptions:
+
+| Paper / Dataset | Canonical description |
+|---|---|
+| ImageCAS | 1000 cases, single-center, CCTA artery segmentation |
+| TransCC (Xu et al.) | 3 authors: Chenchu Xu, Meng Li, Xue Wu; Dice 0.730 / IoU 0.582 on ImageCAS |
+| FISH&CHIPS | NHS national CT-FFR implementation program; publication: Fairbairn TA et al. Nat Med 2025;31(6):1903-1910 |
+| [add high-value papers] | [verified description] |
+
+## Reference Sources
+
+### ArXiv MCP
+Search queries used:
+- "[topic] segmentation transformer" (cs.CV, eess.IV)
+- "[topic] deep learning" (cs.LG)
+Date range: last 3 years
+Downloaded papers: [list arXiv IDs]
+
+### PubMed MCP
+MeSH queries used:
+- "Deep Learning"[MeSH] AND "[domain]"[MeSH]
+- "[method]"[MeSH] AND "diagnosis"[MeSH]
+Filters: Review, Clinical Trial
+
+### Zotero
+API: localhost:23119
+Relevant collections:
+- [Collection name 1]: [N papers]
+- [Collection name 2]: [N papers]
+
+## Literature inventory (3-axis grouping)
+
+### Axis 1: Architectural priors
+- **CNN-based**: [list verified refs]
+- **Transformer-based**: [list]
+- **Mamba / state-space**: [list]
+
+### Axis 2: Inductive priors
+- **Topology-aware**: [list]
+- **Multi-task**: [list]
+- **Graph-based**: [list]
+
+### Axis 3: Data regime
+- **Self-supervised**: [list]
+- **Foundation models**: [list]
+- **Federated**: [list]
+- **Physics-informed**: [list]
+
+### Clinical / downstream
+- [list]
+
+## Verdict positions to take (3-5)
+
+Plan the 3-5 verdict sentences in advance:
+- §Methods axis 1 closer: ...
+- §Methods axis 2 closer: ...
+- §Methods axis 3 closer: ...
+- §Clinical translation closer: ...
+- (optional) §Discussion closer: ...
+
+## Writing-time guardrails (from references/)
+
+- Per-claim verification on every `[N]` placed (CITATION_INTEGRITY ▸ Rule 1-5)
+- Self-scan against 9 hallucination patterns every 5-6 paragraphs (HALLUCINATION_PATTERNS.md)
+- Vendor names only in Table 3
+- Equations only in Box 1
+- Max 2 heading levels, no numbered headings
+```
+
+---
+
+## IMPLEMENTATION_PLAN.md Template
+
+```markdown
+# Implementation Plan: [Review Title]
+
+## Phase 0: Paradigm Capture
+**Status**: [Not Started / In Progress / Complete]
+
+- [ ] Identify 2-3 exemplar reviews from target tier
+- [ ] Read carefully (60-90 min each)
+- [ ] Extract style spec to PARADIGM.md
+- [ ] Re-anchor at start of each Phase 4 writing session
+
+## Phase 1: Project Initialization
+**Status**: [Not Started / In Progress / Complete]
+
+- [ ] CLAUDE.md created with terminology + sources + literature inventory skeleton
+- [ ] IMPLEMENTATION_PLAN.md (this file) created
+- [ ] manuscript_draft.md created (empty)
+- [ ] PARADIGM.md linked
+
+## Phase 2: Literature Collection + Verification
+**Status**: [Not Started / In Progress / Complete]
+
+### ArXiv (Deep Learning Methods)
+- [ ] Search "[topic] segmentation" in cs.CV, eess.IV
+- [ ] Search "[topic] transformer/attention" in cs.CV
+- [ ] Download key papers (target: 50-80 — discriminate aggressively)
+- [ ] Read each (abstract + methods + results)
+- [ ] Note actual module names + actual numbers in working notes
+
+### PubMed (Clinical Literature)
+- [ ] Search MeSH: "Deep Learning" AND "[domain]"
+- [ ] Filter by publication type (Review, Clinical Trial)
+- [ ] Collect clinical validation studies (target: 20-40)
+- [ ] PubMed WebFetch on each for metadata
+
+### Zotero (User's local library)
+- [ ] Check existing collections for closed-access papers
+- [ ] Note Zotero item keys for later fulltext retrieval
+
+### Additional sources
+- [ ] WebSearch supplementary (IEEE Xplore, Springer)
+
+### Verification (every entry, before adding)
+- [ ] DOI resolves on Crossref
+- [ ] First + last author verbatim from first-source
+- [ ] Journal, year, vol, issue, pages match
+- [ ] No `xxx` / `[TBD]` placeholders
+
+### Gap analysis
+- [ ] Negative trials covered? (LLM bias: only positive)
+- [ ] Inter-vendor reproducibility covered?
+- [ ] Demographic-bias studies covered?
+- [ ] Recent 6-month preprints covered?
+
+## Phase 3: Outline + 3-Axis Taxonomy
+**Status**: [Not Started / In Progress / Complete]
+
+- [ ] Top-level sections defined (Introduction / Methods / Applications / Translation / Discussion)
+- [ ] §Methods structured as **3 H3 subsections** (3 axes):
+  - [ ] §Methods.Architectural priors
+  - [ ] §Methods.Inductive priors
+  - [ ] §Methods.Data regime
+- [ ] Each paper in literature inventory mapped to an axis
+- [ ] Table 1 / 2 / 3 designs planned
+- [ ] Box 1 (metrics) content planned
+- [ ] Figures (3-5) planned
+- [ ] Verdict positions for 3 axes selected
+
+## Phase 4: Write with Per-Claim Verification
+**Status**: [Not Started / In Progress / Complete]
+
+For each section, micro-workflow (per CITATION_INTEGRITY.md):
+- [ ] Re-read the actual cited papers
+- [ ] Write 2-4 sentences with actual module names + actual numbers
+- [ ] Verify each `[N]` placed (body↔bib, number, direction)
+- [ ] Close axis with verdict sentence
+- [ ] Equations to Box 1, not body
+- [ ] Vendor names to Table 3, not body
+- [ ] Self-scan against 9 hallucination patterns every 5-6 paragraphs
+
+### Section progress
+
+- [ ] Introduction (Clinical background / Technical challenge / Scope)
+- [ ] Datasets and evaluation metrics (Box 1, Table 1)
+- [ ] Methods §Axis 1: Architectural priors
+- [ ] Methods §Axis 2: Inductive priors
+- [ ] Methods §Axis 3: Data regime
+- [ ] Methods Table 2 finalized
+- [ ] Downstream applications
+- [ ] Translation to clinical practice (Table 3)
+- [ ] Outstanding challenges
+- [ ] Future directions
+- [ ] Conclusion
+- [ ] References (cross-checked with body)
+
+## Phase 5: Multi-Agent Peer Review
+**Status**: [Not Started / In Progress / Complete]
+
+- [ ] TeamCreate `manuscript-review`
+- [ ] Spawn `style-reviewer` teammate (Task 1)
+- [ ] Spawn `ref-checker` teammate (Task 2)
+- [ ] Spawn `peer-reviewer` teammate (Task 3)
+- [ ] Spawn `fact-checker` teammate (Task 4)
+- [ ] Synthesize 4 reports into 00_team_synthesis.md
+- [ ] Address all CRITICAL findings
+- [ ] Address HIGH findings agreed by ≥ 2 reviewers
+
+## Phase 6: Submission Prep
+**Status**: [Not Started / In Progress / Complete]
+
+- [ ] Journal selected (reach + match + safety tiers)
+- [ ] Presubmission inquiries sent (reach tier, optional)
+- [ ] Cover letter drafted
+- [ ] Box vs body duplication scan run
+- [ ] Section cross-reference scan run
+- [ ] Figures produced (not placeholders)
+- [ ] Citation format converted for target journal
+- [ ] Final self-check checklist passed
+
+## Literature Sources Summary
+
+| Source | Query / Collection | Papers | Verified | Status |
+|---|---|---|---|---|
+| ArXiv | [query 1] | N | N | [ ] |
+| ArXiv | [query 2] | N | N | [ ] |
+| PubMed | [MeSH query] | N | N | [ ] |
+| Zotero | [collection] | N | N | [ ] |
+
+## Change log
+
+### [Date] - v1.0
+- Initial draft completed through Phase 4
+### [Date] - v1.1
+- Phase 5 peer review found 8 issues; addressed
+### [Date] - v1.2
+- Phase 6 submission prep done; sent to [Journal]
+```
+
+---
+
+## Standard Table Templates
+
+### Table 1: Public Datasets
+
+```markdown
+**Table 1 | Public datasets for [task].**
+
+| Dataset | Year | Cases | Annotation type | Access |
+|---|---|---|---|---|
+| [Name] | 20XX | N | [type] | [link] |
+
+*Cases = unique patients. Where multi-center, the number of sites is given in parentheses. Access notations: O = open, R = restricted (registration), C = commercial.*
+```
+
+### Table 2: Method Comparison
+
+```markdown
+**Table 2 | Representative deep learning methods for [task].**
+
+| Reference | Modality | Family | Architecture | Dataset | Headline metric | Innovation |
+|---|---|---|---|---|---|---|
+| [First-author Year] [N] | CCTA | Topology-aware | nnU-Net + clDice | ImageCAS | Dice 0.812 | First clDice on CCTA |
+
+*Performance numbers are taken from the original publications and should not be compared directly across rows; datasets, splits and metric definitions differ. Family is the most-engaged inductive prior or training regime, not the only one. CCTA = coronary CT angiography; HD95 = 95th-percentile Hausdorff distance; — = not reported.*
+```
+
+### Table 3: Commercial Products
+
+```markdown
+**Table 3 | Commercial AI tools for [domain] with regulatory clearance.**
+
+| Manufacturer | Product | Indication | Underlying technology | Regulatory | Deployment | Key validation evidence |
+|---|---|---|---|---|---|---|
+| HeartFlow | CT-FFR Analysis | CT-FFR | CFD + DL hybrid | FDA cleared (CPT 75580); CE | Cloud-based SaaS | NXT, ADVANCE, PLATFORM, PACIFIC; FISH&CHIPS [N] |
+| Keya Medical | DeepVessel FFR | CT-FFR | DL surrogate of CFD | FDA, NMPA Class III, CE | Cloud + on-site | Multi-centre Chinese validation [N] |
+
+*Listed validation evidence refers to peer-reviewed primary publications, not vendor white papers. NMPA = National Medical Products Administration (China); CFD = computational fluid dynamics.*
+```
+
+---
+
+## Notes
+
+### Why bibliography target removed
+
+v2 set "80-120 references" as a quality criterion. This drove Claude to **pad the bibliography**, and padding encouraged fabrication. v3 has no count target. Cite what supports the argument. If your review naturally has 60 high-quality refs, that's enough. If it needs 150, also fine. Quantity is downstream of substance.
+
+### Why 3-axis Methods is the structural commitment
+
+v2's coronary review produced 10 flat method H3 subsections. The resulting §Methods read as a textbook chapter, not a flagship review. Flagship reviews compress 10+ method variants into ~3 thematic axes that force comparative synthesis. The 3-axis structure is the most important structural fix in v3.

package/dist/skills/medical-imaging-review/references/WORKFLOW.md

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+# 6-Phase Literature Review Workflow
+
+This workflow replaces the v2 "7-phase write-then-QA" structure with a "write-with-verify + multi-agent peer review" structure. Verification is embedded throughout, not bolted on at the end.
+
+---
+
+## Phase 0: Paradigm Capture
+
+**Goal:** Before writing anything, ground the review in 2-3 published flagship-quality exemplars from the target journal tier.
+
+**Why:** LLMs default to a generic "survey paper" register — numbered chapters, hedging language, neutral catalogue, dense subsections. Flagship reviews (Nature Reviews / Nat Med / Lancet family) write very differently. Without an exemplar to anchor against, the draft will drift toward survey-paper style and become hard to retrofit.
+
+**Actions:**
+
+1. Identify 2-3 exemplar reviews from the target journal tier. Selection criterion: same modality or same problem family, published in last 3 years, by recognized authors.
+
+2. Read them carefully (not just skim). Pay attention to:
+   - Heading depth and numbering (most flagship reviews use 2 levels, no numbers)
+   - Paragraph rhythm (topic → evidence → verdict, not topic → list → list → list)
+   - Citation density (1.5-2.5 refs per paragraph typical)
+   - Equation handling (Box vs inline)
+   - Vendor handling (Table vs body)
+   - Authorial voice (do they take positions or stay neutral?)
+   - Box and Figure usage (how many, how dense)
+   - Table count (rarely more than 3)
+
+3. Write the extracted style spec to `PARADIGM.md`. See [PARADIGM.md template](PARADIGM.md) for the exact structure.
+
+**Deliverable:** `PARADIGM.md` in the project root.
+
+**Time budget:** 2-3 hours (reading + spec writing).
+
+---
+
+## Phase 1: Project Initialization
+
+**Goal:** Set up the project files and writing guidelines.
+
+**Actions:**
+
+1. Create `CLAUDE.md` from the [TEMPLATES.md ▸ CLAUDE.md](TEMPLATES.md#claudemd-template) template. Fill in:
+   - Topic-specific terminology table
+   - Reference source configurations (ArXiv / PubMed / Zotero queries)
+   - Expected literature categories (don't commit yet — refine after Phase 2)
+
+2. Create `IMPLEMENTATION_PLAN.md` from [TEMPLATES.md ▸ IMPLEMENTATION_PLAN.md](TEMPLATES.md#implementation_planmd-template). Note the **3-axis** structure for §Methods (not flat).
+
+3. Create empty `manuscript_draft.md`. Leave it empty until Phase 4 — don't pre-populate with placeholder text.
+
+4. Link `PARADIGM.md` and [CITATION_INTEGRITY.md](CITATION_INTEGRITY.md) and [HALLUCINATION_PATTERNS.md](HALLUCINATION_PATTERNS.md) from CLAUDE.md so they're easy to refer back to.
+
+**Deliverable:** Project skeleton with 4 files (PARADIGM.md, CLAUDE.md, IMPLEMENTATION_PLAN.md, manuscript_draft.md).
+
+**Time budget:** 1 hour.
+
+---
+
+## Phase 2: Literature Collection + Verification (simultaneous)
+
+**Goal:** Gather the corpus while verifying each entry's metadata in real time.
+
+**Why simultaneous:** v2 separated collection from verification — collection in Phase 2, verification never. Result: 17 placeholder DOIs and many wrong-author lists shipped to the final draft. v3 verifies on the way in.
+
+**Actions:**
+
+### 2.1 ArXiv (methodological preprints)
+
+```
+Query: "[topic] AND (segmentation OR detection OR classification)"
+Categories: cs.CV, eess.IV, cs.LG
+Date: last 3 years
+Max results: 50-80 per query (NOT 100 — discriminate aggressively)
+```
+
+For each paper added:
+- `mcp__arxiv-mcp-server__download_paper(paper_id)`
+- `mcp__arxiv-mcp-server__read_paper(paper_id)` — read abstract + methods + results
+- Note: actual title, full author list, exact module names, headline numbers, dataset name
+
+### 2.2 PubMed (peer-reviewed clinical literature)
+
+```
+MeSH: "Deep Learning"[MeSH] AND "[domain]"[MeSH]
+Filters: Review or Clinical Study, last 5 years
+```
+
+For each paper added:
+- WebFetch on `https://pubmed.ncbi.nlm.nih.gov/<PMID>/`
+- Note: title, full author list (first 6 + et al.), journal, year, volume, issue, pages, DOI, headline finding direction (positive/negative)
+
+### 2.3 Zotero (user's local library — especially closed-access)
+
+For closed-access journals (Med Image Anal, Eur Radiol, JACC, Lancet family, Nature family) the user often has PDFs in Zotero. Always check before assuming inaccessible.
+
+```
+mcp__zotero__zotero_search_collections(query: "<topic>")
+mcp__zotero__zotero_get_collection_items(collection_key: ..., detail: "summary", limit: 200)
+mcp__zotero__zotero_search_items(query: "<author> <method>", limit: 5)
+mcp__zotero__zotero_get_item_fulltext(item_key: ...)
+```
+
+### 2.4 Verification — apply CITATION_INTEGRITY rules as you collect
+
+For each paper added to the bibliography, before committing the entry:
+
+- [ ] DOI resolves on Crossref (`api.crossref.org/works/<DOI>`)
+- [ ] First and last author names match the first-source verbatim
+- [ ] Journal name, year, volume, issue, pages match
+- [ ] No placeholder strings (`xxx`, `[TBD]`, `?`) anywhere in the entry
+
+If any check fails, do not add the entry. Either resolve the metadata or drop the paper.
+
+See [CITATION_INTEGRITY.md](CITATION_INTEGRITY.md) for the full 5-rule protocol.
+
+### 2.5 Build the literature matrix
+
+| 3-axis | Sub-family | Key papers (verified) | Count | Source |
+|---|---|---|---|---|
+| Architectural priors | CNN | [refs] | N | arXiv |
+| Architectural priors | Transformer | [refs] | N | arXiv |
+| Inductive priors | Topology | [refs] | N | arXiv |
+| ... | ... | ... | ... | ... |
+| Clinical | Validation | [refs] | N | PubMed |
+| Datasets | Public | [refs] | N | mixed |
+
+Note the **3 axes**, not a flat 10-category list. See [DOMAINS.md](DOMAINS.md) for the 3-axis structure per domain.
+
+### 2.6 Gap analysis
+
+After initial collection:
+- Are negative trials covered? (LLM tendency: only cite positive trials → over-rosy review)
+- Are recent 6-month preprints covered? (LLM tendency: stale by training-cutoff date)
+- Are inter-vendor reproducibility studies covered? (LLM tendency: report-only-positives)
+- Are demographic-bias / fairness studies covered? (LLM tendency: ignore entirely)
+
+For each gap, run a targeted search.
+
+**Deliverable:** Literature matrix (in CLAUDE.md or IMPLEMENTATION_PLAN.md) with every entry verified.
+
+**Time budget:** 1-2 days (depending on topic breadth). Most of the time is reading abstracts to discriminate relevance, not searching.
+
+---
+
+## Phase 3: Outline + 3-Axis Method Taxonomy
+
+**Goal:** Lock in section structure + the 3-axis method grouping before writing prose.
+
+**Actions:**
+
+1. Define top-level sections from the [Standard Review Structure](../SKILL.md#standard-review-structure) template. No numbered headings.
+
+2. For §Methods, force yourself into the **3-axis** grouping (NOT a flat 10-subsection list):
+   - Axis 1: Architectural priors (what kind of network)
+   - Axis 2: Inductive priors (what kind of geometric / structural / multi-task bias is built in)
+   - Axis 3: Data regime (how is data used / pre-trained / federated)
+
+   Each axis becomes one H3 subsection. Inside each axis, group method families with bold lead-ins (`**Topology-aware design.**`), not deeper H4 headings.
+
+3. Map each paper from the literature matrix to one (or sometimes two) axes. A paper that's only about a topology loss → axis 2. A paper that's a Mamba variant for segmentation → axis 1. A paper about federated learning for cardiac MRI → axis 3.
+
+4. Plan the three tables explicitly:
+   - Table 1: public datasets (name, year, cases, annotation type, access)
+   - Table 2: representative methods (with modality / family / dataset / metric — pick 12-20 papers across all 3 axes)
+   - Table 3: commercial products (manufacturer / product / regulatory / validation evidence)
+
+5. Plan Box 1: evaluation metrics with formulas.
+
+6. Plan figures (typically 3-5; overview, taxonomy, representative architectures, workflow).
+
+**Deliverable:** Section outline and 3-axis paper mapping in `IMPLEMENTATION_PLAN.md`.
+
+**Time budget:** 0.5-1 day.
+
+---
+
+## Phase 4: Write with Per-Claim Verification
+
+**Goal:** Produce the manuscript prose, with verification embedded in every paragraph.
+
+**Why per-claim verification:** v2 wrote first and QA'd later. The QA was structural, not factual. Result: shipped fabricated module names and wrong numbers. v3 verifies each claim before committing it.
+
+**Actions per section:**
+
+1. **Write an introduction paragraph** (1-2 paragraphs on motivation + scope). This is the safest part of the section — make it punchy and clear, set up the verdict that will close the section.
+
+2. **For each method family**, repeat this micro-loop:
+
+   a. **Re-read** the cited paper's abstract + relevant methods/results section. Use `read_paper` (arxiv) or `zotero_get_item_fulltext` (closed-access). Do not skip this. If you can't access the paper, do not write its internal architecture.
+
+   b. **Write 2-4 sentences** describing the method's actual contribution, using actual module names and actual numbers. Cite the paper as `[N]`.
+
+   c. **Verify** the [N] you just placed:
+      - Is N's bibliography entry the paper you just read? (body↔bib reconciliation)
+      - Does your sentence's number (Dice / sensitivity / HR) appear in the paper?
+      - Does your sentence's directional claim (lower/higher / increased/decreased) match the paper?
+
+   d. If any verification fails, fix immediately. Do not move on with broken citations — they compound.
+
+3. **Close the section with a verdict sentence** (for 3 of the H3 subsections — pick the most opinionated positions). See [SKILL.md ▸ Verdict Sentences](../SKILL.md#verdict-sentences).
+
+4. **Equations** go into Box 1, not the body. If you find yourself typing a `$$` outside Box 1, stop and move the equation.
+
+5. **Vendor names** go into Table 3, not the body. If you find yourself typing "HeartFlow" / "Cleerly" / etc. outside Table 3, stop and rewrite with category descriptor.
+
+6. **Update bibliography** as you go (don't batch at the end — the body↔bib reconciliation breaks down with batching).
+
+### Self-check during writing
+
+Every 5-6 paragraphs, pause and scan for the 9 hallucination patterns (see [HALLUCINATION_PATTERNS.md](HALLUCINATION_PATTERNS.md)):
+
+- Are author names sounding generic? (pattern 1)
+- Are performance numbers suspiciously round or high? (pattern 2)
+- Am I claiming directional findings I haven't verified? (pattern 3)
+- Am I citing vendor materials as if peer-reviewed? (pattern 4)
+- Are there any `xxx` or `[TBD]` strings? (pattern 5)
+- Are [N] referring to what I think? (pattern 7)
+- Are my metric formulas correct? (pattern 8)
+
+**Deliverable:** `manuscript_draft.md` complete from Introduction through References, with per-claim verification trace in the writing log.
+
+**Time budget:** 3-5 days (the largest phase).
+
+---
+
+## Phase 5: Multi-Agent Peer Review
+
+**Goal:** Before delivering to the user, run a 4-perspective audit.
+
+**Why:** Single-author self-review misses patterns. The 4 specialized agents catch what a single writer doesn't.
+
+**Actions:**
+
+Launch a `manuscript-review` agent team with 4 teammates (see the `ai-review-revision` skill's [references/agent_team_setup.md](../../ai-review-revision/references/agent_team_setup.md) for the exact TeamCreate / TaskCreate / Agent spawn templates):
+
+| Teammate | Focus |
+|---|---|
+| `style-reviewer` | Compare against PARADIGM.md spec; identify register / structural drift |
+| `ref-checker` | Verify every `[N]` body↔bib match; spot-check author lists and DOIs |
+| `peer-reviewer` | Roleplay as flagship-tier journal reviewer; identify missing controversies, weak verdicts, scope drift |
+| `fact-checker` | Cross-check every quantitative claim (Dice, HR, sample size, p-value) against first-source |
+
+After all 4 reports return, synthesize into `review_outputs/00_team_synthesis.md`. For any issue ≥2 reviewers independently flag, treat as hard fix. For single-reviewer flags, judge based on severity.
+
+**If the issues are minor** (handful of style nits, 1-2 minor citation issues): fix them in place and ship.
+
+**If the issues are major** (≥5 hard factual errors, ≥10 citation drift instances, missing major controversies): the right move is to apply the `ai-review-revision` skill's Phase 1 (factual reset) workflow before delivery. This is unusual but possible — and it's a signal that this skill needs further improvement.
+
+**Deliverable:** 4 review reports + synthesis + a final-quality draft.
+
+**Time budget:** 1 day for the multi-agent review, plus fix time depending on findings.
+
+---
+
+## Phase 6: Submission Prep
+
+**Goal:** Format-level finalization for a specific target journal.
+
+Use the `ai-review-revision` skill's [references/phase4_submission_prep.md](../../ai-review-revision/references/phase4_submission_prep.md) for:
+
+- Journal selection (3-tier reach / match / safety)
+- Presubmission inquiry templates
+- Cover letter template
+- Box vs body duplication scan
+- Figure realization (no placeholders at submission)
+- Citation format conversion (`[N]` → `<sup>N</sup>` depending on journal)
+- Self-check checklist
+
+**Deliverable:** Submission-ready package (manuscript + figures + cover letter + author info).
+
+**Time budget:** 0.5-1 week including presubmission inquiry wait.
+
+---
+
+## Total Timeline
+
+For a typical medical-imaging review project:
+
+| Phase | Duration |
+|---|---|
+| Phase 0: Paradigm capture | 2-3 hours |
+| Phase 1: Init | 1 hour |
+| Phase 2: Collect + verify | 1-2 days |
+| Phase 3: Outline + 3-axis taxonomy | 0.5-1 day |
+| Phase 4: Write with per-claim verification | 3-5 days |
+| Phase 5: Multi-agent peer review | 1 day + fix time |
+| Phase 6: Submission prep | 0.5-1 week (incl. presubmission wait) |
+| **Total** | **2-3 weeks of focused work** |
+
+Compare to v2 + downstream fix: typically 1 week of v2 drafting + 2-3 weeks of post-hoc revision. Net the same time, but v3 delivers a submission-ready draft instead of one needing factual reset.