{"id":"f9192b5c-4481-4742-b6e9-6c1b26c00c43","shortId":"XAnSqH","kind":"skill","title":"manage-project","tagline":"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.","description":"# Manage-Project Skill -- Research Project Management\n\n## Purpose\n\nScaffold 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.\n\n---\n\n## Commands\n\n### `/manage-project init {name} --type {type} --journal {journal} [--ssot] [--zotero-collection NAME]`\n\nCreate a complete project scaffold for a new research paper.\n\n**Parameters:**\n- `{name}` -- Project identifier (e.g., `nnunet-skull-fracture`, `rfa-meta-analysis`)\n- `--type` -- Paper type: `original | meta | case | animal | technical | ai_validation | letter`\n- `--journal` -- Target journal: `RYAI | AJR | Radiology | European_Radiology | KJR | INSI | AJNR | generic`\n- `--ssot` -- Emit `SSOT.yaml` (schema v1) from `templates/SSOT.yaml.template` instead of legacy `project.yaml`. Required for Phase 1C auto-enforce (PostToolUse verify-refs hook blocks instead of warns). New projects on or after 2026-04-24 should pass `--ssot`. Legacy in-flight projects stay on `project.yaml` until `/manage-project migrate-ssot` is run.\n- `--zotero-collection NAME` -- Optional. Create a new Zotero collection with `NAME` via pyzotero and populate `library_id` + `collection_key` in the contract. Requires env vars `ZOTERO_API_KEY` + `ZOTERO_LIBRARY_ID` (and optionally `ZOTERO_LIBRARY_TYPE`, default `user`). Graceful degrade: if pyzotero is not installed or credentials are missing, the contract is scaffolded with `library_id: null` / `collection_key: null` and a WARN is printed.\n\n**SSOT template substitutions:** `{{PROJECT_ID}}` → `{name}`, `{{PROJECT_TYPE}}` → 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` — populated manually when the owner links an existing Zotero collection.\n\n**Implementation:** `/manage-project init` is backed by `scripts/init_project.py`. Invoke directly when running outside the skill harness:\n\n```bash\npython3 scripts/init_project.py \\\n    --name {name} --type {type} --journal {journal} [--ssot] \\\n    --project-root {target_dir}\n```\n\n(Run from the `medsci-skills` repo root.)\n\nThe helper writes the contract file (`SSOT.yaml` with `--ssot`, otherwise legacy `project.yaml`), the directory scaffold, minimal stubs required by `scripts/validate_project_contract.py` (`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 — the migrate pipeline is responsible for that marker.\n\n**What it creates:**\n\n```\n{name}/\n├── paper/\n│   ├── main.qmd               <- Main manuscript (Quarto)\n│   ├── sections/\n│   │   ├── abstract.qmd\n│   │   ├── introduction.qmd\n│   │   ├── methods.qmd\n│   │   ├── results.qmd\n│   │   ├── discussion.qmd\n│   │   └── conclusion.qmd\n│   ├── figures/\n│   │   └── .gitkeep\n│   ├── tables/\n│   │   └── table_shells.md    <- Table structure designed before prose\n│   └── supplementary/\n│       └── .gitkeep\n├── analysis/\n│   ├── scripts/\n│   │   └── .gitkeep\n│   └── outputs/\n│       └── .gitkeep\n├── references/\n│   ├── library.bib\n│   └── checklist_{GUIDELINE}.md  <- Loaded from /check-reporting\n├── revision/\n│   └── .gitkeep\n├── submission/\n│   └── .gitkeep\n├── PROJECT.md                <- Project identity and scope\n├── STATUS.md                 <- Current phase, blockers, next actions\n├── CLAIMS.md                 <- Claim-to-result map\n├── DATA_DICTIONARY.md        <- Variable and outcome definitions\n├── ANALYSIS_PLAN.md          <- Primary/secondary analyses\n├── REVIEW_LOG.md             <- Reviewer comments and responses\n├── project_state.json         <- Progress tracking\n└── README.md                  <- Project overview\n```\n\n**Also creates** `project_state.json`:\n\n```json\n{\n  \"name\": \"{name}\",\n  \"type\": \"{type}\",\n  \"journal\": \"{journal}\",\n  \"created\": \"YYYY-MM-DD\",\n  \"target_submission\": null,\n  \"current_phase\": 0,\n  \"phases\": {\n    \"0_init\": \"complete\",\n    \"1_outline\": \"pending\",\n    \"2_tables_figures\": \"pending\",\n    \"3_methods\": \"pending\",\n    \"4_results\": \"pending\",\n    \"5_discussion\": \"pending\",\n    \"6_intro_abstract\": \"pending\",\n    \"7_polish\": \"pending\"\n  },\n  \"word_counts\": {\n    \"abstract\": 0,\n    \"introduction\": 0,\n    \"methods\": 0,\n    \"results\": 0,\n    \"discussion\": 0,\n    \"total\": 0\n  },\n  \"checklist_status\": \"pending\",\n  \"citation_status\": \"unverified\",\n  \"revision_round\": null,\n  \"memory_files\": {\n    \"PROJECT.md\": true,\n    \"STATUS.md\": true,\n    \"CLAIMS.md\": true,\n    \"DATA_DICTIONARY.md\": true,\n    \"ANALYSIS_PLAN.md\": true,\n    \"REVIEW_LOG.md\": true\n  }\n}\n```\n\n---\n\n### `/manage-project migrate-ssot [--no-mark-complete]`\n\nThin 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`.\n\n```bash\npython3 scripts/migrate_project_to_ssot.py \\\n    --project-root . --write --mark-complete\n```\n\n- Default: `--write --mark-complete` (enforce-ready).\n- `--no-mark-complete` flag form: run with `--write` only. Use when the project still has open QC failures — enforcement is deferred until the migration is validated.\n- The migrate script refuses to touch `qc/migration_complete` unless the generated SSOT.yaml passes `validate_project_contract.py` AND `contract_mode=ssot`. Do not `touch qc/migration_complete` manually.\n\nRe-run after resolving failures; the script is idempotent.\n\n---\n\n### `/manage-project status`\n\nReport current progress. Reads `project_state.json`, scans existing files, and checks whether key project memory files are present and aligned.\n\n**Output format:**\n\n```\n## Project Status: {name}\nJournal: {journal} | Type: {type} | Created: {date}\nTarget submission: {date or \"not set\"}\n\n### Phase Progress\n[check] Phase 0: Project Init (complete)\n[check] Phase 1: Outline (complete)\n[check] Phase 2: Tables & Figures (complete)\n[work]  Phase 3: Methods (IN PROGRESS)\n[wait]  Phase 4: Results (pending)\n[wait]  Phase 5: Discussion (pending)\n[wait]  Phase 6: Introduction & Abstract (pending)\n[wait]  Phase 7: Polish (pending)\n\n### Word Counts\nAbstract:     0 / 250 words\nIntroduction: 0 / 600 words\nMethods:      847 / 1000 words  85%\nResults:      0 / 900 words\nDiscussion:   0 / 800 words\nTotal:        847 / 3500 words (journal limit)\n\n### Quality Gates\nCritic score (Methods): 87/100 PASS\nCitations verified: 12/12\nReporting guideline: pending\n\n### Project Memory\nPROJECT.md: present\nSTATUS.md: stale (last updated 12 days ago)\nCLAIMS.md: missing\nDATA_DICTIONARY.md: present\nANALYSIS_PLAN.md: missing\nREVIEW_LOG.md: n/a (not in revision)\n\n### Next Steps\n1. Complete Methods draft (150 words remaining)\n2. Run /analyze-stats for Table 1 and diagnostic accuracy\n3. Begin Results (Phase 4)\n```\n\n### `/manage-project sync-memory`\n\nAudit and refresh project memory files so other agents can work with less ambiguity.\n\n**What it does:**\n- checks for presence of `PROJECT.md`, `STATUS.md`, `CLAIMS.md`, `DATA_DICTIONARY.md`, `ANALYSIS_PLAN.md`, `REVIEW_LOG.md`\n- identifies stale or contradictory project metadata\n- proposes the minimum files to create or update\n- aligns `project_state.json` with the current manuscript phase\n\n**Suggested use cases:**\n- before handing the project to `project-manager`\n- before a large revision cycle\n- when returning to an old folder after weeks or months\n- when multiple collaborators are editing in parallel\n\n---\n\n### `/manage-project checklist`\n\nGenerate a pre-submission checklist covering all quality dimensions.\n\n**Output:** `submission/pre_submission_checklist.md`\n\nRead and output the pre-submission checklist from\n`${CLAUDE_SKILL_DIR}/references/pre_submission_checklist.md`.\n\n---\n\n### `/manage-project timeline {submission_date}`\n\nGenerate a backwards timeline from submission date.\n\n**Example:** `/manage-project timeline 2026-05-01`\n\n**Output:**\n\n```\n## Backwards Timeline to Submission: 2026-05-01\n\nWeek -8 (2026-03-06): Phase 0-2 complete (scaffold, outline, tables)\nWeek -7 (2026-03-13): Methods draft -> critic pass\nWeek -6 (2026-03-20): Results draft -> critic pass + /analyze-stats complete\nWeek -5 (2026-03-27): Discussion draft -> critic pass\nWeek -4 (2026-04-03): Introduction + Abstract -> critic pass\nWeek -3 (2026-04-10): AI pattern removal + /check-reporting (reporting guideline)\nWeek -2 (2026-04-17): /self-review + co-author review\nWeek -1 (2026-04-24): Final revisions + figures at 300 DPI + /lit verification\nSUBMISSION (2026-05-01): Upload to journal portal\n\nCritical path: Statistics must be complete by Week -6.\nRun /analyze-stats as soon as data is available.\n```\n\n---\n\n## Project Scaffold Templates\n\n### PROJECT.md Template\n\n```markdown\n# PROJECT\n\n- Title:\n- Type:\n- Primary question:\n- Target journal/venue:\n- Lead folder:\n- Collaborators:\n- Last updated:\n```\n\n### STATUS.md Template\n\n```markdown\n# STATUS\n\n- Current stage:\n- Current blocker:\n- Next actions:\n  1.\n  2.\n  3.\n- Last updated:\n```\n\n### CLAIMS.md Template\n\n```markdown\n# CLAIMS\n\n| Claim | Supporting result | Source table/figure | Citation status |\n|------|-------------------|---------------------|-----------------|\n| ...  | ...               | ...                 | ...             |\n```\n\n### DATA_DICTIONARY.md Template\n\n```markdown\n# DATA DICTIONARY\n\n| Variable | Definition | Timing | Notes |\n|----------|------------|--------|------|\n| ...      | ...        | ...    | ...  |\n```\n\n### ANALYSIS_PLAN.md Template\n\n```markdown\n# ANALYSIS PLAN\n\n- Primary endpoint:\n- Secondary endpoints:\n- Main comparator:\n- Statistical methods:\n- Validation strategy:\n- Sensitivity analyses:\n```\n\n### REVIEW_LOG.md Template\n\n```markdown\n# REVIEW LOG\n\n| Reviewer comment | Planned action | Status | Location updated |\n|------------------|----------------|--------|------------------|\n| ...              | ...            | ...    | ...              |\n```\n\n---\n\n## Integration with Other Skills\n\nWhen called from `/manage-project init`, automatically:\n1. Load the correct journal profile from `write-paper/references/journal_profiles/{JOURNAL}.md`\n2. Load the correct paper type template from `write-paper/references/paper_types/{TYPE}.md`\n3. Copy the appropriate reporting guideline checklist from `check-reporting/references/checklists/`\n4. Set word count targets based on the journal profile\n\nAfter `/manage-project checklist`, recommend calling:\n- `/self-review` for manuscript quality gate\n- `/search-lit` to verify all citations\n- AI pattern removal (built into `/write-paper` Phase 7)\n\n---\n\n## Project State Conventions\n\n**Phase numbers:**\n- 0 = Init (scaffold created)\n- 1 = Outline approved\n- 2 = Table/Figure shells approved\n- 3 = Methods (critic >= 85)\n- 4 = Results (critic >= 85)\n- 5 = Discussion (critic >= 85)\n- 6 = Introduction + Abstract (critic >= 85)\n- 7 = Polish complete (AI pattern removal + checklist + self-review >= 80)\n\n**Phase status values:** `pending | in_progress | complete | blocked`\n\n## Anti-Hallucination\n\n- **Never fabricate file paths, URLs, DOIs, or package names.** Verify existence before recommending.\n- **Never invent journal metadata, impact factors, or submission policies** without verification at the journal's website.\n- If a tool, package, or resource does not exist or you are unsure, say so explicitly rather than guessing.","tags":["manage","project","medsci","skills","aperivue","agent-skills","biostatistics","claude-code","claude-skills","clinical-research","diagnostic-accuracy","irb-protocol"],"capabilities":["skill","source-aperivue","skill-manage-project","topic-agent-skills","topic-biostatistics","topic-claude-code","topic-claude-skills","topic-clinical-research","topic-diagnostic-accuracy","topic-irb-protocol","topic-literature-review","topic-manuscript","topic-medical-ai","topic-medical-research","topic-meta-analysis"],"categories":["medsci-skills"],"synonyms":[],"warnings":[],"endpointUrl":"https://skills.sh/Aperivue/medsci-skills/manage-project","protocol":"skill","transport":"skills-sh","auth":{"type":"none","details":{"cli":"npx skills add Aperivue/medsci-skills","source_repo":"https://github.com/Aperivue/medsci-skills","install_from":"skills.sh"}},"qualityScore":"0.499","qualityRationale":"deterministic score 0.50 from registry signals: 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