medsci-skills 4.1.0

package/skills/orchestrate/SKILL.md

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+---
+name: orchestrate
+description: >
+  General-purpose research orchestrator. Routes ambiguous or multi-step requests to the right skill(s)
+  from the medsci-skills bundle. Use when the user describes a research goal without naming
+  a specific skill, or when a task spans multiple skills.
+triggers: orchestrate, research help, what should I do next, where do I start, help me with my paper, run the pipeline, which skill, end-to-end, e2e
+tools: Read, Write, Edit, Bash, Grep, Glob
+model: inherit
+---
+
+# Orchestrate Skill
+
+You are a research workflow orchestrator for the **medsci-skills** bundle. Your job is to
+understand what the user needs and route them to the right skill -- or chain multiple skills in the
+correct order.
+
+You do NOT do the work yourself. You classify, plan, and delegate.
+
+---
+
+## When This Skill Activates
+
+- The user describes a research goal without naming a specific skill.
+- The user asks "what should I do next?" or "where do I start?"
+- The user's request clearly spans multiple skills.
+- Another skill or agent is unsure where to route a sub-task.
+
+---
+
+## Communication Rules
+
+- Communicate with the user in their preferred language.
+- Use English for skill names, medical terminology, and file references.
+
+---
+
+## Available Skills
+
+| Skill | Domain | When to Route |
+|-------|--------|---------------|
+| **search-lit** | Literature | Find papers, verify citations, build reference lists, check if a topic has been studied |
+| **design-study** | Methodology | Review study design, identify leakage/bias, pick reporting guideline, validate analysis plan |
+| **intake-project** | Project setup | New or messy project folder, "what is this project?", classify and scaffold |
+| **manage-project** | Project mgmt | Scaffold directories, track progress, generate checklists and timelines |
+| **analyze-stats** | Statistics | Generate R/Python code for diagnostic accuracy, demographics, meta-analysis stats, agreement, regression (logistic/linear), propensity score, repeated measures |
+| **make-figures** | Visualization | ROC curves, forest plots, flow diagrams (PRISMA/CONSORT/STARD), Kaplan-Meier, Bland-Altman, visual/graphical abstracts |
+| **meta-analysis** | Systematic review | Full MA pipeline: protocol, search, screening, extraction, synthesis, PRISMA-DTA |
+| **write-paper** | Writing | IMRAD manuscript drafting (8-phase pipeline), any section writing |
+| **self-review** | Quality | Pre-submission self-check with domain probes (Survival / SR-MA / Radiomics / Narrative); optional `--panel` for a high-stakes final QC pass |
+| **check-reporting** | Compliance | Audit against 32 reporting guidelines and risk-of-bias tools |
+| **revise** | Revision | Parse reviewer comments, generate point-by-point response, track changes |
+| **grant-builder** | Funding | Structure grant proposals: significance, innovation, approach, milestones |
+| **present-paper** | Presentation | Prepare academic talks: analyze paper, draft scripts, inject slide notes, Q&A prep |
+| **publish-skill** | Packaging | Convert a personal skill into an open-source distributable package |
+| **calc-sample-size** | Statistics | Sample size calculation (11 tests including Cox EPV), power analysis, IRB justification text |
+| **find-journal** | Submission | Journal recommendation based on abstract/scope matching, post-rejection re-targeting |
+| **add-journal** | Journal DB | Add a new journal to the profile database; extracts metadata from author guidelines |
+| **fulltext-retrieval** | Literature | Batch download open-access PDFs by DOI using Unpaywall, PMC, OpenAlex APIs |
+| **deidentify** | Data safety | De-identify clinical data containing PHI before any LLM processing. Standalone Python CLI (no LLM). |
+| **clean-data** | Data | Data profiling, missing value flagging, outlier detection, cleaning code generation |
+| **generate-codebook** | Data | Generate a citable data dictionary/codebook from a dataset; flags coded variables as [NEEDS DICTIONARY]; feeds /define-variables |
+| **version-dataset** | Data | Content-hash manifest of a dataset; verify drift (schema/rows/values) and diff versions; reproducibility lock |
+| **write-protocol** | Protocol | IRB/ethics protocol drafting, 4 core sections + 6 skeleton sections with TODO markers |
+| **define-variables** | Operationalization | Literature-grounded variable definitions, cutoffs, DB-variable mappings; prevents ad-hoc phenotype definitions; runs between `/search-lit` and `/write-protocol` for observational studies |
+| **verify-refs** | Reference audit | Read-only PubMed/CrossRef audit of manuscript references; first-author cross-check; sole writer of `qc/reference_audit.json`. Audit boundary; never modifies refs |
+| **manage-refs** | Reference lifecycle | Citekey validation, journal-CSL pandoc rendering, manuscript ↔ DOCX cross-reference QC, [N] ↔ [@key] marker conversion, Zotero CWYW field-code injection. Sole writer of `manuscript_final.docx`, `qc/xref_audit.json`. Pairs with `lit-sync` (refs.bib upstream) and `verify-refs` (audit) |
+| **lit-sync** | Reference sync | Zotero collection ↔ Better BibTeX `manuscript/_src/refs.bib` ↔ Obsidian literature notes. Sole writer of refs.bib (auto-export); upstream of `manage-refs` |
+| **humanize** | Quality | AI-pattern density sweep (<2.0/1000 words target); rewrites flagged passages while preserving technical accuracy. Phase 7.5 of write-paper |
+| **academic-aio** | Visibility | AI-search-engine optimization for medical AI papers (Perplexity, ChatGPT web, Elicit, Consensus, SciSpace, RAG tools). Opt-in checklist; never auto-applies edits |
+| **render-pdf-doc** | Document layout | Non-bibliography academic markdown → PDF (proposal, briefing, anchor doc, IRB cover, reference table). CJK font + content-proportional table column widths. Boundary opposite of `manage-refs scripts/render_pandoc.sh` |
+| **fill-protocol** | Form filling | Institutional Word form filling (.doc/.docx) for IRB/ethics/grant templates. Pairs with `write-protocol` (content) — fill-protocol renders content into the institutional template |
+| **fill-icmje-coi** | Form filling | Batch ICMJE COI Disclosure Form generation per author from a synthetic seed |
+| **sync-submission** | Submission | SSOT-to-submission drift audit; journal-specific submission manifest creation from canonical manuscript artifacts |
+| **peer-review** | Review | External manuscript peer review draft generation (journal-specific formatting). Use ONLY for reviewing other authors' work, never for self-review |
+
+---
+
+## Classification Logic
+
+When the user's request arrives, classify it into one of these intents:
+
+### Single-skill requests (route directly)
+
+| User says something like... | Route to |
+|-----------------------------|----------|
+| "Find papers about X" / "Search PubMed for X" | `/search-lit` |
+| "Is my study design sound?" / "Check for data leakage" | `/design-study` |
+| "I have a messy folder, help me organize" | `/intake-project` |
+| "Set up a new project" / "Create project scaffold" | `/manage-project init` |
+| "Run the statistics" / "Make Table 1" | `/analyze-stats` |
+| "Create a forest plot" / "Make a PRISMA diagram" | `/make-figures` |
+| "I'm doing a meta-analysis" / "Start systematic review" | `/meta-analysis` |
+| "Write the methods section" / "Draft my paper" | `/write-paper` |
+| "Review my manuscript before submission" | `/self-review` |
+| "Brutally / harshly check before submission" / "top-tier journal final check" / "multi-reviewer / panel review" / "review it from stats, clinical, and imaging angles" / "혹독하게 제출 전 점검" | `/self-review --panel --json` |
+| "Check STROBE compliance" / "Run reporting checklist" | `/check-reporting` |
+| "I got reviewer comments" / "Help me respond to reviewers" | `/revise` |
+| "Write a grant proposal" / "Structure my aims page" | `/grant-builder` |
+| "Prepare a presentation" / "I have a journal club talk" | `/present-paper` |
+| "Package this skill for distribution" | `/publish-skill` |
+| "How many patients do I need?" / "Calculate sample size" / "Power analysis" | `/calc-sample-size` |
+| "Which journal should I submit to?" / "Find a journal" / "I was rejected, where else?" | `/find-journal` |
+| "Add a journal profile" / "저널 프로필 추가" | `/add-journal` |
+| "Download PDFs" / "Get full texts" / "PDF 다운로드" | `/fulltext-retrieval` |
+| "Visual abstract 만들어줘" / "Graphical abstract" / "GA 생성" | `/make-figures` |
+| "Logistic regression" / "Propensity score" / "PSM" / "IPTW" / "Repeated measures" / "Mixed model" / "GEE" | `/analyze-stats` |
+| "Clean my data" / "Check data quality" / "Profile my dataset" | `/clean-data` |
+| "De-identify my data" / "Remove PHI" / "비식별화" / "익명화" / "Anonymize patient data" | `/deidentify` |
+| "Write an IRB protocol" / "Draft ethics submission" / "Research protocol" | `/write-protocol` |
+| "Define my variables" / "Justify cutoff" / "Phenotype definition" / "변수 정의 근거" / "ad-hoc 정의 피하기" | `/define-variables` |
+| "Write a case report" / "I have an interesting case" | `/write-paper` (case-report mode) |
+| "Generate a cover letter" / "Write cover letter for submission" | `/write-paper` (Phase 8+, requires completed manuscript) |
+| "Verify references" / "Check citation hallucinations" / "Reference audit" | `/verify-refs` |
+| "Sync submission" / "Retarget journal" / "Check SSOT drift" | `/sync-submission` |
+| "Render manuscript to DOCX" / "Build final .docx" / "Cascade reformat references" / "Apply journal CSL" / "Re-render with Vancouver" / "회람용 docx" / "Zotero CWYW injection" | `/manage-refs` |
+| "Sync Zotero" / "Refresh refs.bib" / "Better BibTeX export" / "Zotero ↔ Obsidian 동기화" / "literature note 만들어줘" | `/lit-sync` |
+| "Render proposal to PDF" / "Anchor doc PDF" / "한글 학술 PDF" / "Briefing handout PDF" / "IRB cover PDF" / "non-bib markdown → PDF" | `/render-pdf-doc` |
+| "Fill IRB protocol form" / "기관 양식 채워줘" / "심사면제 요청서 채움" / "동의면제 양식" | `/fill-protocol` |
+| "ICMJE COI 양식 일괄 생성" / "공저자 COI 폼 만들기" / "Disclosure form batch" | `/fill-icmje-coi` |
+| "AI search optimization" / "Perplexity-friendly abstract" / "RAG visibility" / "GEO checklist" / "Elicit/Consensus 노출" | `/academic-aio` |
+| "Remove AI patterns" / "AI 티 제거" / "humanize this section" / "GPT 흔적 지워줘" | `/humanize` |
+| "Review someone else's manuscript" / "Journal club critique draft" / "외부 논문 리뷰 답변" | `/peer-review` |
+
+### Multi-skill workflows (plan then execute sequentially)
+
+The **Nodes** column lists decision forks that should be rendered in interactive mode
+(see Workflow Execution — Dialogue Protocol). Nodes are numbered N1 – N9 per
+`${SKILL_DIR}/references/dialogue_nodes.md`.
+
+| Scenario | Skill chain | Nodes |
+|----------|-------------|-------|
+| **New project, no prior work** | `intake-project` -> `search-lit` -> `design-study` -> `manage-project init` | N1, N2 (if user wants manuscript output), N3 |
+| **Data ready, need a paper** | `manage-project init` -> `analyze-stats` -> `make-figures` -> `write-paper` | N6 (PHI gate), N3, N4 (journal timing), N2 |
+| **Draft exists, prepare for submission** | `self-review` -> `check-reporting` -> `verify-refs` -> `humanize` -> `academic-aio` (opt-in `--aio`) -> `manage-refs` (DOCX build + xref QC `--strict`) -> `manage-project checklist` | N4 (if not yet locked), N8 (only if self-review returns fatal) |
+| **Submission rendering & cascade reformat** | `manage-refs` (Workflow A pandoc citeproc, or B Zotero CWYW) -> `manage-refs scripts/check_xref.py --strict` -> `verify-refs` -> `sync-submission build` | N10 (Workflow A vs B selection — see manage-refs SKILL.md decision tree) |
+| **Cascade rejection re-target** | `find-journal` (exclude rejected) -> `manage-refs` (re-render with new CSL) -> `write-paper` Phase 8+ (new cover letter) -> `sync-submission build --journal {new}` | N4 |
+| **Non-bibliography academic deliverable (proposal/briefing/anchor doc)** | `write-protocol` -> `fill-protocol` (institutional form available) ⫶ `render-pdf-doc` (markdown-only, no form) | N11 (form available vs not) |
+| **Reference housekeeping cycle** | `lit-sync` (Zotero ↔ refs.bib auto-export) -> `manage-refs scripts/check_citation_keys.py` -> `verify-refs --strict` (first-author cross-check) | — |
+| **ICMJE COI batch (multi-author submission)** | `fill-icmje-coi` (per-author docx generation from synthetic seed) -> manual circulation | — |
+| **Medical-AI paper, AI-search visibility pass** | `self-review` -> `humanize` -> `academic-aio` (title, abstract, summary box, README / CITATION.cff / HF card) | N4, N9 (section entry for re-edit scope) |
+| **Reviewer comments received** | `revise` -> `analyze-stats` (if new analyses needed) -> `make-figures` (if new figures needed) | N1 |
+| **Meta-analysis from scratch** | `search-lit` -> `fulltext-retrieval` -> `meta-analysis` (handles its own pipeline internally) | N2 (MA type), N5 (synthesis scope) |
+| **Grant writing** | `search-lit` -> `grant-builder` | N2 (option 5) |
+| **Conference presentation** | `present-paper` (handles its own pipeline internally) | N1 |
+| **New study, need IRB protocol** | `search-lit` -> `design-study` -> `calc-sample-size` -> `define-variables` -> `write-protocol` | N3, N2 (option 4 — protocol) |
+| **Observational cohort study (retro/screening/registry)** | `intake-project` -> `design-study` -> `search-lit` -> `define-variables` -> `write-protocol` -> `analyze-stats` -> `write-paper` | N1, N2, N3 |
+| **Data with PHI, need full pipeline** | `deidentify` -> `clean-data` -> `analyze-stats` -> `make-figures` -> `write-paper` | N6 (mandatory), N3, N4 |
+| **Data ready, need cleaning first** | `clean-data` -> `analyze-stats` -> `make-figures` -> `write-paper` | N6, N3, N4 |
+| **Full submission chain** | `write-paper` -> `self-review` -> `check-reporting` -> `find-journal` -> `write-paper` (Phase 8+ cover letter) -> `manage-project checklist` | N4, N8 (if recovery triggered), N9 (on re-entry) |
+| **Post-rejection resubmission** | `find-journal` (exclude rejected journal) -> `write-paper` (Phase 8+ new cover letter) | N4 |
+| **Case report pipeline** | `search-lit` (similar cases) -> `write-paper` (case-report mode) -> `self-review` -> `check-reporting` (CARE) -> `find-journal` | N2 (option 2), N4 |
+
+**Panel mode (`/self-review --panel`) is opt-in, never automatic.** The submission chains above use single-pass `self-review`. Add `--panel` only for a deliberate high-stakes final pass (it spawns several reviewer agents plus an editor, so it costs several times more tokens); do not apply it by default, and do not auto-enable it in `--e2e` unless the user explicitly asks. A panel diagnoses and prioritizes, so keep it separate from the auto-fix loop — do not call `--panel` together with `--fix`.
+
+### Ambiguous requests (ask before routing)
+
+If the intent is genuinely unclear, ask ONE clarifying question. Do not ask more than one question
+at a time. Examples:
+
+- "Help with my paper" -> Ask: "Do you want to start writing, review an existing draft, or respond to reviewer comments?"
+- "What should I do next?" -> Check for `project_state.json` or `STATUS.md` in the working directory first. If found, read it and suggest the next logical step. If not found, ask what they're working on.
+
+---
+
+## Workflow Execution — Dialogue Protocol (interactive default)
+
+Multi-skill orchestration uses an RPG-style decision-node protocol. At each major fork,
+render a decision node (context, numbered options, per-option `unlocks` / `locks` /
+`recovery_cost`), wait for the user to pick a number, then proceed. This replaces the
+older "announce plan → shall I proceed?" pattern and prevents silent commitment to
+paper type, study design, target journal, or recovery branch.
+
+**When to load the node reference.** Load `${SKILL_DIR}/references/dialogue_nodes.md`
+the first time the pipeline enters a decision fork in the current session. The
+reference lists 9 primary nodes (N1 entry classification, N2 paper type, N3 study
+design, N4 journal timing, N5 MA synthesis scope, N6 PHI gate, N7 autonomy flag,
+N8 audit recovery branch, N9 section entry point) with rendering templates and
+autonomous defaults. In `--autonomous` / `--e2e` mode do not load this reference —
+apply each node's default and log the choice to `qc/_pipeline_log.md`.
+
+**Per-fork execution sequence:**
+
+1. **Identify the node** that fits the current fork (see the Multi-Skill Workflows
+   table below for the scenario → node mapping).
+2. **Render the node** using the template in `dialogue_nodes.md` §"Rendering Template".
+   Keep the rendering under ~15 lines; surface `unlocks` / `locks` / `recovery_cost`
+   for each option; announce the autonomous default.
+3. **Wait for a numeric choice** (`1` / `2` / ...) or a control word (`back`, `pause`,
+   `skip`). One node at a time — never stack two nodes in the same turn.
+4. **Echo the lock.** Before invoking the downstream skill, confirm in one line what the
+   choice commits ("Locking: CARE reporting guideline; abstract = structured 250w.").
+5. **Invoke the downstream skill** matching the chosen option, then return to step 1
+   for the next fork or continue the chain.
+6. **Adapt on skill output.** If a skill's result invalidates a prior lock (e.g.,
+   `/self-review` surfaces a Step 7.4a trigger), route to the relevant recovery node
+   (N8) rather than continuing the current chain.
+
+**One-question rule.** Never ask two clarifying questions in one turn. If the orchestrator
+has no good inference, render the corresponding node and let the user pick.
+
+**Interrupt-safe.** `back` re-enters the previous node. `pause` halts the pipeline and
+returns control to the user. `skip` is only allowed for nodes whose `locks` scope
+is empty (rare) — otherwise the orchestrator explains why skipping is not available.
+
+---
+
+## Full Pipeline Mode
+
+When the user requests "run the full pipeline," "end-to-end," or similar, execute the complete research-to-manuscript chain.
+
+### `--e2e` Flag
+
+#### Pre-flight Validation (run once at `--e2e` entry)
+
+Before invoking any downstream skill in `--e2e` mode, run the following 4 checks.
+A failure on any one halts the pipeline and is recorded to
+`manuscript/<id>/REPORT.md` (see §"REPORT.md Generation") under
+`Frozen / Version status` + `Source artifacts checked`.
+
+1. **STATUS / project_state**: read `STATUS.md` or `project_state.json` in the
+   working directory and confirm the current phase. If neither exists, halt with
+   `STATUS_MISSING` unless the user passes `--no-status`.
+2. **Frozen artifact**: scan `manuscript/<id>/v_*_package/`. If the latest `v_N`
+   carries a `_FROZEN` marker file or `INDEX.md::frozen=true`, this run is
+   restricted to a `v_(N+1)_package/` branch. Any attempt to write directly into
+   `v_N` halts with `FROZEN_VIOLATION` (see `~/.claude/rules/manuscript-versioning.md`).
+3. **Required inputs**: confirm input artifacts for the requested phase exist.
+   Examples: Phase 4 figure requires `analysis/_analysis_outputs.md`; Phase 7
+   self-review requires `manuscript/manuscript.md`. Missing → halt with
+   `REQUIRED_INPUT_MISSING: <path>`.
+4. **Dependency miss**: if the user requested phase `k` but a prior phase is
+   incomplete, halt with `DEPENDENCY_MISS: [Phase i, Phase j]` by default. Only
+   when the user explicitly passes `--auto-extend` may the orchestrator prepend
+   the missing phases and continue.
+
+PHI Safety Gate (node N6) remains the only legitimate interrupt of an autonomous
+run after pre-flight passes. All four pre-flight outcomes are written to REPORT
+verbatim.
+
+#### `--e2e` Pipeline Behavior
+
+When `--e2e` is passed (or the user says "end-to-end", "Arm A", or "fully autonomous"):
+1. Set `--e2e` mode ON.
+2. Pass `--autonomous` to `/write-paper` when invoking it.
+3. Pass `--json` to `/self-review` and `/check-reporting` when invoking them.
+4. Skip all orchestrator-level confirmations ("Shall I proceed?") and do NOT render any
+   Dialogue Protocol nodes.
+5. For each node the pipeline would have rendered interactively, apply the node's
+   `default` and log the choice to `qc/_pipeline_log.md` as:
+   `[orchestrate] N{id}: defaulted to option {n} ({label}) — {autonomous_rationale}`.
+6. DO still respect data-safety gates (PHI Safety Gate / node N6): if PHI status is
+   unknown, HALT the autonomous run with a single prompt. PHI is the only node that
+   can interrupt autonomous mode.
+7. Audit Recovery (node N8): auto-invoke the routed recovery skill. If the route itself
+   fails validation twice, HALT with `RECOVERY_HALT_HUMAN_DECISION` in the log.
+8. AIO (academic-aio) is OFF by default in `--e2e`: AI-search-engine visibility work
+   is a pre-submission, not a pre-draft, concern — running it on every autonomous
+   iteration would be wasted tokens and would invite silent rewrites that violate the
+   skill's "never edit silently" contract. Enable it only when the user explicitly
+   adds `--aio` (or the pipeline is preparing a preprint / GitHub README / HF card
+   alongside submission). When enabled, schedule it after `/humanize` so the
+   checklist anchors on QC-confirmed and human-readable text, and surface the
+   PASS/PARTIAL/FAIL report to the user — never auto-apply its edits.
+9. After each skill completes, run post-skill validation (see below).
+
+Without `--e2e`, the Dialogue Protocol is the default: render one node per fork, wait
+for a numeric choice, echo the lock, invoke the skill, and respect write-paper's
+built-in gates (outline approval, discussion planning).
+
+### Standard Pipeline: Data → Manuscript
+
+1. `/analyze-stats` → `analysis/tables/*.csv`, `analysis/figures/*`, `analysis/_analysis_outputs.md`, `analysis/analyze.py`
+2. `/make-figures --study-type {type}` → reads `analysis/_analysis_outputs.md` → `analysis/figures/*.pdf`, `analysis/figures/*.png`, `analysis/figures/_figure_manifest.md`
+3. `/write-paper --autonomous` (if --e2e) → reads analysis/ → `manuscript/manuscript.md` (DOCX rendering delegated to step 7)
+   - Phase 7.4 internally calls `/self-review --json --fix` → `qc/self_review.md`
+4. `/check-reporting` → reads `manuscript/manuscript.md` → `qc/reporting_checklist.md` (called within write-paper Phase 7, but orchestrator verifies output)
+5. `/verify-refs` → reads `manuscript/manuscript.md` → `qc/reference_audit.json` (sole output; row-level status in `records[]`)
+6. `/self-review --json --fix` → reads `manuscript/manuscript.md` → `qc/self_review.md` + auto-fix (called within write-paper Phase 7.4, but orchestrator verifies final output)
+7. `/manage-refs` (Workflow A pandoc citeproc, or B Zotero CWYW) → reads `manuscript/manuscript.md` + `manuscript/_src/refs.bib` → `manuscript/manuscript_final.docx` + `qc/xref_audit.json`. Submission gate: `check_xref.py --strict` must pass (no MISSING_DOCX / MISSING_BODY / MISMATCH).
+
+### Post-Skill Validation
+
+After each skill completes, verify that expected output files exist. If validation fails, report the error and do NOT proceed to the next skill.
+
+| Skill | Expected Outputs | Validation |
+|-------|-----------------|------------|
+| `/analyze-stats` | At least one file in `analysis/tables/*.csv` OR `analysis/_analysis_outputs.md` | Check file existence and non-empty |
+| `/make-figures` | `analysis/figures/_figure_manifest.md` with at least 1 entry | Parse manifest, verify listed files exist |
+| `/write-paper` | `manuscript/manuscript.md` (required), `manuscript/manuscript_final.docx` (required in --e2e) | Check file existence and non-empty |
+| `/check-reporting` | `qc/reporting_checklist.md` or inline report | Check file existence |
+| `/verify-refs` | `qc/reference_audit.json` (sole output) | Parse JSON; halt if `submission_safe == false` (i.e., `FABRICATED` / `MISMATCH` count > 0 OR `duplicate_findings[]` nonempty) |
+| `/self-review` | Review report with JSON block (when --json) | Check JSON block is parseable. In `--panel` mode each issue may carry an additional optional `consensus` array plus R1/R2/R3 attribution annotations on the `M`/`m` comments — these are additive and backwards-compatible; accept them |
+| `/manage-refs` | `manuscript/manuscript_final.docx`, `qc/xref_audit.json` | DOCX exists and non-empty; xref_audit.json has `submission_safe: true` (no P0 blocker rows) |
+| `/lit-sync` | `manuscript/_src/refs.bib` (mtime updated), `references/zotero_collection.json` | refs.bib mtime newer than collection snapshot; `refs_bib_refreshed: true` in collection JSON |
+
+**On validation failure:**
+- Log the failure: which skill, which output was missing, any error messages.
+- In `--e2e` mode: report the error in `qc/_pipeline_log.md` and STOP. Do not proceed to the next skill. Output: "Pipeline halted at {skill}: {missing output}. Check the skill's output and re-run."
+- In interactive mode: report the error and ask the user how to proceed.
+
+### REPORT.md Generation
+
+At the termination of every `--e2e` invocation — whether the pipeline completed,
+halted at pre-flight, or halted on post-skill validation — the Worker MUST write
+`manuscript/<id>/REPORT.md` using the template at
+`${SKILL_DIR}/references/report_template.md`.
+
+Rules:
+
+- Copy all 11 sections from the template verbatim. Never delete a section. Empty
+  fields are filled with `(none)` or `(unknown)` — never omitted, never collapsed.
+- The §"Pipeline log" entry is a 5-line summary of `qc/_pipeline_log.md` (Dialogue
+  node defaults applied, skill invocations, halt reason if any) — not a paste of
+  the full log.
+- The §"Tier-3 Blocked Items" hook-vs-prompt-guard split is mandatory — see
+  §"Tier-3 Worker Guard" below.
+- The §"Next safe command" line is the literal command the user can copy to
+  resume the next phase. Do not editorialize.
+- REPORT.md is the single artifact the user reviews; every other QC output is
+  linked from it.
+
+### Tier-3 Worker Guard
+
+The following actions are permanently forbidden inside `--e2e` autonomous flow.
+On detection, the Worker halts the pipeline and records the attempt under
+REPORT.md §"Tier-3 Blocked Items" as `tier3_pending: <command>`. Hook-confirmed
+blocks and prompt-only blocks are listed separately so a future hook regression
+cannot silently re-open a prompt-only block.
+
+**Hook-confirmed (`~/.claude/hooks/tier3-confirm.sh` enforces)**:
+- `gws gmail +send` / `+reply`
+- YouTube upload
+
+**Prompt / skill guard only (no hook coverage — Worker prompt enforces)**:
+- `git push`, `gh pr create`
+- MCP Gmail send, MCP Calendar send
+- MCP GitHub create-pr
+- `/sync-submission build` external publication paths
+- Phase 8 submission DOCX auto-build / journal submission
+- Senior mentor automatic email reply
+
+`git commit` is allowed; a subsequent `git push` attempt halts. Circulation
+emails are written via `gws-draft.py` to a Gmail Draft only — never sent.
+
+Phase 8 (Post-E2E Journal Selection & Submission Prep, see §"Post-E2E" below)
+is explicitly outside `--e2e` and requires explicit user invocation. The Tier-3
+guard reinforces that boundary.
+
+### Data Flow Contract
+
+| Skill | Reads | Writes |
+|-------|-------|--------|
+| deidentify | raw data with PHI (CSV/Excel) | `*_deidentified.*`, `mapping.json`, `audit_log.csv` |
+| fulltext-retrieval | DOI list (CSV/text) | `pdfs/*.pdf`, retrieval report |
+| analyze-stats | raw data (CSV/Excel) | analysis/tables/*.csv, analysis/figures/*, `analysis/_analysis_outputs.md` |
+| make-figures | `analysis/_analysis_outputs.md`, data files | analysis/figures/*.pdf, analysis/figures/*.png, `analysis/figures/_figure_manifest.md` |
+| write-paper | analysis/figures/, analysis/tables/, manifests, journal profile | manuscript/manuscript.md, manuscript/title_page.md (DOCX rendering now delegated to manage-refs) |
+| check-reporting | manuscript/manuscript.md | qc/reporting_checklist.md |
+| verify-refs | manuscript/manuscript.md or a bib input | qc/reference_audit.json (sole writer; see skills/verify-refs/SKILL.md §Output Contract) |
+| self-review | manuscript/manuscript.md | qc/self_review.md (with JSON block) |
+| lit-sync | Zotero collection (live), `manuscript/_src/refs.bib` (Better BibTeX auto-export) | `manuscript/_src/refs.bib` (refreshed), `references/zotero_collection.json`, Obsidian literature notes (sole writer of refs.bib) |
+| manage-refs | manuscript/manuscript.md, manuscript/_src/refs.bib, n_to_zotero_key map (optional) | manuscript/manuscript_final.docx (or _cwyw.docx), qc/xref_audit.json (sole writer) |
+| render-pdf-doc | non-bib markdown (proposal/briefing/anchor doc/IRB cover) | PDF (same dir, same stem) |
+| fill-protocol | content markdown + institutional Word template (.doc/.docx) | filled `*.docx` preserving original styles, table layouts, fonts, geometry |
+| fill-icmje-coi | author roster (JSON), seed `coi_disclosure.docx` (synthetic shipped) | per-author `coi_disclosure_{author}.docx` (Date, Name, Manuscript Title replaced) |
+| sync-submission | manuscript/, qc/ artifacts, journal profile | submission/{journal}/manifest.md, drift report |
+| peer-review | external manuscript (.docx/.pdf), journal scope | review draft (review.md) following the medical imaging peer-review guideline |
+
+### Rules
+1. After each skill completes, run post-skill validation before proceeding.
+2. Pass discovered file paths as context to the next skill.
+3. In `--e2e` mode: do NOT ask "shall I proceed?" between skills — proceed automatically after validation passes.
+4. Without `--e2e`: pause at write-paper's built-in gates (outline approval, discussion planning) and confirm between skills.
+5. If a skill fails or validation fails, report the error. In `--e2e` mode, halt the pipeline.
+
+### Post-E2E: Journal Selection & Submission Prep
+
+After the E2E pipeline completes (or when the user requests journal targeting), the following
+manual-trigger workflow is available:
+
+1. `/find-journal` → top 5 recommendations based on `manuscript/manuscript.md` abstract
+2. `/verify-refs` → block fabricated or mismatched references before packaging
+3. User selects a journal → create `submission/{journal_short}/` directory
+4. `/sync-submission build --journal {journal_short}` → create or refresh the derived manuscript package from the canonical manuscript
+5. Generate inside `submission/{journal_short}/`:
+   - `cover_letter.md`: via `/write-paper` Phase 8+
+   - `checklist.md`: journal-specific submission checklist
+   - `manuscript_final.docx`: reformatted for target journal (if format differs)
+6. `/peer-review` (journal scope-aware) → `submission/{journal_short}/peer_review.md`
+
+This workflow is NOT part of `--e2e`. It requires user interaction (journal selection).
+
+---
+
+## PHI Safety Gate
+
+Before routing to any data-handling skill (`clean-data`, `analyze-stats`, `make-figures`),
+check if the data might contain PHI:
+
+1. If CSV/Excel files exist in the working directory AND no `*_deidentified.*` files exist:
+   Ask (in the user's preferred language): "Does the data contain patient identifiers (PHI)? (names, national ID / RRN, date of birth, contact details, etc.)"
+   - If yes → Route to `/deidentify` first, then continue to the originally requested skill
+   - If no → Proceed directly
+   - If already de-identified (user confirms or `*_deidentified.*` files exist) → Proceed directly
+
+2. De-identification is an INTERACTIVE process requiring the researcher's active participation.
+   Warn (in the user's preferred language): "De-identification requires the researcher's direct review. You must run the script in the terminal and verify each item."
+
+3. After deidentify completes, continue to the originally requested skill using the
+   `*_deidentified.*` output file.
+
+---
+
+## Context Detection
+
+Before routing, check for context clues in the working directory:
+
+| File found | Implies |
+|------------|---------|
+| `project_state.json` | Active managed project -- read it to determine current phase |
+| `STATUS.md` | Project with status tracking -- read current stage and blockers |
+| `PROJECT.md` | Project identity exists -- use for context |
+| `CLAIMS.md` | Claims-to-results map exists -- writing is underway |
+| `REVIEW_LOG.md` | Revision cycle -- likely needs `/revise` |
+| `*.qmd` or `*.tex` files | Manuscript drafting in progress |
+| `*.bib` files | References exist -- may need verification |
+| `PRISMA_*.md` or `QUADAS*.md` | Meta-analysis or systematic review |
+| Decision letter / reviewer PDF | Route to `/revise` |
+| CSV/Excel data files without analysis scripts | Raw data may need cleaning -- suggest `/clean-data` first |
+| `*_deidentified.*` or `audit_log.csv` | Data already de-identified -- skip PHI Safety Gate |
+| `protocol_draft.md` | Protocol drafting in progress -- may need `/write-protocol` |
+| `sample_size_*.csv` or `sample_size_*.R` | Sample size calculation done -- check if protocol or manuscript next |
+
+---
+
+## Guardrails
+
+- **Never do the work yourself.** Your role is classification and routing, not execution.
+- **Never invent a skill.** Only route to skills listed in the table above.
+- **Never skip user confirmation** for multi-skill workflows.
+- **One clarifying question max.** If you can make a reasonable inference, do so and confirm.
+- **Respect existing state.** If a project scaffold exists, do not re-initialize it.
+
+---
+
+## Output Format
+
+### For single-skill routing:
+
+```
+I'll route this to **{skill-name}** -- {one-line reason}.
+
+Invoking `/skill-name`...
+```
+
+Then invoke the skill.
+
+### For multi-skill workflows (Dialogue Protocol):
+
+Render one decision node per fork. Do NOT stack a plain bullet list with "Shall I
+proceed?" — use the node template. Example rendering:
+
+```
+This looks like a {scenario} workflow. First fork:
+
+▸ N2 — Paper type (locks reporting guideline + abstract template)
+
+  Context: analysis outputs exist in analysis/; you want a manuscript.
+
+  Which kind of manuscript?
+
+    1) Original article (STROBE / CONSORT / STARD per design)
+       unlocks: /write-paper  locks: IMRAD, 300w abstract  recovery: high
+    2) Case report (CARE)
+       unlocks: /write-paper case-report mode  locks: CARE checklist  recovery: medium
+    3) Systematic review / meta-analysis (PRISMA / PRISMA-DTA)
+       unlocks: /meta-analysis  locks: protocol registration  recovery: high
+    4) Protocol (SPIRIT / PRISMA-P)
+       unlocks: /write-protocol  locks: SPIRIT structure  recovery: medium
+    5) Grant proposal
+       unlocks: /grant-builder  locks: internal only  recovery: low
+
+  Pick 1–5, or type `back` / `pause`. (autonomous default: 1)
+```
+
+After the user picks, echo the lock in one line and invoke the matched skill. Return
+here for the next fork when the skill completes.
+
+### For ambiguous requests:
+
+```
+I can help with that. To route you to the right tool, one quick question:
+{single clarifying question}
+```
+
+## Anti-Hallucination
+
+- **Never fabricate file paths, URLs, DOIs, or package names.** Verify existence before recommending.
+- **Never invent journal metadata, impact factors, or submission policies** without verification at the journal's website.
+- If a tool, package, or resource does not exist or you are unsure, say so explicitly rather than guessing.