Intake-Project Skill

Canonical Manuscript Folder Structure

/manage-project init scaffolds new projects; its script is the source of truth for that tree, including the qc/ folder the QC skills write to. Use the layout below to reorganize an existing project that was never scaffolded, mapping each artifact into one of these slots or into a folder the init scaffold or another skill already writes to.

{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
├── qc/                                # QC reports the skills write (self-review, checklists, audits)
├── 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/                       # review notes (QC reports go in qc/ at the root)
│   ├── 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, reporting checklists, cross-reference and reference audits) live in qc/ at the project root, where the skills that produce them write them, 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 through /manage-project init — 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:

## 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