[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/long-running-operation.ts

@@ -0,0 +1,77 @@
+import { z } from "zod";
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
+
+// Tool input schema
+const LongRunningOperationSchema = z.object({
+  duration: z
+    .number()
+    .default(10)
+    .describe("Duration of the operation in seconds"),
+  steps: z.number().default(5).describe("Number of steps in the operation"),
+});
+
+// Tool configuration
+const name = "long-running-operation";
+const config = {
+  title: "Long Running Operation Tool",
+  description: "Demonstrates a long running operation with progress updates",
+  inputSchema: LongRunningOperationSchema,
+};
+
+/**
+ * Registers a tool to demonstrate long-running operations on the server.
+ *
+ * This function defines and registers a tool with the provided server instance that performs a
+ * long-running operation defined by a specific duration and number of steps. The progress
+ * of the operation is reported back to the client through notifications.
+ *
+ * The tool processes the operation in steps, with each step having equal duration.
+ * Progress notifications are sent back to the client at each step, if a `progressToken`
+ * is provided in the metadata. At the end of the operation, the tool returns a message
+ * indicating the completion of the operation, including the total duration and steps.
+ *
+ * @param {McpServer} server - The server instance where the tool should be registered.
+ * The server is responsible for receiving and handling requests, as well as sending progress notifications.
+ */
+export const registerLongRunningOperationTool = (server: McpServer) => {
+  server.registerTool(
+    name,
+    config,
+    async (args, extra): Promise<CallToolResult> => {
+      const validatedArgs = LongRunningOperationSchema.parse(args);
+      const { duration, steps } = validatedArgs;
+      const stepDuration = duration / steps;
+      const progressToken = extra._meta?.progressToken;
+
+      for (let i = 1; i < steps + 1; i++) {
+        await new Promise((resolve) =>
+          setTimeout(resolve, stepDuration * 1000)
+        );
+
+        if (progressToken !== undefined) {
+          await server.server.notification(
+            {
+              method: "notifications/progress",
+              params: {
+                progress: i,
+                total: steps,
+                progressToken,
+              },
+            },
+            { relatedRequestId: extra.requestId }
+          );
+        }
+      }
+
+      return {
+        content: [
+          {
+            type: "text",
+            text: `Long running operation completed. Duration: ${duration} seconds, Steps: ${steps}.`,
+          },
+        ],
+      };
+    }
+  );
+};