Update Readme.md and documentation

Readme.md

@@ -4,20 +4,20 @@
 
 A comprehensive WordPress plugin that implements the [Model Context Protocol (MCP)](https://modelcontextprotocol.io) to expose WordPress functionality through standardized interfaces. This plugin enables AI models and applications to interact with WordPress sites securely using multiple transport protocols and enterprise-grade authentication.
 
-## Features
+## ✨ Features
 
--   **Dual Transport Protocols**: STDIO and HTTP-based (Streamable) transports
--   **JWT Authentication**: Secure token-based authentication with management UI
--   **Admin Interface**: React-based token management and settings dashboard
--   **AI-Friendly APIs**: JSON-RPC 2.0 compliant endpoints for AI integration
--   **Extensible Architecture**: Custom tools, resources, and prompts support
--   **WordPress Feature API**: Adapter for standardized WordPress functionality
--   **Experimental REST API CRUD Tools**: Generic tools for any WordPress REST API endpoint
--   **Comprehensive Testing**: 200+ test cases covering all protocols and authentication
--   **High Performance**: Optimized routing and caching mechanisms
--   **Enterprise Security**: Multi-layer authentication and audit logging
+-   🔄 **Dual Transport Protocols**: STDIO and HTTP-based (Streamable) transports
+-   🔐 **JWT Authentication**: Secure token-based authentication with management UI
+-   🎛️ **Admin Interface**: React-based token management and settings dashboard
+-   🤖 **AI-Friendly APIs**: JSON-RPC 2.0 compliant endpoints for AI integration
+-   🏗️ **Extensible Architecture**: Custom tools, resources, and prompts support
+-   🔌 **WordPress Feature API**: Adapter for standardized WordPress functionality
+-   🧪 **Experimental REST API CRUD Tools**: Generic tools for any WordPress REST API endpoint
+-   🧪 **Comprehensive Testing**: 200+ test cases covering all protocols and authentication
+-   ⚡ **High Performance**: Optimized routing and caching mechanisms
+-   🔒 **Enterprise Security**: Multi-layer authentication and audit logging
 
-## Architecture
+## 🏗️ Architecture
 
 The plugin implements a dual transport architecture:
 
@@ -42,7 +42,7 @@ WordPress MCP Plugin
 | **STDIO**      | `/wp/v2/wpmcp`            | WordPress-style | JWT + App Passwords | Legacy compatibility |
 | **Streamable** | `/wp/v2/wpmcp/streamable` | JSON-RPC 2.0    | JWT only            | Modern AI clients    |
 
-## Installation
+## 🚀 Installation
 
 ### Quick Install
 
@@ -61,7 +61,7 @@ composer install --no-dev
 npm install && npm run build
 ```
 
-## Authentication Setup
+## 🔐 Authentication Setup
 
 ### JWT Token Generation
 
@@ -164,7 +164,7 @@ npx @modelcontextprotocol/inspector \
 }
 ```
 
-## Usage
+## 🎯 Usage
 
 ### With MCP Clients
 
@@ -196,9 +196,9 @@ The streamable transport provides a direct JSON-RPC 2.0 compliant endpoint, whil
 | `prompts/list`   | List available prompts   | Both              |
 | `prompts/get`    | Get prompt template      | Both              |
 
-### Experimental REST API CRUD Tools
+### 🧪 Experimental REST API CRUD Tools
 
-**EXPERIMENTAL FEATURE**: This functionality is experimental and may change or be removed in future versions.
+⚠️ **EXPERIMENTAL FEATURE**: This functionality is experimental and may change or be removed in future versions.
 
 When enabled via `Settings > WordPress MCP > Enable REST API CRUD Tools`, the plugin provides three powerful generic tools that can interact with any WordPress REST API endpoint:
 
@@ -232,7 +232,7 @@ When enabled via `Settings > WordPress MCP > Enable REST API CRUD Tools`, the pl
 -   **Standards Compliant**: Uses standard HTTP methods (GET, POST, PATCH, DELETE)
 -   **Permission Safe**: Inherits WordPress user capabilities and respects endpoint permissions
 
-## Development
+## 🔧 Development
 
 ### Project Structure
 
@@ -260,17 +260,18 @@ You can extend the MCP functionality by adding custom tools through your own plu
 <?php
 declare(strict_types=1);
 
-namespace Automattic\WordpressMcp\Tools;
+use Automattic\WordpressMcp\Core\RegisterMcpTool;
 
 class MyCustomTool {
-    public function register(): void {
-        add_action('wp_mcp_register_tools', [$this, 'register_tool']);
+    public function __construct() {
+        add_action('wordpress_mcp_init', [$this, 'register_tools']);
     }
 
-    public function register_tool(): void {
-        WPMCP()->register_tool([
+    public function register_tools(): void {
+        new RegisterMcpTool([
             'name' => 'my_custom_tool',
             'description' => 'My custom tool description',
+            'type' => 'read', // or 'action' for tools that modify data
             'inputSchema' => [
                 'type' => 'object',
                 'properties' => [
@@ -279,13 +280,19 @@ class MyCustomTool {
                 'required' => ['param1']
             ],
             'callback' => [$this, 'execute'],
+            'permission_callback' => [$this, 'check_permissions'], // optional
         ]);
     }
 
     public function execute(array $args): array {
         // Your tool logic here
         return ['result' => 'success'];
     }
+
+    public function check_permissions(): bool {
+        // Optional: Add custom permission checks
+        return current_user_can('edit_posts');
+    }
 }
 ```
 
@@ -297,15 +304,15 @@ You can extend the MCP functionality by adding custom resources through your own
 <?php
 declare(strict_types=1);
 
-namespace Automattic\WordpressMcp\Resources;
+use Automattic\WordpressMcp\Core\RegisterMcpResource;
 
 class MyCustomResource {
-    public function register(): void {
-        add_action('wp_mcp_register_resources', [$this, 'register_resource']);
+    public function __construct() {
+        add_action('wordpress_mcp_init', [$this, 'register_resources']);
     }
 
-    public function register_resource(): void {
-        WPMCP()->register_resource([
+    public function register_resources(): void {
+        new RegisterMcpResource([
             'uri' => 'custom://my-resource',
             'name' => 'My Custom Resource',
             'description' => 'Custom resource description',
@@ -350,7 +357,7 @@ npm run build
 npm run start
 ```
 
-## Security
+## 🔒 Security
 
 ### Best Practices
 
@@ -364,14 +371,14 @@ npm run start
 
 ### Security Features
 
--   JWT signature validation
--   Token expiration and revocation
--   User capability inheritance
--   Secure secret key generation
--   Audit logging for security events
--   Protection against malformed requests
+-   ✅ JWT signature validation
+-   ✅ Token expiration and revocation
+-   ✅ User capability inheritance
+-   ✅ Secure secret key generation
+-   ✅ Audit logging for security events
+-   ✅ Protection against malformed requests
 
-## Testing Coverage
+## 📊 Testing Coverage
 
 The plugin includes extensive testing:
 
@@ -383,7 +390,7 @@ The plugin includes extensive testing:
 
 View detailed testing documentation in [`tests/README.md`](tests/README.md).
 
-## Configuration
+## 🔧 Configuration
 
 ### Environment Variables
 
@@ -413,9 +420,9 @@ The plugin provides granular control over CRUD operations:
 -   **Enable Delete Tools**: ⚠️ Allow DELETE operations via MCP tools (use with caution)
 -   **Enable REST API CRUD Tools**: 🧪 Enable experimental generic REST API access tools
 
-**Security Note**: Delete operations can permanently remove data. Only enable delete tools if you trust all users with MCP access.
+⚠️ **Security Note**: Delete operations can permanently remove data. Only enable delete tools if you trust all users with MCP access.
 
-## Contributing
+## 🤝 Contributing
 
 We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md).
 
@@ -427,7 +434,7 @@ We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.
 4. Set up WordPress test environment
 5. Run tests with `vendor/bin/phpunit`
 
-## Documentation
+## 📚 Documentation
 
 -   **Documentation Overview**: [docs/README.md](docs/README.md)
 -   **Client Setup Guide**: [docs/client-setup.md](docs/client-setup.md)
@@ -438,19 +445,18 @@ We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.
 -   **Register MCP Tools**: [docs/register-mcp-tools.md](docs/register-mcp-tools.md)
 -   **Register MCP Prompts**: [docs/register-mcp-prompt.md](docs/register-mcp-prompt.md)
 -   **Register MCP Resources**: [docs/register-mcp-resources.md](docs/register-mcp-resources.md)
--   **Troubleshooting Guide**: [docs/troubleshooting.md](docs/troubleshooting.md)
 -   **Testing Guide**: [tests/README.md](tests/README.md)
 
-## Support
+## 🆘 Support
 
 For support and questions:
 
--   **Documentation**: [docs/README.md](docs/README.md)
--   **Bug Reports**: [GitHub Issues](https://github.com/Automattic/wordpress-mcp/issues)
--   **Discussions**: [GitHub Discussions](https://github.com/Automattic/wordpress-mcp/discussions)
--   **Contact**: Reach out to the maintainers
+-   📖 **Documentation**: [docs/README.md](docs/README.md)
+-   🐛 **Bug Reports**: [GitHub Issues](https://github.com/Automattic/wordpress-mcp/issues)
+-   💬 **Discussions**: [GitHub Discussions](https://github.com/Automattic/wordpress-mcp/discussions)
+-   ✉️ **Contact**: Reach out to the maintainers
 
-## License
+## 📄 License
 
 This project is licensed under the [GPL v2 or later](LICENSE).