Enforce MCP initialization phases and server capabilities

changelog.d/unreleased/4848.fixed.md

@@ -0,0 +1,25 @@
+---
+category: fixed
+issues:
+  - 4848
+affected:
+  - src/CodeIndex/Mcp/McpServer.Initialization.cs
+  - src/CodeIndex/Mcp/McpServer.MessageDispatch.Single.cs
+  - src/CodeIndex/Mcp/McpServer.Transport.ConcurrentLoop.cs
+  - src/CodeIndex/Mcp/McpServer.Transport.cs
+  - src/CodeIndex/Mcp/McpServer.cs
+  - src/CodeIndex/Mcp/McpToolHandlers.cs
+  - tests/CodeIndex.Tests/McpAuditLogTests.cs
+  - tests/CodeIndex.Tests/McpServerProtocolTests.cs
+  - tests/CodeIndex.Tests/McpServerTests.cs
+  - DEVELOPER_GUIDE.md
+  - TESTING_GUIDE.md
+---
+
+## English
+
+- **MCP sessions now enforce one initialization and protocol-correct capability direction (#4848)** — The server rejects duplicate initialization without replacing established session state, advertises only server-provided capabilities, and requests client roots after the initialized notification only when roots support was negotiated. Repeated initialized notifications coalesce into one tracked roots refresh that participates in transport teardown.
+
+## 日本語
+
+- **MCP session で初期化を1回に制限し、capability の方向を protocol に合わせました（#4848）** — 確立済み session state を置き換えずに重複初期化を拒否し、server 提供 capability だけを公開します。また、roots support を交渉した場合に限り、initialized notification 後に client roots を要求します。initialized notification が再送されても、追跡対象の roots refresh 1件に集約し、transport teardown で drain します。

src/CodeIndex/Mcp/McpServer.DatabaseLifecycle.cs

@@ -147,6 +147,7 @@ public void Dispose()
         if (_disposed)
             return;
         _disposed = true;
+        MarkSessionClosed();
         CloseSharedDb();
         var shutdownCancellationTask = RequestShutdownCancellation();
         if (shutdownCancellationTask.IsCompleted)