Update README with CLI Commands and Project Configuration Guide

[JeremyDev87]

Update README with CLI Commands and Project Configuration Guide

📋 Summary

Comprehensively updates the README to include CLI commands documentation, MCP resources/tools/prompts reference tables, and a complete project configuration guide. This transforms the README from a basic server description into a full user guide.

🎯 Problem

Incomplete Documentation

The previous README was minimal and didn't cover:

• How to use the new codingbuddy init CLI command
• What MCP resources, tools, and prompts are available
• How project configuration works
• How to set up and use configuration files
• How AI uses the configuration

Users had to discover these features through code or trial-and-error.

Missing User Guide

With the addition of CLI commands and project configuration (previous PRs), users needed:

• Quick start guide
• Command reference
• Configuration examples
• File structure explanation
• Usage instructions

✨ Solution

Comprehensive README Update

Transforms the README into a complete user guide covering:

1. Quick Start - Get started in seconds
2. CLI Commands - Reference table for all commands
3. MCP Resources - Available resources reference
4. MCP Tools - Available tools reference
5. MCP Prompts - Available prompts reference
6. Project Configuration - Complete configuration guide

1. Quick Start Section

Added:

• One-command example to get started
• Clear explanation of what codingbuddy init does

Before:

## Features

- **Resources**: Access rule files directly...

After:

## Quick Start

```bash
# Initialize project configuration (AI-powered)
npx codingbuddy init

# This analyzes your project and creates codingbuddy.config.js

Features

### 2. CLI Commands Table

**Added:**
- Reference table for all CLI commands
- Clear descriptions for each command

| Command | Description |
|---------|-------------|
| `codingbuddy init` | Analyze project and generate configuration |
| `codingbuddy --help` | Show help |
| `codingbuddy --version` | Show version |

### 3. MCP Resources Table

**Added:**
- Complete list of available MCP resources
- Descriptions for each resource type

| Resource | Description |
|----------|-------------|
| `config://project` | Project configuration (tech stack, architecture, language) |
| `rules://rules/core.md` | Core workflow rules |
| `rules://rules/project.md` | Project setup rules |
| `rules://agents/{name}.json` | Specialist agent definitions |

### 4. MCP Tools Table

**Added:**
- Complete list of available MCP tools
- Descriptions for each tool

| Tool | Description |
|------|-------------|
| `get_project_config` | Get project configuration settings |
| `search_rules` | Search through rules and guidelines |
| `get_agent_details` | Get detailed profile of a specialist agent |
| `parse_mode` | Parse PLAN/ACT/EVAL workflow mode (includes language setting) |

### 5. MCP Prompts Table

**Added:**
- List of available MCP prompts
- Descriptions for each prompt

| Prompt | Description |
|--------|-------------|
| `activate_agent` | Activate a specialist agent with project context |

### 6. Project Configuration Section

**Added comprehensive guide:**

#### Initialize Configuration
- Basic usage example
- All command options with examples:
  - `--format json` - Output format
  - `--force` - Overwrite existing config
  - Custom project path
  - `--api-key` - API key option

#### Configuration File
- Complete example `codingbuddy.config.js` file
- Comments explaining each section:
  - Language settings
  - Project metadata
  - Technology stack
  - Architecture pattern
  - Coding conventions
  - Testing strategy

#### File Structure
- Visual directory tree showing:
  - `codingbuddy.config.js` - Main configuration
  - `.codingignore` - Ignore patterns
  - `.codingbuddy/` - Additional context directory

#### How AI Uses Configuration
- Clear explanation of how configuration improves AI responses:
  1. Language - AI responds in configured language
  2. Tech Stack - Code examples use configured frameworks
  3. Architecture - Suggestions follow configured patterns
  4. Conventions - AI follows configured naming and style rules

### 7. Updated Environment Variables

**Added:**
- `CODINGBUDDY_PROJECT_ROOT` - Project root for config loading
- `ANTHROPIC_API_KEY` - API key for `codingbuddy init`

### 8. Updated File Paths

**Fixed:**
- `dist/main.js` → `dist/src/main.js` (reflects actual build output structure)
- Clarified difference between `codingbuddy` (CLI) and `codingbuddy-mcp` (MCP server)

### 9. Updated Title and Description

**Before:**
```markdown
# Codingbuddy Rules MCP Server

A NestJS-based Model Context Protocol (MCP) server that exposes the Multi-AI Rules System (`.ai-rules/`) to AI clients.

After:

# Codingbuddy MCP Server

A NestJS-based Model Context Protocol (MCP) server that provides AI coding assistants with project-specific context and rules.

🎯 Benefits

1. Complete User Guide

Users can now understand and use all features from the README alone.

2. Quick Onboarding

Quick Start section gets users running in seconds.

3. Reference Tables

Easy-to-scan tables for commands, resources, tools, and prompts.

4. Configuration Examples

Real-world examples show users exactly how to configure their projects.

5. Clear Structure

Well-organized sections make information easy to find.

📖 Before/After Comparison

Before

• Basic server description
• Minimal feature list
• No CLI documentation
• No configuration guide
• Outdated paths

After

• Complete user guide
• Quick start section
• CLI commands reference
• MCP resources/tools/prompts tables
• Comprehensive configuration guide
• Updated paths and environment variables

🔗 Related Documentation

• TICKET-004: CLI Init Command
• TICKET-005: MCP Config Integration
• EPIC-000: User Configuration System

✅ Acceptance Criteria

• Quick Start section added
• CLI commands documented
• MCP resources/tools/prompts tables added
• Project configuration guide added
• Configuration file examples included
• File structure explained
• Environment variables updated
• File paths corrected
• Clear distinction between CLI and MCP server commands