[Doc] Move Custom methods to the bottom of the README

Custom methods are an advanced feature and may not be appropriate for the top of the README.md.
Move them to the bottom of the page.

Only sections were reorganized with headings. No content was changed.

Author: koic

README.md

@@ -54,57 +54,6 @@ It implements the Model Context Protocol specification, handling model context r
 - `completion/complete` - Returns autocompletion suggestions for prompt arguments and resource URIs
 - `sampling/createMessage` - Requests LLM completion from the client (server-to-client)
 
-### Custom Methods
-
-The server allows you to define custom JSON-RPC methods beyond the standard MCP protocol methods using the `define_custom_method` method:
-
-```ruby
-server = MCP::Server.new(name: "my_server")
-
-# Define a custom method that returns a result
-server.define_custom_method(method_name: "add") do |params|
-  params[:a] + params[:b]
-end
-
-# Define a custom notification method (returns nil)
-server.define_custom_method(method_name: "notify") do |params|
-  # Process notification
-  nil
-end
-```
-
-**Key Features:**
-
-- Accepts any method name as a string
-- Block receives the request parameters as a hash
-- Can handle both regular methods (with responses) and notifications
-- Prevents overriding existing MCP protocol methods
-- Supports instrumentation callbacks for monitoring
-
-**Usage Example:**
-
-```ruby
-# Client request
-{
-  "jsonrpc": "2.0",
-  "id": 1,
-  "method": "add",
-  "params": { "a": 5, "b": 3 }
-}
-
-# Server response
-{
-  "jsonrpc": "2.0",
-  "id": 1,
-  "result": 8
-}
-```
-
-**Error Handling:**
-
-- Raises `MCP::Server::MethodAlreadyDefinedError` if trying to override an existing method
-- Supports the same exception reporting and instrumentation as standard methods
-
 ### Sampling
 
 The Model Context Protocol allows servers to request LLM completions from clients through the `sampling/createMessage` method.
@@ -502,6 +451,59 @@ When configured, sessions that receive no HTTP requests for this duration are au
 transport = MCP::Server::Transports::StreamableHTTPTransport.new(server, session_idle_timeout: 1800)
 ```
 
+### Advanced
+
+#### Custom Methods
+
+The server allows you to define custom JSON-RPC methods beyond the standard MCP protocol methods using the `define_custom_method` method:
+
+```ruby
+server = MCP::Server.new(name: "my_server")
+
+# Define a custom method that returns a result
+server.define_custom_method(method_name: "add") do |params|
+  params[:a] + params[:b]
+end
+
+# Define a custom notification method (returns nil)
+server.define_custom_method(method_name: "notify") do |params|
+  # Process notification
+  nil
+end
+```
+
+**Key Features:**
+
+- Accepts any method name as a string
+- Block receives the request parameters as a hash
+- Can handle both regular methods (with responses) and notifications
+- Prevents overriding existing MCP protocol methods
+- Supports instrumentation callbacks for monitoring
+
+**Usage Example:**
+
+```ruby
+# Client request
+{
+  "jsonrpc": "2.0",
+  "id": 1,
+  "method": "add",
+  "params": { "a": 5, "b": 3 }
+}
+
+# Server response
+{
+  "jsonrpc": "2.0",
+  "id": 1,
+  "result": 8
+}
+```
+
+**Error Handling:**
+
+- Raises `MCP::Server::MethodAlreadyDefinedError` if trying to override an existing method
+- Supports the same exception reporting and instrumentation as standard methods
+
 ### Unsupported Features (to be implemented in future versions)
 
 - Resource subscriptions