medsci-skills 4.1.0

package/skills/intake-project/SKILL.md

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+---
+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:
+- 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.
+
+---
+
+## 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>`.
+
+---
+
+## 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:
+
+```text
+## Project Intake Summary
+Project: ...
+Type: ...
+Current stage: ...
+Likely target: ...
+
+### What exists
+- ...
+
+### What is missing
+- ...
+
+### Risks / ambiguities
+- ...
+
+### Recommended next actions
+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.

package/skills/intake-project/skill.yml

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+schema_version: 2
+name: intake-project
+layer: D
+owner_domain: project_intake
+
+when_to_use: "Intake and normalize a new research project: classify type, summarize state, flag missing inputs, recommend next steps, and scaffold lightweight memory files."
+when_NOT_to_use: "Ongoing project tracking (use manage-project)."
+
+inputs:
+  - "raw project description / existing files"
+outputs:
+  - "project classification"
+  - "state summary"
+  - "scaffolded memory files"
+side_effects:
+  - scaffolds_project_files
+downstream_consumers:
+  - manage-project
+  - design-study
+forbidden_actions:
+  - overwrite_existing_project_artifacts
+  - fabricate_missing_inputs
+
+# v2.1 quality card
+purpose: "Normalize a new or messy project into a classified, summarized starting point with scaffolded memory."
+safety_boundaries:
+  - "Scaffolds new lightweight files; does not overwrite existing project artifacts."
+  - "Flags missing inputs rather than inventing them."
+known_limitations:
+  - "Classification is heuristic and may need correction on unusual projects."
+  - "No standalone demo; a setup step, not an analysis."
+validation_commands:
+  - "review the scaffolded files and correct the classification if needed"
+evidence_surface: manual_workflow