Introduce server sessions (#198)

Introduce a `ServerSession` to manage multiple connections to the mcp
server. `Protocall` logic of the `Server` was moved to `ServerSession`,
while MCP resources logic remained in `Server`

## Motivation and Context
1. Fix the multiple connection issues reported for SSE transport
2. Avoid server duplications during configurations: currently every connection
creates a session, but the server stays single

## How Has This Been Tested?

Added `SseIntegrationTest` and `WebSocketIntegrationTest` integration
tests to check connection with single and multiple clients

## Breaking Changes

This change caused several depreciations:
1. The `Server` -> `Protocol` inheritance (which caused single
connection issue) should be removed in future releases, now, all the
methods inherited from `Protocall` marked as `Deprecated` with a
`Warning`
2. Websocket Ktor server initialization changes in order not to create
server instance per connection

## Types of changes

- [ ] Bug fix (non-breaking change which fixes an issue)
- [x] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update

## Checklist
<!-- Go over all the following points, and put an `x` in all the boxes
that apply. -->
- [x] I have read the [MCP
Documentation](https://modelcontextprotocol.io)
- [x] My code follows the repository's style guidelines
- [x] New and existing tests pass locally
- [x] I have added appropriate error handling
- [x] I have added or updated documentation as needed

## Additional context
<!-- Add any other context, implementation notes, or design decisions
-->

---------

Co-authored-by: devcrocod <devcrocod@gmail.com>

samples/kotlin-mcp-server/src/commonMain/kotlin/server.kt

@@ -23,6 +23,7 @@ import io.modelcontextprotocol.kotlin.sdk.TextResourceContents
 import io.modelcontextprotocol.kotlin.sdk.Tool
 import io.modelcontextprotocol.kotlin.sdk.server.Server
 import io.modelcontextprotocol.kotlin.sdk.server.ServerOptions
+import io.modelcontextprotocol.kotlin.sdk.server.ServerSession
 import io.modelcontextprotocol.kotlin.sdk.server.SseServerTransport
 import io.modelcontextprotocol.kotlin.sdk.server.mcp
 
@@ -94,33 +95,33 @@ fun configureServer(): Server {
 }
 
 suspend fun runSseMcpServerWithPlainConfiguration(port: Int) {
-    val servers = ConcurrentMap<String, Server>()
+    val serverSessions = ConcurrentMap<String, ServerSession>()
     println("Starting sse server on port $port. ")
     println("Use inspector to connect to the http://localhost:$port/sse")
 
+    val server = configureServer()
+
     embeddedServer(CIO, host = "0.0.0.0", port = port) {
         install(SSE)
         routing {
             sse("/sse") {
                 val transport = SseServerTransport("/message", this)
-                val server = configureServer()
 
                 // For SSE, you can also add prompts/tools/resources if needed:
                 // server.addTool(...), server.addPrompt(...), server.addResource(...)
 
-                servers[transport.sessionId] = server
+                val serverSession = server.connect(transport)
+                serverSessions[transport.sessionId] = server.connect(transport)
 
-                server.onClose {
+                serverSession.onClose {
                     println("Server closed")
-                    servers.remove(transport.sessionId)
+                    serverSessions.remove(transport.sessionId)
                 }
-
-                server.connect(transport)
             }
             post("/message") {
                 println("Received Message")
                 val sessionId: String = call.request.queryParameters["sessionId"]!!
-                val transport = servers[sessionId]?.transport as? SseServerTransport
+                val transport = serverSessions[sessionId]?.transport as? SseServerTransport
                 if (transport == null) {
                     call.respond(HttpStatusCode.NotFound, "Session not found")
                     return@post

samples/weather-stdio-server/src/main/kotlin/io/modelcontextprotocol/sample/server/McpWeatherServer.kt

@@ -114,9 +114,9 @@ fun `run mcp server`() {
     )
 
     runBlocking {
-        server.connect(transport)
+        val session = server.connect(transport)
         val done = Job()
-        server.onClose {
+        session.onClose {
             done.complete()
         }
         done.join()