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Command Reference

Setup Commands

Basic Usage

./setup.sh              # Smart setup - detects what needs to be done
./setup.sh preview      # Show what would be installed/updated
./setup.sh minimal      # Install essential tools only  
./setup.sh fix          # Run diagnostics and fix common issues
./setup.sh warp         # Configure Warp terminal optimizations
./setup.sh info         # Learn about installed tools, aliases & features
./setup.sh help         # Show help message

# Backup management (automatic - runs during setup)
./setup.sh backup         # List all backups
./setup.sh backup clean   # Manually remove old backups (also automatic)
./setup.sh backup migrate # Migrate legacy backups to new structure

Advanced Options

# Use environment variables instead of flags
SETUP_VERBOSE=1 ./setup.sh      # Verbose output
SETUP_JOBS=8 ./setup.sh         # Custom parallel jobs
SETUP_LOG=file.log ./setup.sh   # Log to file
SETUP_NO_WARP=true ./setup.sh   # Skip Warp auto-detection

# Advanced interactive mode
./setup.sh advanced     # Interactive menu for all options

# Git configuration
git config --global core.editor # Automatically set to vim/nvim if available

Information Commands

./setup.sh info              # Show help categories
./setup.sh info tools        # List all installed tools with descriptions
./setup.sh info aliases      # Show all shell aliases
./setup.sh info functions    # Show custom shell functions
./setup.sh info features     # Show special features and enhancements
./setup.sh info examples     # Show usage examples for common tasks
./setup.sh info search fd    # Search for specific tool/command
./setup.sh info all          # Show everything (paginated)

# After setup, use the alias:
devhelp                      # Quick access to info command
devhelp tools                # Show tools
devhelp search ripgrep       # Search for ripgrep

Git Helpers

Conventional Commits

./scripts/setup-git-hooks.sh # Set up conventional commit hooks
./scripts/commit-helper.sh   # Interactive commit message creator
./scripts/commit-helper.sh --quick # Quick mode with fewer prompts

# Shell aliases (after running setup):
gci                          # Interactive commit helper
gcft "message"               # Quick feat commit
gcfs scope "message"         # Scoped feat commit
commit-help                  # Show commit format reference

Branch Cleanup

# Clean up stale remote-tracking branches
gclean                       # Interactive cleanup of gone branches
gclean --force               # Skip confirmation prompts
git-cleanup-branches         # Full function name (same as gclean)
gprune                       # Just prune remote branches

# Manual cleanup (what gclean does automatically):
git remote prune origin
git branch -vv | grep ": gone]" | awk '{print $1}' | xargs git branch -d

MCP Server Management

Claude Desktop

./scripts/setup-claude-mcp.sh           # Install and configure MCP servers
./scripts/setup-claude-mcp.sh --check   # Check MCP server status
./scripts/setup-claude-mcp.sh --update  # Update MCP servers
./scripts/setup-claude-mcp.sh --remove  # Remove MCP configuration

./scripts/fix-mcp-servers.sh            # Fix/repair MCP configuration
./scripts/fix-mcp-servers.sh --no-api-keys  # Only setup servers without API keys
./scripts/fix-mcp-servers.sh --servers filesystem,memory,git  # Setup specific servers
./scripts/debug-mcp-servers.sh          # Test and debug MCP installations

Claude Code CLI

./scripts/setup-claude-code-mcp.sh      # Add MCP servers to user scope (global)
./scripts/setup-claude-code-mcp.sh --scope project  # Add to project scope (.mcp.json)
./scripts/setup-claude-code-mcp.sh --scope user     # Add to user scope (default)

# After setup, use MCP servers in Claude Code:
claude mcp list              # List configured MCP servers
claude mcp add <server>      # Add a new MCP server
claude mcp remove <server>   # Remove an MCP server

# Update Exa MCP server specifically
./scripts/update-exa-mcp.sh              # Update the Exa search server

Package Synchronization

The --sync flag detects and installs new packages added to configuration files:

  • Checks homebrew/Brewfile for new formulae/casks
  • Syncs VS Code extensions from vscode/extensions.txt
  • Installs missing global npm packages from nodejs-config/global-packages.txt
  • Updates Python packages from python/requirements.txt
  • Use --sync --minimal to sync only essential packages from Brewfile.minimal

Other Scripts

./scripts/cleanup-artifacts.sh  # Periodic maintenance and cleanup
./scripts/health-check.sh       # System health verification
./scripts/setup-terminal-fonts.sh  # Install Nerd Fonts for terminal
./scripts/benchmark-vscode-extensions.sh  # Benchmark VS Code extension install times
./scripts/update.sh             # Update all tools and dependencies
./scripts/uninstall.sh          # Clean removal with backups
./scripts/rollback.sh           # Restore from previous backups

Agentic Workflow Setup

./scripts/setup-claude-agentic.sh               # System setup: plugins, LSP deps, templates
./scripts/setup-claude-agentic.sh --init [DIR]   # Bootstrap agents/skills in a project
./scripts/setup-claude-agentic.sh --check        # Check if templates are up-to-date
./scripts/setup-claude-agentic.sh --update       # Update templates + re-deploy to project
claude-init-agentic [DIR]                        # CLI alias (symlinked to ~/.local/bin/)

Agent Helper Scripts

./scripts/claude-agents/agent-benchmarks.sh      # Benchmark agent execution patterns
./scripts/claude-agents/demo-agents.sh            # Demo agent workflow coordination
./scripts/claude-agents/test-agent-workflows.sh   # Test agent workflow integration