manage-project

这段内容是审核时保存的快照。外部来源才是完整且最新的版本。

---
name: manage-project
description: "Research project management for medical manuscripts. Scaffold project structure, track writing progress across phases, maintain project memory files, generate submission checklists and backwards timelines. Commands: init, status, sync-memory, checklist, timeline."
triggers: manage project, project init, project status, submission checklist, project scaffold, create project, new paper project
tools: Read, Write, Edit, Bash, Grep, Glob
model: inherit
---

# Manage-Project Skill -- Research Project Management

## Purpose

Scaffold new research projects, track manuscript writing progress, maintain lightweight project memory, generate pre-submission checklists, and create backwards submission timelines. Integrates with all other writing skills and the project-manager agent.

---

## Commands

### `/manage-project init {name} --type {type} --journal {journal} [--ssot] [--zotero-collection NAME]`

Create a complete project scaffold for a new research paper.

**Parameters:**
- `{name}` -- Project identifier (e.g., `nnunet-skull-fracture`, `rfa-meta-analysis`)
- `--type` -- Paper type: `original | meta | case | animal | technical | ai_validation | letter`
- `--journal` -- Target journal: `RYAI | AJR | Radiology | European_Radiology | KJR | INSI | AJNR | generic`
- `--ssot` -- Emit `SSOT.yaml` (schema v1) from `templates/SSOT.yaml.template` instead of legacy `project.yaml`. Required for Phase 1C auto-enforce (the PostToolUse verify-refs hook blocks instead of warns). New projects should pass `--ssot`; legacy in-flight projects stay on `project.yaml` until `/manage-project migrate-ssot` is run.
- `--zotero-collection NAME` -- Optional. Create a Zotero collection via pyzotero and populate `library_id` + `collection_key` in the contract. Requires `ZOTERO_API_KEY` + `ZOTERO_LIBRARY_ID` (optionally `ZOTERO_LIBRARY_TYPE`, default `user`). **Graceful degrade:** with pyzotero missing or credentials absent, the contract is scaffolded with `library_id: null` / `collection_key: null` and a WARN is printed.

**SSOT template substitutions:** `{{PROJECT_ID}}` → `{name}`; `{{PROJECT_TYPE}}` → the SSOT
`project_type` enum mapped from `--type` (`original → original_research`, `meta → meta_analysis`,
`case → case_report`, `ai_validation → ai_validation`, else `other`). Without
`--zotero-collection`, `library_id` / `collection_key` stay `null` until the owner links an
existing collection.

**Implementation:** backed by `scripts/init_project.py`. Invoke it directly when running outside
the skill harness (from the `medsci-skills` repo root):

```bash
python3 scripts/init_project.py \
    --name {name} --type {type} --journal {journal} [--ssot] \
    --project-root {target_dir}
```

The helper writes the contract file (`SSOT.yaml` with `--ssot`, else legacy `project.yaml`), the
directory scaffold, the minimal stubs `scripts/validate_project_contract.py` requires
(`manuscript/index.qmd`, `artifact_manifest.json`, `qc/status.json`), the memory-file templates,
and `project_state.json`. **`qc/migration_complete` is NOT written by init** — that marker belongs
to the migrate pipeline.

**Do not hand-build the scaffold.** The script is the source of truth for the tree and for
`project_state.json`; a hand-built one drifts from what the contract validator expects.

**Read on demand:**

| File | Read it when | Cost if read blindly |
|---|---|---|
| `references/init_scaffold.md` | you need to know where a scaffolded file lands, or what a `project_state.json` field means | ~1,400 tokens describing output the script already produces for you |

---
### `/manage-project migrate-ssot [--no-mark-complete]`

Thin wrapper over `scripts/migrate_project_to_ssot.py` that converts a legacy `project.yaml` project into SSOT.yaml form and, by default, touches `qc/migration_complete` so Phase 1C `auto` mode switches from `warn` to `enforce`.

```bash
python3 scripts/migrate_project_to_ssot.py \
    --project-root . --write --mark-complete
```

-