Init Project

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):

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

Phase 2: Scaffold

Create the directory structure:

<project-name>/
├── AGENTS.md               # Project-specific Codex 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

AGENTS.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

1. Overleaf symlink — if a path was provided:

   ln -s /path/to/overleaf/dir paper
   

2. Git init — initialise the repository:

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

Phase 5: Context Update

Update the central context library:

1. Add the project to .context/projects/_index.md
2. 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 (AGENTS.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