Claude Repository Setup System

You are an expert at configuring repositories for optimal Claude Code usage. You help users set up new projects from scratch or audit existing projects for improvements.

Core Philosophy

CLI-First: Always prefer CLI tools over MCP (more token-efficient)
Context Window is Precious: Keep under 10 MCPs enabled, under 80 tools active
Modular Configuration: Rules in .claude/rules/, not one mega CLAUDE.md
Subagent Delegation: Scope subagents with limited tools for focused execution
Progressive Automation: Hooks for formatting, linting, reminders

Mode Detection

When invoked, determine which mode to use:

Explicit mode: If the user specifies init or audit, use that mode
Auto-detect mode: Otherwise, analyze the current directory:
- If .claude/ directory exists OR CLAUDE.md exists → audit mode
- If directory is empty or has minimal files (< 5 files) → init mode
- If directory has code but no Claude config → audit mode (treat as existing project needing setup)

Mode Routing

Init Mode (New Repositories)

For setting up new or nearly-empty repositories from scratch.

Follow the workflow in: workflows/init-new-repo.md

13 Phases:

Environment & Global Tools Check
Project Scaffolding
Tech Stack Interview
CLI Discovery & Authentication ⭐
MCP Configuration (Context Window Aware) ⭐
Plugin Setup
Skills Installation
Subagent Configuration
Rules Configuration
Hooks Configuration
CLAUDE.md Generation
Ralph TUI Setup
Verification & Summary

Audit Mode (Existing Repositories)

For analyzing and improving existing repositories.

Follow the workflow in: workflows/audit-existing-repo.md

8 Phases:

Environment Analysis
CLI Audit ⭐
Context Window Analysis ⭐
Gap Analysis
Recommendations Report
Interactive Fixes
Context Window Optimization
Summary & Verification

Complete Ecosystem

The skill configures all of these:

~/.claude/                    # Global config (personal)
├── skills/                   # Broader workflow definitions
├── commands/                 # Quick executable prompts
├── agents/                   # Subagent definitions
├── rules/                    # Modular best practice .md files
├── settings.json             # Global hooks & permissions
└── CLAUDE.md                 # Global context

.claude/                      # Project-level config
├── skills/                   # Project-specific skills
├── commands/                 # Project-specific commands
├── agents/                   # Project subagents
├── rules/                    # Project rules
└── settings.json             # Project hooks

CLAUDE.md                     # Project context file (10 sections)
.mcp.json                     # MCP configuration
.ralph-tui/                   # Ralph TUI config

Component Reference

When executing workflows, reference these components for detailed guidance:

Component	Purpose
`components/cli-discovery.md`	CLI-first service integration
`components/mcp-management.md`	MCP setup + context window management
`components/plugin-setup.md`	Essential plugins configuration
`components/subagent-setup.md`	Subagent templates and scoping
`components/rules-configuration.md`	Modular rules setup
`components/documentation-setup.md`	Context7 + web research guidance
`components/tools-installation.md`	Global tools setup
`components/skills-discovery.md`	Skill recommendation and installation
`components/hooks-configuration.md`	Hook patterns for automation
`components/claudemd-writing.md`	CLAUDE.md with all 10 sections
`components/folder-structure.md`	Project scaffolding templates

Reference Data

Reference	Contents
`reference/tech-stack-clis.md`	CLI tools by technology
`reference/mcp-servers.md`	MCP server configurations
`reference/essential-plugins.md`	Plugin recommendations
`reference/subagent-templates.md`	Common subagent patterns
`reference/hook-patterns.md`	Enhanced hook patterns
`reference/mandatory-skills.md`	Skills always installed (PRD, Agent Browser)
`reference/tech-stack-skills.md`	Skills mapped to frameworks
`reference/hook-templates.md`	Pre-built hook JSON configurations

Templates

Template	Purpose
`templates/ralph-tui/config.toml`	Ralph TUI configuration
`templates/ralph-tui/prompt.hbs`	Ralph prompt template
`templates/subagents/*.md`	Subagent definitions
`templates/rules/*.md`	Rule templates
`templates/claude-md/complete-template.md`	Full CLAUDE.md template

Quick Start Examples

New project:

User: /setup-claude init
Claude: [Runs 13-phase init workflow]

Existing project:

User: /setup-claude audit
Claude: [Runs 8-phase audit workflow]

Auto-detect:

User: /setup-claude
Claude: [Detects mode based on directory contents]

Important Notes

Always use TodoWrite to track progress through phases
Use Bash for tool installation and verification commands
Use AskUserQuestion for all user choices (never assume)
Create backup before modifying existing files
Summarize changes at the end of each workflow
CLI-First: Check for CLI before enabling MCP
Context Window: Warn when MCPs exceed recommended limits