Skip to content

quick-reference.md

Latest commit

 

History

History
340 lines (252 loc) · 8.9 KB

quick-reference.md

File metadata and controls

340 lines (252 loc) · 8.9 KB
Raw
title Quick Reference
description Command cheat sheet for agents, skills, teams, Git, R, and shell operations
category reference
agents
teams
skills

Quick Reference

Command cheat sheet for invoking agents, skills, and teams through Claude Code, plus essential Git, R, shell, and WSL commands.

Agents, Skills, and Teams

Invoking Skills (Slash Commands)

Skills are invoked as slash commands in Claude Code when symlinked into .claude/skills/:

# Make a skill available as a slash command
ln -s ../../skills/submit-to-cran .claude/skills/submit-to-cran

# In Claude Code, invoke with:
/submit-to-cran

# Other examples
/commit-changes
/security-audit-codebase
/review-skill-format

Skills can also be referenced in conversation: "Use the create-r-package skill to scaffold this."

Spawning Agents

Agents are spawned as subagents via Claude Code's Task tool. Ask Claude Code directly:

"Use the r-developer agent to add Rcpp integration"
"Spawn the security-analyst to audit this codebase"
"Have the code-reviewer check this PR"

Agents are discovered from .claude/agents/ (symlinked to agents/ in this project).

Activating Teams

Teams are activated by asking Claude Code to use them. Claude reads the team definition from teams/, then spawns each listed member as a subagent via the Agent tool (subagent_type) and coordinates them with SendMessage under the session's single implicit team (TeamCreate is a gated FleetView/cloud-only fallback):

"Use the r-package-review team to review this package"
"Spin up the scrum-team for this sprint"
"Launch the tending team for a meditation session"

Note: Teams are not auto-discovered from .claude/teams/ like agents and skills. Team definitions are blueprints that Claude reads directly from teams/ when asked.

Available teams: r-package-review, gxp-compliance-validation, fullstack-web-dev, ml-data-science-review, devops-platform-engineering, tending, dyad, scrum-team, opaque-team, agentskills-alignment, entomology, analytical-chemistry, gpu-acceleration, physical-computing, translation-campaign, synoptic-mind, caveman-spellbook, visual-pr-review.

Registry Lookups

# Count skills, agents, teams
grep "total_skills" skills/_registry.yml
grep "total_agents" agents/_registry.yml
grep "total_teams" teams/_registry.yml

# List all domains
grep "^  [a-z]" skills/_registry.yml | head -50

# List all agents
grep "^  - id:" agents/_registry.yml

# List all teams
grep "^  - id:" teams/_registry.yml

README Automation

# Regenerate all READMEs from registries
npm run update-readmes

# Check if READMEs are up to date (CI dry-run)
npm run check-readmes

WSL-Windows Integration

Path Conversion

# Windows to WSL
C:\Users\Name\Documents  ->  /mnt/c/Users/Name/Documents
D:\dev\projects          ->  /mnt/d/dev/projects

# Access Windows R from WSL (adjust version)
"/mnt/c/Program Files/R/R-4.5.0/bin/R.exe"
"/mnt/c/Program Files/R/R-4.5.0/bin/Rscript.exe"

# Open current directory in Windows Explorer
explorer.exe .

R Package Development

Development Cycle

devtools::load_all()        # Load package for development
devtools::document()        # Update documentation
devtools::test()            # Run tests
devtools::check()           # Full package check
devtools::install()         # Install package

Quick Checks

devtools::test_file("tests/testthat/test-feature.R")
devtools::run_examples()
devtools::spell_check()
urlchecker::url_check()

CRAN Submission

devtools::check_win_devel()     # Windows builder
devtools::check_win_release()   # Windows builder
rhub::rhub_check()              # R-hub multi-platform
devtools::release()             # Interactive CRAN submission

Scaffolding

usethis::use_r("function_name")           # New R file
usethis::use_test("function_name")        # New test file
usethis::use_vignette("guide_name")       # New vignette
usethis::use_mit_license()                # Add MIT license
usethis::use_github_action_check_standard() # CI/CD

Git Commands

Daily Operations

git status                 # Show working tree status
git diff                   # Show unstaged changes
git diff --staged          # Show staged changes
git log --oneline -10      # Recent commits

git add filename           # Stage specific file
git commit -m "message"    # Commit with message
git commit --amend         # Amend last commit

git checkout -b new-branch # Create and switch to branch
git merge feature-branch   # Merge branch

Remote Operations

git remote -v              # List remotes
git fetch origin           # Fetch changes
git pull origin main       # Pull and merge
git push origin main       # Push to remote
git push -u origin branch  # Push new branch

Useful Aliases

git config --global alias.st status
git config --global alias.co checkout
git config --global alias.br branch
git config --global alias.ci commit
git config --global alias.last 'log -1 HEAD'

Claude Code and MCP

Session Management

claude                     # Start Claude Code
claude mcp list            # List configured MCP servers
claude mcp get r-mcptools  # Get server details

Configuration Files

Claude Code (CLI/WSL):      ~/.claude.json
Claude Desktop (GUI/Win):   %APPDATA%\Claude\claude_desktop_config.json

MCP Servers

# R integration
claude mcp add r-mcptools stdio \
  "/mnt/c/Program Files/R/R-4.5.0/bin/Rscript.exe" \
  -e "mcptools::mcp_server()"

# Hugging Face
claude mcp add hf-mcp-server \
  -e HF_TOKEN=your_token_here \
  -- mcp-remote https://huggingface.co/mcp

Shell Commands

Navigation and Search

pwd                        # Print working directory
ls -la                     # List files with details
tree                       # Show directory tree
z project-name             # Jump to frequent directory

rg "pattern"               # Ripgrep search
rg -t r "pattern"          # Search only R files
fd "pattern"               # User-friendly find
fd -e R                    # Find by extension

File Operations

mkdir -p path/to/dir       # Create nested directories
cp -r source/ dest/        # Copy directory recursively
tar -czf archive.tar.gz dir/  # Create compressed tar
tar -xzf archive.tar.gz      # Extract tar.gz
du -sh directory           # Directory size
df -h                      # Disk space usage

Process Management

htop                       # Interactive process viewer
ps aux | grep process      # Find specific process
kill PID                   # Kill process by ID

Keyboard Shortcuts

Terminal (Bash)

Ctrl+A    Beginning of line       Ctrl+E    End of line
Ctrl+K    Delete to end           Ctrl+U    Delete to beginning
Ctrl+W    Delete previous word    Ctrl+R    Search history
Ctrl+L    Clear screen            Ctrl+C    Cancel command

tmux

Ctrl+A |       Split vertically     Ctrl+A -      Split horizontally
Ctrl+A arrows  Navigate panes       Ctrl+A d      Detach session

VS Code

Ctrl+`         Open terminal        Ctrl+P        Quick open file
Ctrl+Shift+P   Command palette      F1            Command palette

Environment Variables

printenv              # All environment variables
echo $PATH            # PATH variable
export VAR=value      # Set for current session

# Set permanently
echo 'export VAR=value' >> ~/.bashrc
source ~/.bashrc

Package Managers

# APT
sudo apt update && sudo apt install package

# npm
npm install -g package       # Install globally
npm list -g --depth=0        # List global packages

# R (renv)
renv::init()                 # Initialize renv
renv::install("package")     # Install package
renv::snapshot()             # Save lockfile
renv::restore()              # Restore from lockfile

Troubleshooting

R Package Issues

which R                               # R location
R --version                           # R version
Rscript -e ".libPaths()"             # Library paths
echo $RSTUDIO_PANDOC                  # Check pandoc path

WSL Issues

wsl --list --verbose   # List WSL distributions
wsl --status           # WSL status
ip addr                # IP addresses

Git Issues

git config --list          # Show all config
git remote show origin     # Show remote details
git status --porcelain     # Machine-readable status

Related Resources