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

Adding simulated logging and refactoring subscriptions to not need to track transports

* Updated architecture.md

* In server/index.ts
  - remove import of Transport
  - import beginSimulatedLogging and stopSimulatedLogging
  - in clientConnected()
    - change argument to sessionId? instead of transport
    - add call to beginSimulatedLogging
    - send server and sessionId to beginSimulatedResourceUpdates and beginSimulatedLogging
  - in cleanup()
    - add call to stopSimulatedLogging passing sessionId

* Added server/logging.ts
  - Initialize logsUpdateIntervals to Map session ID to the interval for sending logging messages to the client
  - in beginSimulatedLogging()
    - create an array of logging meesages, customized with the sessionId if present
    - if the interval for the sessionId hasn't been set, create one, calling server.sendLoggingMessage with a random message to the client each time the interval elapses
  - in stopSimulatedLogging()
    - if a logging interval exists for the sessionId, clear it and remove it

* In subscriptions.ts
  - remove import of Transport
  - remove transports map
  - in beginSimulatedResourceUpdates()
    - change arguments to server and sessionId
    - check for the subsUpdateInterval for the session
    - remove all transport storage and interaction
    - instead use the server to send the notification
 - in stopSimulatedResourceUpdates()
   - remove management of transports map

* In sse.ts and streamableHttp.ts
  - when calling clientConnected, pass sessionId instead of transport

* In stdio.ts,
- when calling clientConnected, pass nothing instead of transport

* In subscriptions.ts
  - updated inline doc

src/everything/resources/subscriptions.ts

@@ -1,5 +1,4 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { Transport } from "@modelcontextprotocol/sdk/shared/transport.js";
 import {
   SubscribeRequestSchema,
   UnsubscribeRequestSchema,
@@ -11,12 +10,6 @@ const subscriptions: Map<string, Set<string | undefined>> = new Map<
   Set<string | undefined>
 >();
 
-// Track transport by session id
-const transports: Map<string | undefined, Transport> = new Map<
-  string | undefined,
-  Transport
->();
-
 // Interval to send notifications to subscribers
 const subsUpdateIntervals: Map<string | undefined, NodeJS.Timeout | undefined> =
   new Map<string | undefined, NodeJS.Timeout | undefined>();
@@ -105,35 +98,28 @@ export const setSubscriptionHandlers = (server: McpServer) => {
 
 /**
  * Starts the process of simulating resource updates and sending server notifications
- * to subscribed clients at regular intervals. If the update interval is already active,
- * invoking this function will not start another interval.
+ * to the client for the resources they are subscribed to. If the update interval is
+ * already active, invoking this function will not start another interval.
  *
- * Note that tracking and sending updates on the transport of the subscriber allows for
- * multiple clients to be connected and independently receive only updates about their
- * own subscriptions. Had we used `server.notification` instead, all clients would
- * receive updates for all subscriptions.
- *
- * @param {Transport} transport - The transport to the subscriber
+ * @param server
+ * @param sessionId
  */
-export const beginSimulatedResourceUpdates = (transport: Transport) => {
-  const sessionId = transport?.sessionId;
-  if (!transports.has(sessionId)) {
-    // Store the transport
-    transports.set(sessionId, transport);
-
-    // Set the interval to send notifications to the subscribers
+export const beginSimulatedResourceUpdates = (
+  server: McpServer,
+  sessionId: string | undefined
+) => {
+  if (!subsUpdateIntervals.has(sessionId)) {
+    // Set the interval to send resource update notifications to this client
     subsUpdateIntervals.set(
       sessionId,
       setInterval(async () => {
-        // Send notifications to all subscribers for each URI
+        // Search all URIs for ones this client is subscribed to
         for (const uri of subscriptions.keys()) {
           const subscribers = subscriptions.get(uri) as Set<string | undefined>;
 
-          // Get the transport for the subscriber and send the notification
+          // If this client is subscribed, send the notification
           if (subscribers.has(sessionId)) {
-            const transport = transports.get(sessionId) as Transport;
-            await transport.send({
-              jsonrpc: "2.0",
+            await server.server.notification({
               method: "notifications/resources/updated",
               params: { uri },
             });
@@ -162,8 +148,4 @@ export const stopSimulatedResourceUpdates = (sessionId?: string) => {
     clearInterval(subsUpdateInterval);
     subsUpdateIntervals.delete(sessionId);
   }
-  // Remove transport for the session
-  if (transports.has(sessionId)) {
-    transports.delete(sessionId);
-  }
 };