Commands Cheatsheet

Quick reference for every command available in the Research Project Flow template.

Project commands

These commands work inside any project built from the template.

/init

Initializes a new CLAUDE.md file in the current directory. Use this to set up the AI’s project instructions from scratch.

> /init

When to use: If you are starting a project without the template, or if you want to create a fresh CLAUDE.md tailored to your project. The template already includes a CLAUDE.md, so you only need this for new or non-template projects. You can also borrow the CLAUDE.md from this template and adapt it.

/status

Scans the project and reports its current state.

> /status

Shows: pipeline steps and last run dates, uncommitted changes, Dropbox conflicts, stale logs, scratch files.

When to use: Start of every session. The AI runs this automatically when you launch Claude Code in a project with CLAUDE.md.

/run

Executes a pipeline step with logging and validation.

> /run                    # prompts for which step
> /run 05_merge           # runs a specific step
> /run --all              # runs the full pipeline
> /run --from 05          # runs from step 05 forward

What it does:

  1. Validates the script exists
  2. Executes it via run_all.sh
  3. Captures the log to output/logs/
  4. Reads the log and reports results

/check

Full integrity audit of the project.

> /check

Verifies:

  • Every script in the pipeline table exists and has a valid header
  • Script inputs/outputs match the pipeline table in the README
  • params.do values match the README Parameters table
  • Referenced data files exist
  • Manuscript \input references point to existing files
  • Table/figure map matches actual output files

/add-step

Scaffolds a new pipeline step end-to-end.

> /add-step

Prompts for: step number, language (Stata/R/Python), description, inputs, outputs.

Creates:

  • The script file with a structured header
  • An entry in the README pipeline table
  • A registration in 00_run.do
  • A registration in run_all.sh

/handoff

Writes a session summary for future reference or co-author communication.

> /handoff

Produces: a markdown file in session_logs/ with:

  • Files created or modified
  • Outputs regenerated
  • Open questions or next steps
  • Git status at time of handoff

/git

Stages, commits, and pushes all changes.

> /git

What it does:

  1. Stages all tracked and new files
  2. Writes a descriptive commit message based on changes
  3. Commits
  4. Pushes to the remote

No confirmation prompt — it runs immediately. Use when your project is in a clean, working state.

Terminal commands

These are standard terminal commands you will use alongside Claude Code.

Command Purpose
claude Launch Claude Code in the current directory
cd ~/Dropbox/my-project Navigate to your project
git status Check for uncommitted changes
git log --oneline -10 View recent commits
./run_all.sh "script_name" Run a pipeline step directly
./run_all.sh --all Run the full pipeline directly

Keyboard shortcuts in Claude Code

Shortcut Action
Enter Send message
Esc Cancel current operation
Ctrl+C Exit Claude Code
Up arrow Scroll through message history