Init Project — Research Project Scaffolder

Interactive project setup: answer questions, get a ready-to-use research project directory.

Protocol

Phase 1: Interview

Ask the user these questions using AskUserQuestion (adapt based on what's already known):

Project name — short name for the directory (e.g., nudge-experiment)
Paper title — working title for the paper
Research question — one sentence
Target journal/venue — where you plan to submit
Co-authors — names and affiliations (if any)
Parent directory — where to create the project (default: ~/Research/)
Overleaf path — path to Overleaf-synced directory for symlink (optional)
Methodology — experimental, observational, theoretical, simulation, mixed

Phase 2: Scaffold

Create the directory structure:

<project-name>/
├── CLAUDE.md               # Project-specific Claude instructions
├── README.md               # Project overview
├── MEMORY.md               # Knowledge base (seeded with template)
├── paper/                  # → Overleaf symlink (or empty dir)
├── code/
│   ├── python/             # Python scripts
│   └── R/                  # R scripts
├── data/
│   ├── raw/                # Original data (never modified)
│   └── processed/          # Cleaned/transformed data
├── results/                # Analysis outputs
├── figures/                # Generated figures
├── docs/                   # Project documentation
├── correspondence/         # Referee reports, cover letters
│   └── referee2/           # Referee 2 agent reports
├── log/                    # Session logs
│   └── plans/              # Saved plans
└── .gitignore

Phase 3: Populate Files

CLAUDE.md — project-specific instructions:

Paper title and research question
Co-authors and target venue
Methodology and key conventions
Pointer to project context files

README.md — human-readable overview:

Project title and description
Directory structure explanation
How to compile the paper
Co-author information

MEMORY.md — seeded with research project template:

Notation Registry (empty)
Estimand Registry (empty)
Key Decisions (empty)
Citations (empty)
Anti-Patterns (empty)
Code Pitfalls (empty)

.gitignore — standard research project ignores:

Build artifacts (out/, *.aux, *.log)
Data files (data/raw/*.csv, data/raw/*.xlsx)
Python/R artifacts (__pycache__/, .Rhistory)
OS files (.DS_Store)

Phase 4: Git & Symlinks

Overleaf symlink — if a path was provided:
```
ln -s /path/to/overleaf/dir paper
```

Git init — initialise the repository:

git init
git add .
git commit -m "Initial project scaffold"

Phase 5: Context Update

Update the central context library:

Add the project to .context/projects/_index.md
Create .context/projects/papers/<project-name>.md with metadata

Output

Print a summary of what was created:

Project created: ~/Research/<project-name>/
  Directories: 12
  Files: 4 (CLAUDE.md, README.md, MEMORY.md, .gitignore)
  Overleaf: linked / not configured
  Git: initialised with initial commit

Next steps:
  1. Start writing in paper/ (or link Overleaf)
  2. Add code to code/python/ or code/R/
  3. Run /session-log when you finish working

init-project