diff --git a/README.md b/README.md
index d46bc35..2ee409b 100644
--- a/README.md
+++ b/README.md
@@ -34,8 +34,8 @@ Fast MCP solves all these problems by providing a clean, Ruby-focused implementa
 - 🚀 **Real-time Updates** - Subscribe to changes for interactive applications
 - 🎯 **Dynamic Filtering** - Control tool/resource access based on request context (permissions, API versions, etc.)
 
-
 ## 💎 What Makes FastMCP Great
+
 ```ruby
 # Define tools for AI models to use
 server = FastMcp::Server.new(name: 'popular-users', version: '1.0.0')
@@ -109,7 +109,7 @@ Control which tools and resources are available based on request context:
 class AdminTool < FastMcp::Tool
   tags :admin, :dangerous
   description "Perform admin operations"
-  
+
   def call
     # Admin only functionality
   end
@@ -118,7 +118,7 @@ end
 # Filter tools based on user permissions
 server.filter_tools do |request, tools|
   user_role = request.params['role']
-  
+
   case user_role
   when 'admin'
     tools # Admins see all tools
@@ -131,6 +131,7 @@ end
 ```
 
 ### 🚂 Fast Ruby on Rails implementation
+
 ```shell
 bundle add fast-mcp
 bin/rails generate fast_mcp:install
@@ -155,20 +156,13 @@ FastMcp.mount_in_rails(
   # allowed_ips: ['127.0.0.1', '::1']
   # authenticate: true,       # Uncomment to enable authentication
   # auth_token: 'your-token' # Required if authenticate: true
-) do |server|
-  Rails.application.config.after_initialize do
-    # FastMcp will automatically discover and register:
-    # - All classes that inherit from ApplicationTool (which uses ActionTool::Base)
-    # - All classes that inherit from ApplicationResource (which uses ActionResource::Base)
-    server.register_tools(*ApplicationTool.descendants)
-    server.register_resources(*ApplicationResource.descendants)
-    # alternatively, you can register tools and resources manually:
-    # server.register_tool(MyTool)
-    # server.register_resource(MyResource)
-  end
-end
+  # tools_dir: Rails.root.join('app/tools'), # This is the default directory for tools
+  # resources_dir: Rails.root.join('app/resources'), # This is the default directory for resources
+)
 ```
+
 The install script will also:
+
 - add app/resources folder
 - add app/tools folder
 - add app/tools/sample_tool.rb
@@ -187,7 +181,7 @@ These are automatically set up in Rails applications. You can use either naming
 
 ```ruby
 # Using Rails-style naming:
-class MyTool < ActionTool::Base
+class MyTool < ApplicationTool
   description "My awesome tool"
 
   arguments do
@@ -219,7 +213,10 @@ class ApplicationResource < ActionResource::Base
 end
 ```
 
+Tools and resources are automatically registered in the server when they are inherited from ApplicationTool and ApplicationResource. Inheriting off of ActionTool::Base or FastMcp::Tool will not require you to register them manually.
+
 ### Easy Sinatra setup
+
 I'll let you check out the dedicated [sinatra integration docs](./docs/sinatra_integration.md).
 
 ## 🚀 Quick Start
@@ -282,17 +279,21 @@ Clone this project, then give it a go !
 ```shell
 npx @modelcontextprotocol/inspector examples/server_with_stdio_transport.rb
 ```
+
 Or to test with an SSE transport using a rack middleware:
+
 ```shell
 npx @modelcontextprotocol/inspector examples/rack_middleware.rb
 ```
 
 Or to test over SSE with an authenticated rack middleware:
+
 ```shell
 npx @modelcontextprotocol/inspector examples/authenticated_rack_middleware.rb
 ```
 
 You can test your custom implementation with the official MCP inspector by using:
+
 ```shell
 # Test with a stdio transport:
 npx @modelcontextprotocol/inspector path/to/your_ruby_file.rb
@@ -321,6 +322,7 @@ end
 ### Integrating with Claude Desktop
 
 Add your server to your Claude Desktop configuration at:
+
 - macOS: `~/Library/Application Support/Claude/claude_desktop_config.json`
 - Windows: `%APPDATA%\Claude\claude_desktop_config.json`
 
@@ -329,28 +331,27 @@ Add your server to your Claude Desktop configuration at:
   "mcpServers": {
     "my-great-server": {
       "command": "ruby",
-      "args": [
-        "/Users/path/to/your/awesome/fast-mcp/server.rb"
-      ]
+      "args": ["/Users/path/to/your/awesome/fast-mcp/server.rb"]
     }
   }
 }
 ```
 
 ## How to add a MCP server to Claude, Cursor, or other MCP clients?
+
 Please refer to [configuring_mcp_clients](docs/configuring_mcp_clients.md)
 
 ## 📊 Supported Specifications
 
-| Feature | Status |
-|---------|--------|
-| ✅ **JSON-RPC 2.0** | Full implementation for communication |
-| ✅ **Tool Definition & Calling** | Define and call tools with rich argument types |
-| ✅ **Resource & Resource Templates Management** | Create, read, update, and subscribe to resources |
-| ✅ **Transport Options** | STDIO, HTTP, and SSE for flexible integration |
-| ✅ **Framework Integration** | Rails, Sinatra, Hanami, and any Rack-compatible framework |
-| ✅ **Authentication** | Secure your AI endpoints with token authentication |
-| ✅ **Schema Support** | Full JSON Schema for tool arguments with validation |
+| Feature                                         | Status                                                    |
+| ----------------------------------------------- | --------------------------------------------------------- |
+| ✅ **JSON-RPC 2.0**                             | Full implementation for communication                     |
+| ✅ **Tool Definition & Calling**                | Define and call tools with rich argument types            |
+| ✅ **Resource & Resource Templates Management** | Create, read, update, and subscribe to resources          |
+| ✅ **Transport Options**                        | STDIO, HTTP, and SSE for flexible integration             |
+| ✅ **Framework Integration**                    | Rails, Sinatra, Hanami, and any Rack-compatible framework |
+| ✅ **Authentication**                           | Secure your AI endpoints with token authentication        |
+| ✅ **Schema Support**                           | Full JSON Schema for tool arguments with validation       |
 
 ## 🗺️ Use Cases
 
@@ -406,6 +407,7 @@ FastMcp.authenticated_rack_middleware(app,
 Check out the [examples directory](examples) for more detailed examples:
 
 - **🔨 Basic Examples**:
+
   - [Simple Server](examples/server_with_stdio_transport.rb)
   - [Tool Examples](examples/tool_examples.rb)
 
diff --git a/lib/fast_mcp.rb b/lib/fast_mcp.rb
index de75bf1..f305f69 100644
--- a/lib/fast_mcp.rb
+++ b/lib/fast_mcp.rb
@@ -7,6 +7,9 @@
 module FastMcp
   class << self
     attr_accessor :server
+
+    attr_accessor :tools_dir
+    attr_accessor :resources_dir
   end
 end
 
@@ -102,18 +105,20 @@ def self.register_tools(*tools)
 
   # Register a resource with the MCP server
   # @param resource [FastMcp::Resource] The resource to register
+  # @option options [Boolean] :notify Whether to notify subscribers about the list change
   # @return [FastMcp::Resource] The registered resource
-  def self.register_resource(resource)
+  def self.register_resource(resource, notify: true)
     self.server ||= FastMcp::Server.new(name: 'mcp-server', version: '1.0.0')
-    self.server.register_resource(resource)
+    self.server.register_resource(resource, notify: notify)
   end
 
   # Register multiple resources at once
   # @param resources [Array<FastMcp::Resource>] The resources to register
+  # @option options [Boolean] :notify Whether to notify subscribers about the list change
   # @return [Array<FastMcp::Resource>] The registered resources
-  def self.register_resources(*resources)
+  def self.register_resources(*resources, notify: true)
     self.server ||= FastMcp::Server.new(name: 'mcp-server', version: '1.0.0')
-    self.server.register_resources(*resources)
+    self.server.register_resources(*resources, notify: notify)
   end
 
   # Mount the MCP middleware in a Rails application
@@ -127,6 +132,8 @@ def self.register_resources(*resources)
   # @option options [Logger] :logger The logger to use
   # @option options [Boolean] :authenticate Whether to use authentication
   # @option options [String] :auth_token The authentication token
+  # @option options [String] :tools_dir The directory to load tools from
+  # @option options [String] :resources_dir The directory to load resources from
   # @option options [Array<String,Regexp>] :allowed_origins List of allowed origins for DNS rebinding protection
   # @yield [server] A block to configure the server
   # @yieldparam server [FastMcp::Server] The server to configure
@@ -148,6 +155,9 @@ def self.mount_in_rails(app, options = {})
     options[:logger] = logger
     options[:allowed_origins] = allowed_origins
 
+    self.tools_dir = options.delete(:tools_dir) || Rails.root.join('app/tools')
+    self.resources_dir = options.delete(:resources_dir) || Rails.root.join('app/resources')
+
     # Create or get the server
     self.server = FastMcp::Server.new(name: name, version: version, logger: logger)
     yield self.server if block_given?
diff --git a/lib/generators/fast_mcp/install/templates/fast_mcp_initializer.rb b/lib/generators/fast_mcp/install/templates/fast_mcp_initializer.rb
index e2eac52..0531869 100644
--- a/lib/generators/fast_mcp/install/templates/fast_mcp_initializer.rb
+++ b/lib/generators/fast_mcp/install/templates/fast_mcp_initializer.rb
@@ -28,15 +28,6 @@
   # allowed_ips: ['127.0.0.1', '::1']
   # authenticate: true,       # Uncomment to enable authentication
   # auth_token: 'your-token', # Required if authenticate: true
-) do |server|
-  Rails.application.config.after_initialize do
-    # FastMcp will automatically discover and register:
-    # - All classes that inherit from ApplicationTool (which uses ActionTool::Base)
-    # - All classes that inherit from ApplicationResource (which uses ActionResource::Base)
-    server.register_tools(*ApplicationTool.descendants)
-    server.register_resources(*ApplicationResource.descendants)
-    # alternatively, you can register tools and resources manually:
-    # server.register_tool(MyTool)
-    # server.register_resource(MyResource)
-  end
-end
+  # tools_dir: Rails.root.join('app/tools'), # This is the default directory for tools
+  # resources_dir: Rails.root.join('app/resources'), # This is the default directory for resources
+)
diff --git a/lib/mcp/railtie.rb b/lib/mcp/railtie.rb
index 6938b89..0222fce 100644
--- a/lib/mcp/railtie.rb
+++ b/lib/mcp/railtie.rb
@@ -4,14 +4,14 @@
 require 'fileutils'
 require_relative '../mcp/server'
 
-# Create ActionTool and ActionResource modules at load time
-unless defined?(ActionTool)
+# Create ActionTool and ActionResource modules when using Rails
+if !defined?(ActionTool) && defined?(Rails)
   module ::ActionTool
     Base = FastMcp::Tool
   end
 end
 
-unless defined?(ActionResource)
+if !defined?(ActionResource) && defined?(Rails)
   module ::ActionResource
     Base = FastMcp::Resource
   end
@@ -20,19 +20,29 @@ module ::ActionResource
 module FastMcp
   # Railtie for integrating Fast MCP with Rails applications
   class Railtie < Rails::Railtie
-    # Add tools and resources directories to autoload paths
-    initializer 'fast_mcp.setup_autoload_paths' do |app|
-      app.config.autoload_paths += %W[
-        #{app.root}/app/tools
-        #{app.root}/app/resources
-      ]
+
+    # Auto-register all tools and resources after the application is fully loaded
+    config.after_initialize do |app|
+      FastMcp::Railtie.eager_load_and_register_tools_and_resources
     end
 
     # Auto-register all tools and resources after the application is fully loaded
-    config.after_initialize do
-      # Load all files in app/tools and app/resources directories
-      Dir[Rails.root.join('app', 'tools', '**', '*.rb')].each { |f| require f }
-      Dir[Rails.root.join('app', 'resources', '**', '*.rb')].each { |f| require f }
+    config.to_prepare do
+      FastMcp.server.clear_tools!
+      FastMcp.server.clear_resources!
+
+      FastMcp::Railtie.eager_load_and_register_tools_and_resources
+    end
+
+    def self.eager_load_and_register_tools_and_resources
+      Rails.autoloaders.main.eager_load_dir(FastMcp.tools_dir)
+      Rails.autoloaders.main.eager_load_dir(FastMcp.resources_dir)
+
+      tools = ApplicationTool.descendants.sort_by(&:name)
+      resources = ApplicationResource.descendants.sort_by(&:name)
+
+      FastMcp.server.register_tools(*tools)
+      FastMcp.server.register_resources(*resources, notify: false)
     end
 
     # Add rake tasks
diff --git a/lib/mcp/server.rb b/lib/mcp/server.rb
index 029808b..71a4da8 100644
--- a/lib/mcp/server.rb
+++ b/lib/mcp/server.rb
@@ -60,22 +60,30 @@ def register_tool(tool)
       tool.server = self
     end
 
+    # Clear all tools from the server
+    def clear_tools!
+      @tools = {}
+    end
+
     # Register multiple resources at once
     # @param resources [Array<Resource>] Resources to register
-    def register_resources(*resources)
+    # @option options [Boolean] :notify Whether to notify subscribers about the list change
+    def register_resources(*resources, notify: true)
       resources.each do |resource|
-        register_resource(resource)
+        register_resource(resource, notify: notify)
       end
     end
 
     # Register a resource with the server
-    def register_resource(resource)
+    # @param resource [Resource] Resource to register
+    # @option options [Boolean] :notify Whether to notify subscribers about the list change
+    def register_resource(resource, notify: true)
       @resources << resource
 
       @logger.debug("Registered resource: #{resource.resource_name} (#{resource.uri})")
       resource.server = self
       # Notify subscribers about the list change
-      notify_resource_list_changed if @transport
+      notify_resource_list_changed if @transport && notify
 
       resource
     end
@@ -97,6 +105,11 @@ def remove_resource(uri)
       end
     end
 
+    # Clear all resources from the server
+    def clear_resources!
+      @resources = []
+    end
+
     # Start the server using stdio transport
     def start
       @logger.transport = :stdio