intake-project · diff

git:20260819.bd9e30b to git:20260930.913abeb

18 added, 141 removed. Audit A to A.

---

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

- ## Purpose

- This skill is the front door for a new or messy project. It converts a folder, document bundle, or mixed set of notes into a structured project state that other skills can use safely.

- Use this skill when:

- - a new paper or proposal folder has been created

- - an older folder exists but is poorly organized

- - the user asks "what is this project and what should I do next?"

- - another skill needs a reliable project summary before proceeding

- ---

- ## Communication Rules

- - Communicate with the user in their preferred language.

- - Keep project labels and file names in the language already used by the workspace.

- - Use English for manuscript section names, study design names, and medical/statistical terminology.

- ---

- ## Inputs

- Accept any of the following:

- - a project folder

- - a manuscript draft

- - an abstract or proposal

- - tables/figures plus notes

- - a mixed folder with PDFs, drafts, and analyses

- If information is incomplete, infer cautiously from file names and contents, then label uncertain items clearly.

- ---

- ## Core Tasks

- ### 1. Project classification

- Determine:

- - likely target journal or venue, if recoverable

- ### 2. State reconstruction

- Identify:

- - what already exists

- - what is missing

- - current phase

- - blocking dependencies

- ### 3. Project memory scaffold

- If missing, propose or create lightweight anchor files:

- - `PROJECT.md`

- - `STATUS.md`

- - `CLAIMS.md`

- - `DATA_DICTIONARY.md`

- - `ANALYSIS_PLAN.md`

- - `REVIEW_LOG.md`

- Create only files that are justified by the project type.

- ### 4. Action plan

- Produce the next 3-5 actions in dependency order.

- ---

## 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`, folder entries.

+ - **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.

+ - 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.

- **Why it pays off:** moving version drafts and QC docs off the `manuscript/` top level makes retargeting a different journal a single `cp -r submission/<journal> submission/<new_journal>`.

---

## 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 stage

+ ### Phase 2: Classify project and stage

- Assign one current stage:

- - `idea`

- - `data assembly`

- - `analysis planning`

- - `analysis in progress`

- - `drafting`

- - `revision`

- - `submission prep`

- - `archived/unclear`

+ Determine:

+ - likely target journal or venue — only if the files name one

+ 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 common gaps:

+ 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

+ ### Recommended next actions (3-5, in dependency order)

1. ...

2. ...

3. ...

```

---

- ## Optional File Templates

- ### `PROJECT.md`

- ```md

- # PROJECT

- - Title:

- - Type:

- - Primary question:

- - Target journal/venue:

- - Lead folder:

- - Collaborators:

- - Last updated:

- ```

- ### `STATUS.md`

- ```md

- # STATUS

- - Current stage:

- - Current blocker:

- - Next actions:

- 1.

- 2.

- 3.

- - Last updated:

- ```

- ---

- ## Guardrails

- - Do not invent data values, outcomes, or collaborator roles.

- - Do not assume a target journal unless evidence exists in the files.

- - Do not create a large folder scaffold when the user only wants a quick assessment.

- - If a project appears to mix multiple studies, say so explicitly rather than collapsing them into one.

- ---

## 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`

- ---

- ## What This Skill Does NOT Do

- - It does not write full manuscript sections

- - It does not perform statistical analysis

- - It does not verify citations deeply

- - It does not replace study design review

- ## 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.