Give hosted Codex Apps an independent MCP protocol opt-in (#44318)

## Why

Hosted Codex Apps shared the `mcp_2026_07_28` protocol setting with other MCP servers, preventing independent protocol selection.

## What changed

- Add `features.codex_apps_mcp_2026_07_28`, disabled by default, for the host-owned HTTP `codex_apps` server. Enabling it attempts 2026-07-28 discovery with Legacy fallback.
- Keep other servers, including third-party registrations with Apps-like names or URLs and local stdio servers, governed by `mcp_2026_07_28`.
- Support the new flag through `experimentalFeature/enablement/set` and refresh protocol settings in existing sessions. Track protocol mode per server when deciding whether to reuse connections.

## Testing

Add coverage for independent feature and protocol selection, hosted event-stream protocol selection, standalone Legacy defaults and discovery fallback, and runtime enablement refreshing an existing app-server thread.

GitOrigin-RevId: 640e8e251f0c45e5f4829cc2b73c3082cf42f715

codex-rs/app-server/README.md

@@ -22,6 +22,18 @@ late proofs after the approval is canceled or resolved. Only one native worker
 runs per app-server; if an OS call remains active after cancellation or timeout,
 subsequent local operations return `failed/providerError` until that worker exits.
 
+# Hosted Codex Apps MCP protocol
+
+The host-owned HTTP `codex_apps` server uses Legacy by default in app-server and
+standalone Codex. To discover the 2026-07-28 protocol, set
+`codex_apps_mcp_2026_07_28 = true` under `[features]`, or send a true runtime
+override via `experimentalFeature/enablement/set`. Discovery falls back to Legacy
+when the server does not support it. Explicit config takes precedence.
+The dedicated setting does not apply to third-party HTTP or local `codex_app`
+stdio servers. The existing `mcp_2026_07_28` flag still governs eligible other
+servers, regardless of whether their names or URLs resemble hosted Apps.
+App-server does not persist this selection.
+
 # Thread removal
 
 `thread/archive` and `thread/delete` reject attempts to remove a live internal

codex-rs/app-server/src/request_processors/config_processor.rs

@@ -65,6 +65,7 @@ const BACKGROUND_PAGINATED_ROLLOUT_MIGRATION_FEATURE: &str =
 const SUPPORTED_EXPERIMENTAL_FEATURE_ENABLEMENT: &[&str] = &[
     "auth_elicitation",
     BACKGROUND_PAGINATED_ROLLOUT_MIGRATION_FEATURE,
+    "codex_apps_mcp_2026_07_28",
     "mcp_2026_07_28",
     "memories",
     "mentions_v2",

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

@@ -0,0 +1,128 @@
+//! Verifies that a hosted Apps protocol opt-in refreshes an existing app-server thread.
+
+use std::collections::BTreeMap;
+
+use anyhow::Result;
+use app_test_support::ChatGptAuthFixture;
+use app_test_support::MockResponsesConfig;
+use app_test_support::TestAppServer;
+use app_test_support::write_chatgpt_auth;
+use codex_app_server_protocol::ClientRequest;
+use codex_app_server_protocol::ExperimentalFeatureEnablementSetParams;
+use codex_app_server_protocol::ExperimentalFeatureEnablementSetResponse;
+use codex_app_server_protocol::McpServerToolCallParams;
+use codex_app_server_protocol::McpServerToolCallResponse;
+use codex_app_server_protocol::ThreadStartParams;
+use codex_config::types::AuthCredentialsStoreMode;
+use codex_features::Feature;
+use core_test_support::apps_test_server::AppsTestServer;
+use core_test_support::responses;
+use pretty_assertions::assert_eq;
+use serde_json::Value;
+use serde_json::json;
+use tempfile::TempDir;
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn enabling_hosted_apps_protocol_refreshes_an_existing_thread() -> Result<()> {
+    let server = responses::start_mock_server().await;
+    let apps = AppsTestServer::mount(&server).await?;
+    let codex_home = TempDir::new()?;
+    MockResponsesConfig::new(&server.uri())
+        .with_root_config(&format!("chatgpt_base_url = \"{}\"", apps.chatgpt_base_url))
+        .enable_feature(Feature::Apps)
+        .write(codex_home.path())?;
+    write_chatgpt_auth(
+        codex_home.path(),
+        ChatGptAuthFixture::new("chatgpt-token")
+            .account_id("account-123")
+            .chatgpt_user_id("user-123")
+            .chatgpt_account_id("account-123"),
+        AuthCredentialsStoreMode::File,
+    )?;
+    let mut app_server = TestAppServer::builder()
+        .with_codex_home(codex_home.path())
+        .build_initialized()
+        .await?;
+    let thread_id = app_server
+        .start_thread(ThreadStartParams::default())
+        .await?
+        .thread
+        .id;
+
+    let call_tool = |thread_id: String| McpServerToolCallParams {
+        thread_id,
+        server: "codex_apps".to_string(),
+        tool: "calendar_list_events".to_string(),
+        arguments: Some(json!({ "query": "hello" })),
+        meta: None,
+    };
+    let _: McpServerToolCallResponse = app_server
+        .request(|request_id| ClientRequest::McpServerToolCall {
+            request_id,
+            params: call_tool(thread_id.clone()),
+        })
+        .await?;
+    let methods = server
+        .received_requests()
+        .await
+        .expect("mock server should capture Apps MCP startup requests")
+        .into_iter()
+        .filter(|request| request.url.path() == "/api/codex/ps/mcp")
+        .filter_map(|request| {
+            let body: Value = serde_json::from_slice(&request.body).ok()?;
+            body.get("method")?.as_str().map(str::to_string)
+        })
+        .collect::<Vec<_>>();
+    assert_eq!(
+        methods,
+        [
+            "initialize",
+            "notifications/initialized",
+            "tools/list",
+            "tools/call"
+        ]
+    );
+
+    let enablement = BTreeMap::from([("codex_apps_mcp_2026_07_28".to_string(), true)]);
+    let request_id = app_server
+        .send_experimental_feature_enablement_set_request(ExperimentalFeatureEnablementSetParams {
+            enablement: enablement.clone(),
+        })
+        .await?;
+    let response: ExperimentalFeatureEnablementSetResponse =
+        app_server.read_response(request_id).await?;
+    assert_eq!(response.enablement, enablement);
+
+    let _: McpServerToolCallResponse = app_server
+        .request(|request_id| ClientRequest::McpServerToolCall {
+            request_id,
+            params: call_tool(thread_id),
+        })
+        .await?;
+    let methods = server
+        .received_requests()
+        .await
+        .expect("mock server should capture Apps MCP startup requests")
+        .into_iter()
+        .filter(|request| request.url.path() == "/api/codex/ps/mcp")
+        .filter_map(|request| {
+            let body: Value = serde_json::from_slice(&request.body).ok()?;
+            body.get("method")?.as_str().map(str::to_string)
+        })
+        .collect::<Vec<_>>();
+    assert_eq!(
+        methods,
+        [
+            "initialize",
+            "notifications/initialized",
+            "tools/list",
+            "tools/call",
+            "server/discover",
+            "initialize",
+            "notifications/initialized",
+            "tools/list",
+            "tools/call",
+        ]
+    );
+    Ok(())
+}

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

@@ -1341,9 +1341,9 @@ impl ServerHandler for ToolAppsMcpServer {
             .get("threadId")
             .and_then(|value| value.as_str())
             .unwrap_or_default();
-        let client_capabilities = context.peer.peer_info().map(|request| {
+        let client_capabilities = context.client_capabilities().map(|capabilities| {
             json!({
-                "extensions": request.capabilities.extensions.clone().unwrap_or_default(),
+                "extensions": capabilities.extensions.unwrap_or_default(),
             })
         });
 

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

@@ -53,6 +53,7 @@ mod marketplace_add;
 mod marketplace_remove;
 mod marketplace_upgrade;
 mod mcp_event_stream;
+mod mcp_protocol_default;
 mod mcp_resource;
 mod mcp_resource_origin;
 mod mcp_server_elicitation;

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

@@ -83,9 +83,8 @@ impl ServerHandler for VerificationServer {
     ) -> Result<CallToolResponse, rmcp::ErrorData> {
         assert_eq!(
             context
-                .peer
+                .client_capabilities()
-                .peer_info()
+                .and_then(|capabilities| capabilities.extensions)
-                .and_then(|info| info.capabilities.extensions.clone())
                 .and_then(|extensions| extensions.get(OPENAI_ELICITATION_EXTENSION_ID).cloned())
                 .map(Value::Object),
             Some(json!({"userVerification": {}})),

codex-rs/codex-mcp/src/connection_manager.rs

@@ -160,6 +160,7 @@ impl Drop for McpServerConnection {
 #[derive(Clone)]
 struct McpServerView {
     connection: Arc<McpServerConnection>,
+    protocol_mode: crate::McpProtocolMode,
     metadata: McpServerMetadata,
     tool_filter: ToolFilter,
     tool_timeout: Option<Duration>,
@@ -186,7 +187,6 @@ pub(crate) struct McpConnectionSet {
     servers: HashMap<String, McpServerView>,
     pub(crate) event_stream_connection: Option<Arc<EventStreamConnectionSettings>>,
     disabled_servers: Vec<String>,
-    protocol_mode: crate::McpProtocolMode,
     required_servers: Vec<String>,
     optional_startup_deadline: OnceLock<tokio::time::Instant>,
     tool_plugin_provenance: Arc<ToolPluginProvenance>,
@@ -231,7 +231,8 @@ impl McpConnectionSet {
         let codex_home = config.codex_home.clone();
         let prefix_mcp_tool_names = config.prefix_mcp_tool_names;
         let non_prefixed_mcp_tool_servers = config.non_prefixed_mcp_tool_servers.clone();
-        let protocol_mode = config.protocol_mode;
+        let default_protocol_mode = config.protocol_mode;
+        let host_owned_apps_protocol_mode = config.host_owned_apps_protocol_mode;
         let client_elicitation_capability = config.client_elicitation_capability.clone();
         let tool_plugin_provenance = crate::mcp::tool_plugin_provenance(&config);
         let auth = auth.as_ref();
@@ -313,6 +314,15 @@ impl McpConnectionSet {
             };
             let metadata = McpServerMetadata::from(&server);
             let configured_config = server.config().clone();
+            let protocol_mode = if is_host_owned_codex_apps
+                && matches!(
+                    &configured_config.transport,
+                    McpServerTransportConfig::StreamableHttp { .. }
+                ) {
+                host_owned_apps_protocol_mode
+            } else {
+                default_protocol_mode
+            };
             let configured_tool_filter = ToolFilter::from_config(&configured_config);
             let startup_timeout = configured_config
                 .startup_timeout_sec
@@ -445,13 +455,11 @@ impl McpConnectionSet {
                     && !connection.client.cancel_token.is_cancelled()
                     && previous_view.catalog_item_limit == catalog_item_limit
                     && expected_protocol_mode.is_some()
-                    && reusable_previous
+                    && previous_view.protocol_mode == protocol_mode;
-                        .is_some_and(|previous| previous.protocol_mode == protocol_mode);
                 let unchanged_auth_failure = if connection.identity.as_ref()
                     == Some(&connection_identity)
                     && connection_identity.oauth_store_was_contended
-                    && reusable_previous
+                    && previous_view.protocol_mode == protocol_mode
-                        .is_some_and(|previous| previous.protocol_mode == protocol_mode)
                     && connection.client.startup_complete.load(Ordering::Acquire)
                 {
                     connection
@@ -480,6 +488,7 @@ impl McpConnectionSet {
                         server_name.clone(),
                         McpServerView {
                             connection,
+                            protocol_mode,
                             metadata,
                             tool_filter: configured_tool_filter,
                             tool_timeout: configured_tool_timeout,
@@ -614,6 +623,7 @@ impl McpConnectionSet {
                         startup_trigger,
                         _diagnostics_guard: LIVE_CONNECTIONS.track(),
                     }),
+                    protocol_mode,
                     metadata,
                     tool_filter: configured_tool_filter,
                     tool_timeout: configured_tool_timeout,
@@ -738,7 +748,6 @@ impl McpConnectionSet {
             servers,
             event_stream_connection,
             disabled_servers,
-            protocol_mode,
             required_servers,
             optional_startup_deadline: OnceLock::new(),
             tool_plugin_provenance,
@@ -797,7 +806,6 @@ impl McpConnectionSet {
             servers: HashMap::new(),
             event_stream_connection: None,
             disabled_servers: Vec::new(),
-            protocol_mode: crate::McpProtocolMode::Legacy,
             required_servers: Vec::new(),
             optional_startup_deadline: OnceLock::new(),
             tool_plugin_provenance: Arc::new(ToolPluginProvenance::default()),

codex-rs/codex-mcp/src/connection_manager_tests.rs

@@ -106,7 +106,6 @@ impl McpConnectionSet {
             servers: HashMap::new(),
             event_stream_connection: None,
             disabled_servers: Vec::new(),
-            protocol_mode: crate::McpProtocolMode::Legacy,
             required_servers: Vec::new(),
             optional_startup_deadline: OnceLock::new(),
             tool_plugin_provenance: Arc::new(ToolPluginProvenance::default()),
@@ -132,6 +131,7 @@ impl McpConnectionSet {
             name,
             McpServerView {
                 tool_filter: ToolFilter::default(),
+                protocol_mode: crate::McpProtocolMode::Legacy,
                 connection: Arc::new(McpServerConnection {
                     identity: None,
                     client,
@@ -1985,6 +1985,97 @@ fn codex_apps_env_bearer_token_bypasses_shared_tools_cache() {
     ));
 }
 
+#[tokio::test]
+async fn hosted_apps_protocol_mode_is_independent_of_generic_mode() -> anyhow::Result<()> {
+    let codex_home = tempdir()?;
+    let server_config: McpServerConfig =
+        serde_json::from_value(serde_json::json!({ "url": "http://127.0.0.1:1/ps/mcp" }))?;
+
+    for (generic_mode, hosted_mode) in [
+        (
+            crate::McpProtocolMode::Legacy,
+            crate::McpProtocolMode::V20260728,
+        ),
+        (
+            crate::McpProtocolMode::V20260728,
+            crate::McpProtocolMode::Legacy,
+        ),
+    ] {
+        let mut config = crate::mcp::tests::test_mcp_config(codex_home.path().to_path_buf());
+        config.protocol_mode = generic_mode;
+        config.host_owned_apps_protocol_mode = hosted_mode;
+        let mut catalog = crate::ResolvedMcpCatalog::builder();
+        catalog.register(crate::McpServerRegistration::from_hosted_apps(
+            "test-host",
+            /*contribution_order*/ 0,
+            server_config.clone(),
+        ));
+        catalog.register(crate::McpServerRegistration::from_config(
+            "third_party".to_string(),
+            server_config.clone(),
+        ));
+        config.mcp_server_catalog = catalog.build();
+
+        let startup_cancellation_token = CancellationToken::new();
+        startup_cancellation_token.cancel();
+        let manager = McpConnectionSet::new(
+            /*previous*/ None,
+            McpPublicationGate::already_published(),
+            McpRuntimeInput {
+                startup_policy: McpStartupPolicy::Eager,
+                config: Arc::new(config),
+                plugins_available: false,
+                ready_selected_capability_roots: Vec::new(),
+                mcp_servers: HashMap::from([
+                    (
+                        CODEX_APPS_MCP_SERVER_NAME.to_string(),
+                        EffectiveMcpServer::configured(server_config.clone()),
+                    ),
+                    (
+                        "third_party".to_string(),
+                        EffectiveMcpServer::configured(server_config.clone()),
+                    ),
+                ]),
+                submit_id: "protocol-mode-scope".to_string(),
+                tx_event: None,
+                startup_cancellation_token,
+                runtime_context: McpRuntimeContext::new(
+                    Arc::new(environment_manager_without_environments()),
+                    codex_home.path().to_path_buf(),
+                ),
+                codex_apps_tools_cache: ConnectorRuntimeManager::default(),
+                tool_catalog_cache: McpToolCatalogCache::default(),
+                codex_apps_tools_cache_key: ConnectorRuntimeContextKey::personal(
+                    /*account_id*/ None, /*chatgpt_user_id*/ None,
+                ),
+                client_mcp_extensions: ClientMcpExtensions::default(),
+                auth: None,
+                auth_manager: None,
+                elicitation_reviewer: None,
+                elicitation_lifecycle: None,
+            },
+            ElicitationRequestRouter::default(),
+        )
+        .await;
+
+        assert_eq!(
+            manager.servers[CODEX_APPS_MCP_SERVER_NAME].protocol_mode,
+            hosted_mode
+        );
+        assert_eq!(manager.servers["third_party"].protocol_mode, generic_mode);
+        assert_eq!(
+            manager
+                .event_stream_connection
+                .as_ref()
+                .expect("hosted Apps event stream")
+                .protocol_mode,
+            hosted_mode
+        );
+    }
+
+    Ok(())
+}
+
 #[tokio::test]
 async fn codex_apps_extension_does_not_share_host_owned_tools_cache() -> anyhow::Result<()> {
     let codex_home = tempdir()?;
@@ -2005,6 +2096,7 @@ async fn codex_apps_extension_does_not_share_host_owned_tools_cache() -> anyhow:
     let server_config: McpServerConfig =
         serde_json::from_value(serde_json::json!({ "url": "http://127.0.0.1:1" }))?;
     let mut config = crate::mcp::tests::test_mcp_config(codex_home.path().to_path_buf());
+    config.host_owned_apps_protocol_mode = crate::McpProtocolMode::V20260728;
     let mut catalog = crate::ResolvedMcpCatalog::builder();
     catalog.register(crate::McpServerRegistration::from_extension(
         CODEX_APPS_MCP_SERVER_NAME.to_string(),
@@ -2049,6 +2141,11 @@ async fn codex_apps_extension_does_not_share_host_owned_tools_cache() -> anyhow:
     .await;
 
     let client = manager.test_client(CODEX_APPS_MCP_SERVER_NAME);
+    assert_eq!(
+        manager.servers[CODEX_APPS_MCP_SERVER_NAME].protocol_mode,
+        crate::McpProtocolMode::Legacy,
+        "an ordinary extension named codex_apps must not inherit the hosted protocol default"
+    );
     assert!(
         client.codex_apps_tools_cache_context.is_none(),
         "an extension must not receive the host-owned Apps cache"
@@ -4907,6 +5004,7 @@ async fn manager_with_reusable_ready_server(
     manager.servers.insert(
         "docs".to_string(),
         McpServerView {
+            protocol_mode: crate::McpProtocolMode::Legacy,
             connection: Arc::new(McpServerConnection {
                 identity: Some(reusable_server_identity("docs", config, runtime_context)),
                 client: create_ready_async_managed_client(tools).await,
@@ -5226,6 +5324,7 @@ async fn reconciliation_reuses_connection_without_relisting_regular_tools() -> a
     previous.servers.insert(
         "docs".to_string(),
         McpServerView {
+            protocol_mode: crate::McpProtocolMode::Legacy,
             connection: Arc::new(McpServerConnection {
                 identity: Some(reusable_server_identity("docs", &config, &runtime_context)),
                 client: AsyncManagedClient {

codex-rs/codex-mcp/src/mcp/mod.rs

@@ -172,8 +172,10 @@ pub struct McpConfig {
     pub prefix_mcp_tool_names: bool,
     /// MCP servers whose model-visible tool namespaces omit the `mcp__` prefix.
     pub non_prefixed_mcp_tool_servers: Vec<String>,
-    /// Protocol compatibility policy captured when this MCP configuration is created.
+    /// Protocol mode for servers other than the host-owned Codex Apps registration.
     pub protocol_mode: McpProtocolMode,
+    /// Independent protocol mode for the trusted, HTTP Codex Apps registration.
+    pub host_owned_apps_protocol_mode: McpProtocolMode,
     /// Client-side elicitation capabilities advertised during MCP initialization.
     pub client_elicitation_capability: ElicitationCapability,
     /// Resolved MCP registrations keyed by logical server name.

codex-rs/codex-mcp/src/mcp/mod_tests.rs

@@ -42,6 +42,7 @@ pub(crate) fn test_mcp_config(codex_home: PathBuf) -> McpConfig {
         prefix_mcp_tool_names: true,
         non_prefixed_mcp_tool_servers: Vec::new(),
         protocol_mode: McpProtocolMode::Legacy,
+        host_owned_apps_protocol_mode: McpProtocolMode::Legacy,
         client_elicitation_capability: ElicitationCapability::default(),
         mcp_server_catalog: ResolvedMcpCatalog::default(),
         connector_snapshot: codex_connectors::ConnectorSnapshot::default(),

codex-rs/core/config.schema.json

@@ -701,6 +701,9 @@
             "code_mode_prewarm": {
               "type": "boolean"
             },
+            "codex_apps_mcp_2026_07_28": {
+              "type": "boolean"
+            },
             "codex_git_commit": {
               "type": "boolean"
             },
@@ -6190,6 +6193,9 @@
         "code_mode_prewarm": {
           "type": "boolean"
         },
+        "codex_apps_mcp_2026_07_28": {
+          "type": "boolean"
+        },
         "codex_git_commit": {
           "type": "boolean"
         },

codex-rs/core/src/config/config_tests.rs

@@ -7018,7 +7018,7 @@ async fn to_mcp_config_flows_mcp_tool_prefix_from_feature() -> std::io::Result<(
 }
 
 #[tokio::test]
-async fn to_mcp_config_flows_mcp_2026_feature_from_config() -> std::io::Result<()> {
+async fn to_mcp_config_flows_independent_mcp_2026_features() -> std::io::Result<()> {
     let codex_home = TempDir::new()?;
     let mut config = Config::load_from_base_config_with_overrides(
         ConfigToml::default(),
@@ -7030,13 +7030,42 @@ async fn to_mcp_config_flows_mcp_2026_feature_from_config() -> std::io::Result<(
         plugins_manager_for_config(&config, auth_manager_from_optional_auth(/*auth*/ None));
 
     let mcp_config = config.to_mcp_config(&plugins_manager).await;
-    assert_eq!(mcp_config.protocol_mode, codex_mcp::McpProtocolMode::Legacy);
+    assert_eq!(
+        (
+            mcp_config.protocol_mode,
+            mcp_config.host_owned_apps_protocol_mode,
+        ),
+        (
+            codex_mcp::McpProtocolMode::Legacy,
+            codex_mcp::McpProtocolMode::Legacy,
+        )
+    );
 
     let _ = config.features.enable(Feature::Mcp20260728);
     let mcp_config = config.to_mcp_config(&plugins_manager).await;
     assert_eq!(
-        mcp_config.protocol_mode,
+        (
-        codex_mcp::McpProtocolMode::V20260728
+            mcp_config.protocol_mode,
+            mcp_config.host_owned_apps_protocol_mode,
+        ),
+        (
+            codex_mcp::McpProtocolMode::V20260728,
+            codex_mcp::McpProtocolMode::Legacy,
+        )
+    );
+
+    let _ = config.features.disable(Feature::Mcp20260728);
+    let _ = config.features.enable(Feature::CodexAppsMcp20260728);
+    let mcp_config = config.to_mcp_config(&plugins_manager).await;
+    assert_eq!(
+        (
+            mcp_config.protocol_mode,
+            mcp_config.host_owned_apps_protocol_mode,
+        ),
+        (
+            codex_mcp::McpProtocolMode::Legacy,
+            codex_mcp::McpProtocolMode::V20260728,
+        )
     );
 
     Ok(())

codex-rs/core/src/config/mod.rs

@@ -1792,6 +1792,11 @@ impl Config {
                 Vec::new()
             },
             protocol_mode: self.mcp_protocol_mode(),
+            host_owned_apps_protocol_mode: if self.features.enabled(Feature::CodexAppsMcp20260728) {
+                McpProtocolMode::V20260728
+            } else {
+                McpProtocolMode::Legacy
+            },
             client_elicitation_capability: if self.features.enabled(Feature::AuthElicitation) {
                 ElicitationCapability::new()
                     .with_form(FormElicitationCapability::new())

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

@@ -1931,6 +1931,18 @@ impl Session {
             config.mcp_servers = next_config.mcp_servers.clone();
             config.mcp_optional_startup_grace = next_config.mcp_optional_startup_grace;
             config.mcp_oauth_credentials_store_mode = next_config.mcp_oauth_credentials_store_mode;
+            if let Err(err) = config.features.set_enabled(
+                Feature::Mcp20260728,
+                next_config.features.enabled(Feature::Mcp20260728),
+            ) {
+                warn!("failed to refresh MCP protocol config: {err}");
+            }
+            if let Err(err) = config.features.set_enabled(
+                Feature::CodexAppsMcp20260728,
+                next_config.features.enabled(Feature::CodexAppsMcp20260728),
+            ) {
+                warn!("failed to refresh Codex Apps MCP protocol config: {err}");
+            }
             if let Err(err) = config.features.set_enabled(
                 Feature::SecretAuthStorage,
                 next_config.features.enabled(Feature::SecretAuthStorage),
@@ -1987,6 +1999,18 @@ impl Session {
         config.mcp_servers = next_config.mcp_servers;
         config.mcp_optional_startup_grace = next_config.mcp_optional_startup_grace;
         config.mcp_oauth_credentials_store_mode = next_config.mcp_oauth_credentials_store_mode;
+        if let Err(err) = config.features.set_enabled(
+            Feature::Mcp20260728,
+            next_config.features.enabled(Feature::Mcp20260728),
+        ) {
+            warn!("failed to refresh MCP protocol config: {err}");
+        }
+        if let Err(err) = config.features.set_enabled(
+            Feature::CodexAppsMcp20260728,
+            next_config.features.enabled(Feature::CodexAppsMcp20260728),
+        ) {
+            warn!("failed to refresh Codex Apps MCP protocol config: {err}");
+        }
         if let Err(err) = config.features.set_enabled(
             Feature::SecretAuthStorage,
             next_config.features.enabled(Feature::SecretAuthStorage),

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

@@ -0,0 +1,64 @@
+//! Verifies the hosted Apps protocol choice in standalone Codex sessions.
+
+use codex_features::Feature;
+use codex_login::CodexAuth;
+use codex_mcp::CODEX_APPS_MCP_SERVER_NAME;
+use core_test_support::apps_test_server::AppsTestServer;
+use core_test_support::responses;
+use core_test_support::skip_if_no_network;
+use core_test_support::test_codex::test_codex;
+use core_test_support::wait_for_mcp_server;
+use pretty_assertions::assert_eq;
+use serde_json::Value;
+use test_case::test_case;
+
+#[derive(Clone, Copy)]
+enum HostedProtocolSetting {
+    Default,
+    Enabled,
+}
+
+#[test_case(HostedProtocolSetting::Default, &["initialize", "notifications/initialized", "tools/list"]; "defaults_to_legacy")]
+#[test_case(HostedProtocolSetting::Enabled, &["server/discover", "initialize", "notifications/initialized", "tools/list"]; "opt_in_discovers_and_falls_back_to_legacy")]
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn standalone_codex_apps_respects_protocol_setting(
+    setting: HostedProtocolSetting,
+    expected_methods: &[&str],
+) -> anyhow::Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = responses::start_mock_server().await;
+    let apps_base_url = AppsTestServer::mount(&server).await?.chatgpt_base_url;
+    let fixture = test_codex()
+        .with_auth(CodexAuth::create_dummy_chatgpt_auth_for_testing())
+        .with_config(move |config| {
+            config
+                .features
+                .enable(Feature::Apps)
+                .expect("test config should allow Apps override");
+            if matches!(setting, HostedProtocolSetting::Enabled) {
+                config
+                    .features
+                    .enable(Feature::CodexAppsMcp20260728)
+                    .expect("test config should allow Apps protocol override");
+            }
+            config.chatgpt_base_url = apps_base_url;
+        })
+        .build_with_auto_env(&server)
+        .await?;
+
+    wait_for_mcp_server(&fixture.codex, CODEX_APPS_MCP_SERVER_NAME).await?;
+    let methods = server
+        .received_requests()
+        .await
+        .expect("mock server should capture Apps MCP startup requests")
+        .into_iter()
+        .filter(|request| request.url.path() == "/api/codex/ps/mcp")
+        .filter_map(|request| {
+            let body: Value = serde_json::from_slice(&request.body).ok()?;
+            body.get("method")?.as_str().map(str::to_string)
+        })
+        .collect::<Vec<_>>();
+    assert_eq!(methods, expected_methods);
+    Ok(())
+}

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

@@ -52,6 +52,7 @@ mod client_websockets;
 mod cloud_config;
 mod code_mode;
 mod code_mode_elicitation;
+mod codex_apps_protocol;
 mod codex_delegate;
 mod collaboration_instructions;
 mod compact;

codex-rs/features/src/lib.rs

@@ -209,6 +209,8 @@ pub enum Feature {
     EnableMcpApps,
     /// Enable MCP protocol version 2026-07-28 support.
     Mcp20260728,
+    /// Enable MCP protocol version 2026-07-28 for the host-owned Codex Apps server.
+    CodexAppsMcp20260728,
     /// Let RMCP coordinate OAuth refresh through the configured credential store.
     McpOAuthRefreshCoordination,
     /// Removed compatibility flag for the legacy Apps MCP path override.
@@ -1303,6 +1305,12 @@ pub const FEATURES: &[FeatureSpec] = &[
         stage: Stage::UnderDevelopment,
         default_enabled: false,
     },
+    FeatureSpec {
+        id: Feature::CodexAppsMcp20260728,
+        key: "codex_apps_mcp_2026_07_28",
+        stage: Stage::UnderDevelopment,
+        default_enabled: false,
+    },
     FeatureSpec {
         id: Feature::McpOAuthRefreshCoordination,
         key: "mcp_oauth_refresh_coordination",

codex-rs/features/src/tests.rs

@@ -93,6 +93,30 @@ fn cwd_relative_turn_diffs_is_an_opt_in_map_feature() {
     assert!(!features.enabled(Feature::CwdRelativeTurnDiffs));
 }
 
+#[test]
+fn codex_apps_mcp_protocol_can_be_enabled_independently_of_generic_mcp() {
+    let features_toml = FeaturesToml::from(BTreeMap::from([
+        (Feature::CodexAppsMcp20260728.key().to_string(), true),
+        (Feature::Mcp20260728.key().to_string(), false),
+    ]));
+    let features = Features::from_sources(
+        FeatureConfigSource {
+            features: Some(&features_toml),
+            ..Default::default()
+        },
+        FeatureConfigSource::default(),
+        FeatureOverrides::default(),
+    );
+
+    assert_eq!(
+        (
+            features.enabled(Feature::CodexAppsMcp20260728),
+            features.enabled(Feature::Mcp20260728),
+        ),
+        (true, false),
+    );
+}
+
 #[test]
 fn default_enabled_features_are_stable() {
     for spec in crate::FEATURES {