Fix #3234 -

"Everything Server crashes when multiple clients reconnect"

* In index.ts
  - added a variable to hold the initialize timeout
  - store the timeout in the oninitialized handler
  - clear the timeout in the cleanup callback

* In roots.ts
  - In the catch block of syncRoots, log the error to the console via .error rather than attempting to send to the client because the most probable case here is that we don't have a connection.

src/everything/server/roots.ts

@@ -63,15 +63,10 @@ export const syncRoots = async (server: McpServer, sessionId?: string) => {
           );
         }
       } catch (error) {
-        await server.sendLoggingMessage(
-          {
-            level: "error",
-            logger: "everything-server",
-            data: `Failed to request roots from client: ${
-              error instanceof Error ? error.message : String(error)
-            }`,
-          },
-          sessionId
+        console.error(
+          `Failed to request roots from client ${sessionId}: ${
+            error instanceof Error ? error.message : String(error)
+          }`
         );
       }
     };