[codex] preserve runtime MCP servers across client capability refresh

codex-rs/app-server/README.md

@@ -232,7 +232,7 @@ Example with notification opt-out:
 - `mcpServer/oauth/login` — start an OAuth login for a configured MCP server; returns an `authorization_url` and later emits `mcpServer/oauthLogin/completed` once the browser flow finishes.
 - `tool/requestUserInput` — prompt the user with 1–3 short questions for a tool call and return their answers (experimental).
 - `config/mcpServer/reload` — reload MCP server config from disk and queue a refresh for loaded threads (applied on each thread's next active turn); returns `{}`. Use this after editing `config.toml` without restarting the server.
-- `mcpServerStatus/list` — enumerate configured MCP servers with their tools, auth status, server info, plus resources/resource templates for `full` detail; supports optional `threadId` and cursor+limit pagination. If `threadId` is omitted, the server reads from the latest global config directly. If `detail` is omitted, the server defaults to `full`.
+- `mcpServerStatus/list` — enumerate configured MCP servers with their tools, auth status, server info, plus resources/resource templates for `full` detail; supports optional `threadId` and cursor+limit pagination. With `threadId`, the response is a point-in-time snapshot of the MCP manager generation currently installed for that thread. If `threadId` is omitted, the server reads from the latest global config directly. If `detail` is omitted, the server defaults to `full`.
 - `mcpServer/resource/read` — read a resource from a configured MCP server by optional `threadId`, `server`, and `uri`, returning text/blob resource `contents`. If `threadId` is omitted, the server reads from the latest MCP config directly.
 - `mcpServer/tool/call` — call a tool on a thread's configured MCP server by `threadId`, `server`, `tool`, optional `arguments`, and optional `_meta`, returning the MCP tool result.
 - `windowsSandbox/setupStart` — start Windows sandbox setup for the selected mode (`elevated` or `unelevated`); accepts an optional absolute `cwd` to target setup for a specific workspace, returns `{ started: true }` immediately, and later emits `windowsSandbox/setupCompleted`.

codex-rs/app-server/tests/suite/v2/mcp_server_status.rs

@@ -214,7 +214,7 @@ url = "{mcp_server_url}/mcp"
 }
 
 #[tokio::test]
-async fn mcp_server_status_list_never_advertises_uninstalled_codex_apps() -> Result<()> {
+async fn mcp_server_status_list_reflects_installed_manager_generation() -> Result<()> {
     let server = create_mock_responses_server_sequence_unchecked(Vec::new()).await;
     let (apps_server_url, apps_server_handle) = start_apps_mcp_server("calendar_lookup").await?;
     let codex_home = TempDir::new()?;

codex-rs/core/src/codex_thread.rs

@@ -593,7 +593,7 @@ impl CodexThread {
         self.codex.session.runtime_mcp_config(config).await
     }
 
-    /// Returns the MCP inventory installed for this thread.
+    /// Returns a point-in-time snapshot of the MCP inventory installed for this thread.
     pub async fn mcp_server_status_snapshot(
         &self,
         config: &crate::config::Config,

codex-rs/core/src/session/mcp.rs

@@ -444,8 +444,9 @@ impl Session {
         }
 
         let config = self.get_config().await;
+        let mcp_servers = self.runtime_mcp_servers(config.as_ref()).await;
         let refresh_config = McpServerRefreshConfig {
-            mcp_servers: serde_json::to_value(config.mcp_servers.get())?,
+            mcp_servers: serde_json::to_value(mcp_servers)?,
             mcp_oauth_credentials_store_mode: serde_json::to_value(
                 config.mcp_oauth_credentials_store_mode,
             )?,

codex-rs/core/tests/suite/mcp_refresh_cleanup.rs

@@ -6,6 +6,10 @@ use std::time::Duration;
 use codex_config::DEFAULT_MCP_SERVER_ENVIRONMENT_ID;
 use codex_config::types::McpServerConfig;
 use codex_config::types::McpServerTransportConfig;
+use codex_mcp::CODEX_APPS_MCP_SERVER_NAME;
+use codex_protocol::mcp::CallToolResult;
+use core_test_support::apps_test_server::AppsTestServer;
+use core_test_support::apps_test_server::apps_enabled_builder;
 use core_test_support::process::process_is_alive;
 use core_test_support::process::wait_for_pid_file;
 use core_test_support::process::wait_for_process_exit;
@@ -14,6 +18,62 @@ use core_test_support::skip_if_no_network;
 use core_test_support::stdio_server_bin;
 use core_test_support::test_codex::test_codex;
 use core_test_support::wait_for_mcp_server;
+use pretty_assertions::assert_eq;
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn elicitation_capability_refresh_preserves_host_owned_codex_apps() -> anyhow::Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = responses::start_mock_server().await;
+    let apps_server = AppsTestServer::mount(&server).await?;
+    let fixture = apps_enabled_builder(apps_server.chatgpt_base_url)
+        .build(&server)
+        .await?;
+    wait_for_mcp_server(&fixture.codex, CODEX_APPS_MCP_SERVER_NAME).await?;
+
+    responses::mount_sse_once(
+        &server,
+        responses::sse(vec![
+            responses::ev_response_created("resp-1"),
+            responses::ev_assistant_message("msg-1", "done"),
+            responses::ev_completed("resp-1"),
+        ]),
+    )
+    .await;
+    fixture
+        .codex
+        .set_openai_form_elicitation_support(/*supported*/ true)
+        .await?;
+    fixture.submit_turn("refresh MCP servers").await?;
+
+    let result = fixture
+        .codex
+        .call_mcp_tool(
+            CODEX_APPS_MCP_SERVER_NAME,
+            "calendar_create_event",
+            Some(serde_json::json!({
+                "title": "Team sync",
+                "starts_at": "2026-06-24T17:00:00Z",
+            })),
+            /*meta*/ None,
+        )
+        .await?;
+    assert_eq!(
+        result,
+        CallToolResult {
+            content: vec![serde_json::json!({
+                "type": "text",
+                "text": "called calendar_create_event for Team sync at 2026-06-24T17:00:00Z with ",
+            })],
+            structured_content: Some(serde_json::json!({ "_codex_apps": null })),
+            is_error: Some(false),
+            meta: None,
+        }
+    );
+
+    fixture.codex.shutdown_and_wait().await?;
+    Ok(())
+}
 
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
 async fn refresh_shuts_down_superseded_mcp_stdio_server() -> anyhow::Result<()> {