Manage-Project Skill -- Research Project Management

Commands

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

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, but not sufficient, for Phase 1C auto-enforce (the PostToolUse verify-refs hook blocks instead of warns): enforce also needs qc/migration_complete, which init does not write. After init, run migrate_project_to_ssot.py --project-root {target_dir} --mark-complete to validate the SSOT.yaml and write the marker. 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). With pyzotero or the credentials missing, 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.

Run scripts/init_project.py:

python3 "${CLAUDE_SKILL_DIR}/scripts/init_project.py" \
    --name {name} --type {type} --journal {journal} [--ssot] \
    --project-root {target_dir}

It 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 stubs, and project_state.json. qc/migration_complete is NOT written by init — that marker belongs to the migrate script. For an --ssot project, run it with --mark-complete (no project.yaml needed): it validates the existing SSOT.yaml and writes the marker only on PASS. Until then the reference hook stays in warn mode.

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 ${CLAUDE_SKILL_DIR}/references/init_scaffold.md only when you need to know where a scaffolded file lands or what a project_state.json field means.

After the script, copy the matching reporting-guideline checklist from ${CLAUDE_SKILL_DIR}/../check-reporting/references/checklists/ into references/checklist_{GUIDELINE}.md.

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

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. On an SSOT-native project (SSOT.yaml present, no project.yaml — e.g. init --ssot) there is nothing to convert: --mark-complete validates the existing SSOT.yaml and writes the marker on PASS; SSOT.yaml is not rewritten.

python3 "${CLAUDE_SKILL_DIR}/scripts/migrate_project_to_ssot.py" \
    --project-root . --write --mark-complete

• --no-mark-complete: run with --write only. Use it when the project still has open QC failures — enforcement is deferred until the migration is validated.
• 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.

Re-run after resolving failures; the script is idempotent.

/manage-project status

Report current progress: read project_state.json, scan the existing files, and check whether the project memory files are present and aligned. Take word-count limits from the target journal's profile, ${CLAUDE_SKILL_DIR}/../write-paper/references/journal_profiles/{JOURNAL}.md, not from memory. Lay the report out as in ${CLAUDE_SKILL_DIR}/references/status_output_format.md.

/manage-project sync-memory

Audit and refresh the project memory files:

• check for PROJECT.md, STATUS.md, CLAIMS.md, DATA_DICTIONARY.md, ANALYSIS_PLAN.md, REVIEW_LOG.md
• identify stale or contradictory project metadata
• propose the minimum files to create or update; create them from ${CLAUDE_SKILL_DIR}/references/scaffold_templates.md
• align project_state.json with the current manuscript phase

/manage-project checklist

Read the pre-submission checklist from ${CLAUDE_SKILL_DIR}/references/pre_submission_checklist.md and write it to submission/pre_submission_checklist.md. Then recommend /self-review (manuscript quality gate), /verify-refs (citation verification) and AI pattern removal (/write-paper Phase 7).

/manage-project timeline {submission_date}

Generate a backwards timeline from the submission date, in the layout of ${CLAUDE_SKILL_DIR}/references/timeline_example.md.

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Project State Conventions

Phase numbers:

• 0 = Init (scaffold created)
• 1 = Outline approved
• 2 = Table/Figure shells approved
• 3 = Methods (critic >= 85)
• 4 = Results (critic >= 85)
• 5 = Discussion (critic >= 85)
• 6 = Introduction + Abstract (critic >= 85)
• 7 = Polish complete (AI pattern removal + checklist + self-review >= 80)

Phase status values: pending | in_progress | complete | blocked