/init-project

Initialize the current workspace as a Research Paper Factory project. Work from the workspace root.

Steps

1. Check for an existing setup. If docs/_backbone/_STATE.md or a CLAUDE.md containing "Research Paper Factory" already exists, report what is present and ask the user whether to update missing pieces only (default) or re-initialize. Never overwrite existing backbone files.

2. Create the folder structure (skip any that exist):

   data/raw/  data/processed/  scripts/  docs/_backbone/  docs/plans/  docs/details/
   output/figures/  output/slides/  jobs/slurm/logs/
   

3. Write the project contract. Copy ${CLAUDE_PLUGIN_ROOT}/templates/PROJECT_CLAUDE.md to CLAUDE.md in the workspace root. If a CLAUDE.md already exists, append the contract under a # Research Paper Factory heading instead of overwriting.

4. Seed backbone files in docs/_backbone/ (only if missing):

   • _STATE.md — phase "Initialized", today's date, empty checkpoint
   • _STATUS.md — project name (from the command argument, or ask), status "New"
   • _INDEX.md — table with the files just created
   • _LESSONS.md — empty with header explaining [LEARN:category] tag format
   • _STYLE.md — header noting "fill in journal target and table conventions"

5. Bootstrap the pipeline map. Run:

   python "${CLAUDE_PLUGIN_ROOT}/scripts/pipeline_bootstrap.py" .
   

   If it fails (e.g. no Python), copy ${CLAUDE_PLUGIN_ROOT}/templates/_PIPELINE.yaml to docs/_backbone/_PIPELINE.yaml instead.

6. Protect raw data. Confirm to the user that the plugin's PreToolUse hook blocks writes to data/raw/.

7. Report what was created and suggest next steps: run /research-factory:strategist to plan the project, or /research-factory:idea-lab to brainstorm ideas. Remind the user that the memory-charter skill will create _CHARTER.md + _DECISIONS.md on first strategic planning session.

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