feat: make built-in MCPs first-class runtime servers (#21356)

## DISCLAIMER
This is experimental and no production service must rely on this

## Why

Built-in MCPs are product-owned runtime capabilities, but they were
previously flattened into the same config-backed stdio path as
user-configured servers. That made them depend on a hidden `codex
builtin-mcp` re-exec path, exposed them through config-oriented CLI
flows, and erased distinctions the runtime needs to preserve—most
notably whether an MCP call should count as external context for
memory-mode pollution.

## What changed

- Model product-owned built-ins separately from config-backed MCP
servers via `BuiltinMcpServer` and `EffectiveMcpServer`.
- Launch built-ins in process through a reusable async transport instead
of the hidden `builtin-mcp` stdio subcommand.
- Keep config-oriented CLI operations such as `codex mcp
list/get/login/logout` scoped to configured servers, while merging
built-ins only into the effective runtime server set.
- Retain server metadata after launch so parallel-tool support and
context classification come from the live server set; built-in
`memories` is now classified as local Codex state rather than external
context.

## Test plan

- `cargo test -p codex-mcp`
- `cargo test -p codex-core --test suite
builtin_memories_mcp_call_does_not_mark_thread_memory_mode_polluted_when_configured`

---------

Co-authored-by: Codex <noreply@openai.com>

codex-rs/cli/src/main.rs

@@ -123,10 +123,6 @@ enum Subcommand {
     /// Start Codex as an MCP server (stdio).
     McpServer,
 
-    /// Internal: start a Codex-shipped MCP server (stdio).
-    #[clap(hide = true, name = "builtin-mcp")]
-    BuiltinMcp(BuiltinMcpCommand),
-
     /// [experimental] Run the app server or related tooling.
     AppServer(AppServerCommand),
 
@@ -179,13 +175,6 @@ enum Subcommand {
     Features(FeaturesCli),
 }
 
-#[derive(Debug, Args)]
-struct BuiltinMcpCommand {
-    name: String,
-    #[arg(long)]
-    codex_home: PathBuf,
-}
-
 #[derive(Debug, Parser)]
 #[command(bin_name = "codex plugin")]
 struct PluginCli {
@@ -820,15 +809,6 @@ async fn cli_main(arg0_paths: Arg0DispatchPaths) -> anyhow::Result<()> {
             )?;
             codex_mcp_server::run_main(arg0_paths.clone(), root_config_overrides).await?;
         }
-        Some(Subcommand::BuiltinMcp(command)) => {
-            reject_remote_mode_for_subcommand(
-                root_remote.as_deref(),
-                root_remote_auth_token_env.as_deref(),
-                "builtin-mcp",
-            )?;
-            let codex_home = AbsolutePathBuf::try_from(command.codex_home)?;
-            codex_builtin_mcps::run_builtin_mcp_server(&command.name, &codex_home).await?;
-        }
         Some(Subcommand::Mcp(mut mcp_cli)) => {
             reject_remote_mode_for_subcommand(
                 root_remote.as_deref(),

codex-rs/cli/src/mcp_cmd.rs

@@ -397,7 +397,7 @@ async fn run_login(config_overrides: &CliConfigOverrides, login_args: LoginArgs)
     let mcp_manager = McpManager::new(Arc::new(PluginsManager::new(
         config.codex_home.to_path_buf(),
     )));
-    let mcp_servers = mcp_manager.effective_servers(&config, /*auth*/ None).await;
+    let mcp_servers = mcp_manager.configured_servers(&config).await;
 
     let LoginArgs { name, scopes } = login_args;
 
@@ -450,7 +450,7 @@ async fn run_logout(config_overrides: &CliConfigOverrides, logout_args: LogoutAr
     let mcp_manager = McpManager::new(Arc::new(PluginsManager::new(
         config.codex_home.to_path_buf(),
     )));
-    let mcp_servers = mcp_manager.effective_servers(&config, /*auth*/ None).await;
+    let mcp_servers = mcp_manager.configured_servers(&config).await;
 
     let LogoutArgs { name } = logout_args;
 
@@ -482,12 +482,13 @@ async fn run_list(config_overrides: &CliConfigOverrides, list_args: ListArgs) ->
     let mcp_manager = McpManager::new(Arc::new(PluginsManager::new(
         config.codex_home.to_path_buf(),
     )));
-    let mcp_servers = mcp_manager.effective_servers(&config, /*auth*/ None).await;
+    let mcp_servers = mcp_manager.configured_servers(&config).await;
+    let effective_mcp_servers = mcp_manager.effective_servers(&config, /*auth*/ None).await;
 
     let mut entries: Vec<_> = mcp_servers.iter().collect();
     entries.sort_by(|(a, _), (b, _)| a.cmp(b));
     let auth_statuses = compute_auth_statuses(
-        mcp_servers.iter(),
+        effective_mcp_servers.iter(),
         config.mcp_oauth_credentials_store_mode,
         /*auth*/ None,
     )
@@ -737,7 +738,7 @@ async fn run_get(config_overrides: &CliConfigOverrides, get_args: GetArgs) -> Re
     let mcp_manager = McpManager::new(Arc::new(PluginsManager::new(
         config.codex_home.to_path_buf(),
     )));
-    let mcp_servers = mcp_manager.effective_servers(&config, /*auth*/ None).await;
+    let mcp_servers = mcp_manager.configured_servers(&config).await;
 
     let Some(server) = mcp_servers.get(&get_args.name) else {
         bail!("No MCP server named '{name}' found.", name = get_args.name);