intake-project git:20260930.913abebA

Immutable. This exact content never changes and is served at /api/v1/blob/db6fb71fe5cd9360.

---
name: intake-project
description: >
  Intake and normalize a new radiology research project. Classifies project type, summarizes current state,
  identifies missing inputs, recommends next steps, and scaffolds lightweight project memory files.
triggers: new project, intake project, project intake, classify project, organize project, what is this project
tools: Read, Write, Edit, Bash, Grep, Glob
model: inherit
---

# Intake-Project Skill

## Canonical Manuscript Folder Structure

For any manuscript project (cohort, MA, RCT, case series), enforce this structure when scaffolding or reorganizing. Map every new artifact into one of these slots — do not invent ad-hoc folders.

```
{project_root}/
├── HANDOFF.md                         # session handoff entry point
├── README.md                          # project overview
├── data/                              # raw data (NEVER edit; read-only)
├── analysis/                          # reproducible scripts (00_* → 04_*)
├── output/                            # analysis outputs: CSVs, PNGs, intermediates
├── irb/                               # IRB/ethics docs
├── proposal/                          # original protocol / approved proposal
├── reviews/                           # external correspondence
├── manuscript/                        # SOURCE manuscript + drafting
│   ├── manuscript_v{N}.{md,docx,pdf}  # current canonical working version (top level)
│   ├── build_unified_docx.py          # or pandoc wrapper
│   ├── archive/                       # ALL prior versions v1 .. v{N-1}
│   ├── reviews/                       # QC: self_review, peer_review, STROBE/PRISMA, critic
│   ├── figures/                       # figure scripts + rendered PNG/PDF
│   └── tables/                        # table scripts + rendered docx
└── submission/                        # per-journal packages
    └── {journal-slug}/                # e.g., chest/, kjr/
        ├── CHECKLIST.md
        ├── cover_letter.{md,docx,pdf}
        ├── title_page.docx            # separated for double-anonymized
        ├── manuscript_anonymized.{docx,pdf}
        ├── supplement.{docx,pdf}
        ├── strobe_checklist.md        # or PRISMA / CONSORT
        ├── circulation_email.md
        └── figures/                   # submission-ready DPI copies
```

### Rules

- **`manuscript/` = source; `submission/{journal}/` = derived artifacts.** Regenerate submission files from `manuscript/manuscript_v{N}.md`; never edit anonymized/title-page directly.
- **One canonical working version** at `manuscript/manuscript_v{N}.{md,docx,pdf}`. Older versions move to `manuscript/archive/` immediately on version bump.
- **No loose files at project root.** Only `HANDOFF.md`, `README.md`, the project memory files (Phase 3), the contract files `/manage-project init` writes (`SSOT.yaml` or `project.yaml`, `project_state.json`, `artifact_manifest.json`), and folder entries.
- **QC artifacts** (self_review, peer_review, STROBE, critic reports) live in `manuscript/reviews/`, not at manuscript top level.
- **On rejection/retarget:** `cp -r submission/{old} submission/{new}`, then rewrite cover letter and reformat.
- **Double-anonymized journals** (Chest, AJRCCM): title page and anonymized manuscript MUST be separate files under `submission/{journal}/`.
- Keep existing project labels and file names in the language the workspace already uses.

### When to apply

- At project intake: scaffold empty structure — unless the user only wants a quick assessment.
- At first submission prep: create `submission/{journal}/` and populate.
- Mid-project cleanup: when `manuscript/` has >3 versioned files or QC docs at top level, reorganize.
- Before session handoff: reorganize if structure is drifting.

---

## Workflow

### Phase 1: Discover context

1. Read top-level folder names and key files.
2. Detect manuscript-like files, tables, figures, protocols, and analysis outputs.
3. Extract:
   - project title or working title
   - study question
   - dataset or cohort hints
   - collaborators or institutions
   - venue/journal hints

### Phase 2: Classify project and stage

Determine:
- project type: `original | review | meta-analysis | case report | technical note | grant | peer review | challenge | career-doc`
- primary domain: `radiology | medical AI | multimodal LLM | intervention | survival/prognostic | diagnostic accuracy | workflow`
- target output: `paper | abstract | grant | review | rebuttal | CV`
- likely target journal or venue — only if the files name one
- one current stage: `idea | data assembly | analysis planning | analysis in progress | drafting | revision | submission prep | archived/unclear`

If the folder mixes several studies, say so rather than collapsing them into one.

**Gate:** Present the classification (project type, stage, target output) to the user.
Confirm before creating any files — misclassification leads to wrong scaffold and
wrong skill routing.

### Phase 3: Surface missing inputs

Check for blocking dependencies and common gaps:
- no explicit study question
- no target journal
- no analysis plan
- no variable dictionary
- no claims-to-results map
- no review log for revised manuscripts

If missing, propose or create lightweight anchor files — `PROJECT.md`, `STATUS.md`, `CLAIMS.md`,
`DATA_DICTIONARY.md`, `ANALYSIS_PLAN.md`, `REVIEW_LOG.md` — only those the project type justifies.
Read `${CLAUDE_SKILL_DIR}/references/memory_templates.md` when creating `PROJECT.md` or `STATUS.md`.

### Phase 4: Produce normalized summary

Output this structure:

```text
## Project Intake Summary
Project: ...
Type: ...
Current stage: ...
Likely target: ...

### What exists
- ...

### What is missing
- ...

### Risks / ambiguities
- ...

### Recommended next actions (3-5, in dependency order)
1. ...
2. ...
3. ...
```

---

## Handoff Rules

After intake:
- route to `search-lit` if the literature basis is weak
- route to `design-study` if the research question exists but design logic is unclear
- route to `manage-project` if the folder should be scaffolded
- route to `write-paper` only after the project phase is clearly `drafting`