[WIP] Refactor everything server to be more modular and use recommended APIs.

Added long-running-operation tool and improved comments in all tools

* Updated architecture.md

* In tools/
  - add.ts
  - echo.ts
  - toggle-logging.ts
  - toggle-subscriber-updates.ts
    - Add better function and inline docs

* Added tools/long-running-operation.ts
  - similar implementation as in everything v1

* In tools/index.ts
  - import registerLongRunningOperationTool
  - in registerTools
    - registerLongRunningOperationTool

src/everything/tools/toggle-subscriber-updates.ts

@@ -5,6 +5,7 @@ import {
   stopSimulatedResourceUpdates,
 } from "../resources/subscriptions.js";
 
+// Tool configuration
 const name = "toggle-subscriber-updates";
 const config = {
   title: "Toggle Subscriber Updates",
@@ -12,8 +13,23 @@ const config = {
   inputSchema: {},
 };
 
+// Track enabled clients by session id
 const clients: Set<string | undefined> = new Set<string | undefined>();
 
+/**
+ * Registers the `toggle-subscriber-updates` tool with the provided MCP server.
+ * This tool enables or disables simulated resource update notifications for a client.
+ *
+ *
+ * Toggles the state of the updates based on whether the session is already active.
+ * When enabled, the simulated resource updates are sent to the client at a regular interval.
+ * When disabled, updates are stopped for the session.
+ *
+ * The response provides feedback indicating whether simulated updates were started or stopped,
+ * including the session ID.
+ *
+ * @param {McpServer} server - The MCP server instance on which the tool is registered.
+ */
 export const registerToggleSubscriberUpdatesTool = (server: McpServer) => {
   server.registerTool(
     name,