[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/transports/streamableHttp.ts

@@ -49,7 +49,7 @@ app.post("/mcp", async (req: Request, res: Response) => {
           transports.set(sessionId, transport);
 
           // Start simulated logging and subscription updates when a client connects
-          clientConnected(transport);
+          clientConnected(sessionId);
         },
       });