Reference¶

Configuration and command reference documentation.

Configuration¶

Configuration Reference¶

Complete reference for configuring the Claude Code Extended Framework.

Table of Contents¶

CLAUDE.md Configuration
.claude/ Directory Structure
Slash Commands
Rules Configuration
MCP Server Configuration
Environment Variables

CLAUDE.md Configuration¶

The main configuration file loaded by Claude Code CLI.

Structure¶

# Claude Code Configuration - SPARC Development Environment

## 🚨 CRITICAL: CONCURRENT EXECUTION & FILE MANAGEMENT
[Critical rules and patterns]

## Project Overview
[Project description]

## SPARC Commands
[Command reference]

## Available Agents
[Agent listings]

## PM System Overview
[CCPM configuration]

## Rules
[@.claude/rules/*.md references]

Key Sections¶

Concurrent Execution Rules¶

**ABSOLUTE RULES**:
ALL operations MUST be concurrent/parallel in a single message
**NEVER save working files to root folder**
ALWAYS organize files in appropriate subdirectories

File Organization¶

**NEVER save to root folder. Use these directories:**
- `/src` - Source code files
- `/tests` - Test files
- `/docs` - Documentation
- `/config` - Configuration
- `/scripts` - Utility scripts

Agent Coordination¶

**Every Agent MUST:**
- Run hooks before/during/after work
- Update progress via memory
- Follow file-level parallelism
- Make atomic commits

.claude/ Directory Structure¶

commands/¶

Custom slash command definitions.

Structure:

.claude/commands/
├── sc/                    # SuperClaude namespace
│   ├── research.md
│   ├── implement.md
│   ├── test.md
│   └── analyze.md
└── pm/                    # PM system
    ├── prd-new.md
    ├── epic-oneshot.md
    └── issue-start.md

Command File Format:

---
name: command-name
description: Brief description
category: category-name
---

# Command Implementation

Implementation details and logic...

rules/¶

Operational rules and standards.

agent-coordination.md ¶

Rules for parallel agent execution:

# Agent Coordination

## Parallel Execution Principles
1. File-level parallelism
2. Explicit coordination
3. Fail fast
4. Human resolution

## Work Stream Assignment
Each agent gets assigned files/directories

path-standards.md ¶

Path usage standards:

# Path Standards

## Privacy Protection
- Prohibit absolute paths with usernames
- Use relative paths for project files
- Cross-project: `../project-name/file`

github-operations.md ¶

GitHub CLI operation patterns:

# GitHub Operations

## CRITICAL: Repository Protection
Check remote origin before ANY write operation

helpers/¶

Reusable shell script utilities.

Common Helpers:

setup-mcp.sh: MCP server setup
github-setup.sh: GitHub configuration
checkpoint-manager.sh: Session checkpointing
quick-start.sh: Quick setup wizard

Script Standards:

#!/usr/bin/env bash
set -euo pipefail

# All helpers follow:
# - Strict mode
# - Error handling
# - Clear documentation
# - Reusable functions

prds/¶

Product Requirement Documents.

Format:

# PRD: Feature Name

## Overview
[Description]

## Requirements
[Detailed requirements]

## Success Criteria
[Measurable outcomes]

epics/ (gitignored)¶

Epic management and decomposition.

Structure:

.claude/epics/
└── epic-{name}/
    ├── epic.md
    ├── {issue}-analysis.md
    └── updates/
        └── {issue}/
            ├── stream-A.md
            └── stream-B.md

context/¶

Project context files for session persistence.

statusline/¶

Status line configuration for CLI.

Configuration:

.claude/statusline/
├── config.json
└── scripts/
    ├── list-workspaces.sh
    └── switch-workspace.sh

Slash Commands¶

SuperClaude Commands (/sc:*)¶

/sc:research¶

Deep research with adaptive planning.

Usage:

/sc:research "[query]" [--depth quick|standard|deep|exhaustive]

Configuration: .claude/commands/sc/research.md

/sc:implement¶

Implementation with automatic agent selection.

Usage:

/sc:implement "[feature description]"

/sc:test¶

Testing with coverage analysis.

Usage:

/sc:test [--coverage] [--watch]

/sc:analyze¶

Code quality analysis.

Usage:

/sc:analyze [--focus performance|security|quality]

PM Commands (/pm:*)¶

/pm:prd-new¶

Create new Product Requirement Document.

Usage:

/pm:prd-new "[feature name]"

Output: .claude/prds/{name}.md

/pm:epic-oneshot¶

Decompose PRD into epic and sync to GitHub.

Usage:

/pm:epic-oneshot

/pm:issue-start¶

Begin work on GitHub issue.

Usage:

/pm:issue-start <issue-number>

/pm:next¶

Get next priority task.

Usage:

/pm:next

Rules Configuration¶

Enabling/Disabling Rules¶

Rules are referenced in CLAUDE.md:

## Rules
@.claude/rules/agent-coordination.md
@.claude/rules/path-standards.md
@.claude/rules/github-operations.md

Creating Custom Rules¶

Create file in .claude/rules/:

touch .claude/rules/my-rule.md

Document the rule:

# My Rule Title

Clear, actionable rules with examples.

## Section

✅ Correct examples
❌ Incorrect examples

Reference in CLAUDE.md:

@.claude/rules/my-rule.md

MCP Server Configuration¶

Claude Flow (Required)¶

claude mcp add claude-flow npx claude-flow@alpha mcp start

Configuration Options:

{
  "mcpServers": {
    "claude-flow": {
      "command": "npx",
      "args": ["claude-flow@alpha", "mcp", "start"],
      "env": {
        "NODE_ENV": "production"
      }
    }
  }
}

Ruv-Swarm (Optional)¶

claude mcp add ruv-swarm npx ruv-swarm mcp start

Features:

Enhanced swarm coordination
Advanced topology management
Performance benchmarking

Flow-Nexus (Optional)¶

claude mcp add flow-nexus npx flow-nexus@latest mcp start

Requires Registration:

npx flow-nexus@latest register
npx flow-nexus@latest login

Features:

Cloud-based execution
Template marketplace
Real-time collaboration
70+ specialized tools

Verifying MCP Servers¶

# List installed servers
claude mcp list

# Check server status
claude mcp status claude-flow

# View logs
claude mcp logs claude-flow

# Restart server
claude mcp restart claude-flow

Environment Variables¶

Optional Configuration¶

# MCP Server Settings
export CLAUDE_FLOW_ENV=production
export RUV_SWARM_PORT=8080

# PM System
export CCPM_DEFAULT_BASE_BRANCH=main
export CCPM_ISSUE_LABELS=enhancement,feature

# GitHub Integration
export GH_TOKEN=your_github_token  # If not using gh auth

# Custom Settings
export SPARC_DEFAULT_MODE=tdd
export AGENT_CONCURRENCY=5

Loading Environment¶

Create .env file (gitignored):

# .env
CLAUDE_FLOW_ENV=production
CCPM_DEFAULT_BASE_BRANCH=main

Load in session:

source .env

GitHub Automation Configuration¶

Dependabot¶

File: .github/dependabot.yml

version: 2
updates:
  - package-ecosystem: "github-actions"
    directory: "/"
    schedule:
      interval: "weekly"

Workflows¶

Shellcheck: .github/workflows/shellcheck.yml

Triggers: Push/PR to .sh files
Validates: Script syntax and best practices

Health Check: .github/workflows/health-check.yml

Triggers: Weekly + file changes
Validates: Community health files

Auto Label: .github/workflows/auto-label.yml

Triggers: Issue/PR creation
Labels: By title, content, files

Stale: .github/workflows/stale.yml

Triggers: Daily cron
Manages: Stale issues/PRs

CODEOWNERS¶

File: .github/CODEOWNERS

# Default owners
*       @kvnloo

# Documentation
*.md    @kvnloo
/docs/  @kvnloo

# Scripts (security-sensitive)
*.sh    @kvnloo @security-team

Customization Examples¶

Adding a New Command Category¶

Create directory:

mkdir .claude/commands/myapp

Add command:

cat > .claude/commands/myapp/deploy.md <<EOF
---
name: deploy
description: Deploy application
category: myapp
---

# Deploy Command
Implementation...
EOF

Use command:

/myapp:deploy

Custom Agent Configuration¶

Define in CLAUDE.md:

## Custom Agents

### my-agent
- Type: specialized
- Purpose: Custom task automation
- Configuration: .claude/agents/my-agent.yml

Workflow Customization¶

Copy and modify existing workflow:

cp .github/workflows/shellcheck.yml .github/workflows/my-check.yml
# Edit my-check.yml

Configuration Validation¶

Check Configuration¶

# Validate YAML syntax
yamllint .github/workflows/*.yml

# Check bash scripts
shellcheck scripts/*.sh .claude/helpers/*.sh

# Verify markdown
markdownlint docs/*.md

Test Configuration¶

# Test MCP servers
claude mcp status

# Test commands (if available)
/sc:help

# Test scripts
./scripts/checkpoint.sh --dry-run

Troubleshooting Configuration¶

Common Issues¶

MCP server not found:

claude mcp list  # Check if registered
claude mcp add claude-flow npx claude-flow@alpha mcp start

Command not recognized:

Check .claude/commands/ structure
Verify CLAUDE.md loads properly
Ensure file format is correct

Rules not applying:

Check @.claude/rules/*.md references in CLAUDE.md
Verify markdown syntax
Reload Claude Code CLI

For more information:

Getting Started
Architecture Overview
Script Reference

Reference¶

Configuration¶

Configuration Reference¶

Table of Contents¶

CLAUDE.md Configuration¶

Structure¶

Key Sections¶

Concurrent Execution Rules¶

File Organization¶

Agent Coordination¶

.claude/ Directory Structure¶

commands/¶

rules/¶

agent-coordination.md¶

path-standards.md¶

github-operations.md¶

helpers/¶

prds/¶

epics/ (gitignored)¶

context/¶

statusline/¶

Slash Commands¶

SuperClaude Commands (/sc:*)¶

/sc:research¶

/sc:implement¶

/sc:test¶

/sc:analyze¶

PM Commands (/pm:*)¶

/pm:prd-new¶

/pm:epic-oneshot¶

/pm:issue-start¶

/pm:next¶

Rules Configuration¶

Enabling/Disabling Rules¶

Creating Custom Rules¶

MCP Server Configuration¶

Claude Flow (Required)¶

Ruv-Swarm (Optional)¶

Flow-Nexus (Optional)¶

Verifying MCP Servers¶

Environment Variables¶

Optional Configuration¶

Loading Environment¶

GitHub Automation Configuration¶

Dependabot¶

Workflows¶

CODEOWNERS¶

Customization Examples¶

Adding a New Command Category¶

Custom Agent Configuration¶

Workflow Customization¶

Configuration Validation¶

Check Configuration¶

Test Configuration¶

Troubleshooting Configuration¶

Common Issues¶

agent-coordination.md ¶

path-standards.md ¶

github-operations.md ¶