Intake Project

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

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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.

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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.

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Core Tasks

1. Project classification

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, 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.

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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.
• 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}/.

When to apply

• At project intake: scaffold empty structure.
• 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.

Precedent: an STROBE cohort with a mortality endpoint reorganized v1–v6 plus QC docs from the manuscript/ top level so that a reject-retarget path to a different journal requires only cp -r submission/chest submission/<new_journal>.

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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

Assign one current stage:

• idea
• data assembly
• analysis planning
• analysis in progress
• drafting
• revision
• submission prep
• archived/unclear

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:

• no explicit study question
• no target journal
• no analysis plan
• no variable dictionary
• no claims-to-results map
• no review log for revised manuscripts

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
1. ...
2. ...
3. ...

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Optional File Templates

PROJECT.md

# PROJECT

- Title:
- Type:
- Primary question:
- Target journal/venue:
- Lead folder:
- Collaborators:
- Last updated:

STATUS.md

# STATUS

- Current stage:
- Current blocker:
- Next actions:
  1.
  2.
  3.
- Last updated:

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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.

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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

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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.