Extract MCP into codex-mcp crate (#15919)

- Split MCP runtime/server code out of `codex-core` into the new
`codex-mcp` crate. New/moved public structs/types include `McpConfig`,
`McpConnectionManager`, `ToolInfo`, `ToolPluginProvenance`,
`CodexAppsToolsCacheKey`, and the `McpManager` API
(`codex_mcp::mcp::McpManager` plus the `codex_core::mcp::McpManager`
wrapper/shim). New/moved functions include `with_codex_apps_mcp`,
`configured_mcp_servers`, `effective_mcp_servers`,
`collect_mcp_snapshot`, `collect_mcp_snapshot_from_manager`,
`qualified_mcp_tool_name_prefix`, and the MCP auth/skill-dependency
helpers. Why: this creates a focused MCP crate boundary and shrinks
`codex-core` without forcing every consumer to migrate in the same PR.

- Move MCP server config schema and persistence into `codex-config`.
New/moved structs/enums include `AppToolApproval`,
`McpServerToolConfig`, `McpServerConfig`, `RawMcpServerConfig`,
`McpServerTransportConfig`, `McpServerDisabledReason`, and
`codex_config::ConfigEditsBuilder`. New/moved functions include
`load_global_mcp_servers` and
`ConfigEditsBuilder::replace_mcp_servers`/`apply`. Why: MCP TOML
parsing/editing is config ownership, and this keeps config
validation/round-tripping (including per-tool approval overrides and
inline bearer-token rejection) in the config crate instead of
`codex-core`.

- Rewire `codex-core`, app-server, and plugin call sites onto the new
crates. Updated `Config::to_mcp_config(&self, plugins_manager)`,
`codex-rs/core/src/mcp.rs`, `codex-rs/core/src/connectors.rs`,
`codex-rs/core/src/codex.rs`,
`CodexMessageProcessor::list_mcp_server_status_task`, and
`utils/plugins/src/mcp_connector.rs` to build/pass the new MCP
config/runtime types. Why: plugin-provided MCP servers still merge with
user-configured servers, and runtime auth (`CodexAuth`) is threaded into
`with_codex_apps_mcp` / `collect_mcp_snapshot` explicitly so `McpConfig`
stays config-only.

codex-rs/core/src/codex.rs

@@ -265,11 +265,11 @@ use crate::instructions::UserInstructions;
 use crate::mcp::CODEX_APPS_MCP_SERVER_NAME;
 use crate::mcp::McpManager;
 use crate::mcp::auth::compute_auth_statuses;
-use crate::mcp::maybe_prompt_and_install_mcp_dependencies;
 use crate::mcp::with_codex_apps_mcp;
 use crate::mcp_connection_manager::McpConnectionManager;
 use crate::mcp_connection_manager::codex_apps_tools_cache_key;
 use crate::mcp_connection_manager::filter_non_codex_apps_mcp_tools_only;
+use crate::mcp_skill_dependencies::maybe_prompt_and_install_mcp_dependencies;
 use crate::memories;
 use crate::mentions::build_connector_slug_counts;
 use crate::mentions::build_skill_name_counts;
@@ -2000,6 +2000,7 @@ impl Session {
             config.mcp_oauth_credentials_store_mode,
             auth_statuses.clone(),
             &session_configuration.approval_policy,
+            INITIAL_SUBMIT_ID.to_owned(),
             tx_event.clone(),
             sandbox_state,
             config.codex_home.clone(),
@@ -4250,16 +4251,12 @@ impl Session {
     ) {
         let auth = self.services.auth_manager.auth().await;
         let config = self.get_config().await;
+        let mcp_config = config.to_mcp_config(self.services.plugins_manager.as_ref());
         let tool_plugin_provenance = self
             .services
             .mcp_manager
             .tool_plugin_provenance(config.as_ref());
-        let mcp_servers = with_codex_apps_mcp(
-            mcp_servers,
-            self.features.apps_enabled_for_auth(auth.as_ref()),
-            auth.as_ref(),
-            config.as_ref(),
-        );
+        let mcp_servers = with_codex_apps_mcp(mcp_servers, auth.as_ref(), &mcp_config);
         let auth_statuses = compute_auth_statuses(mcp_servers.iter(), store_mode).await;
         let sandbox_state = SandboxState {
             sandbox_policy: turn_context.sandbox_policy.get().clone(),
@@ -4277,6 +4274,7 @@ impl Session {
             store_mode,
             auth_statuses,
             &turn_context.config.permissions.approval_policy,
+            turn_context.sub_id.clone(),
             self.get_tx_event(),
             sandbox_state,
             config.codex_home.clone(),
@@ -4619,8 +4617,6 @@ mod handlers {
     use codex_features::Feature;
     use codex_utils_absolute_path::AbsolutePathBuf;
 
-    use crate::mcp::auth::compute_auth_statuses;
-    use crate::mcp::collect_mcp_snapshot_from_manager;
     use crate::review_prompts::resolve_review_request;
     use crate::rollout::RolloutRecorder;
     use crate::rollout::session_index;
@@ -4629,6 +4625,8 @@ mod handlers {
     use crate::tasks::UserShellCommandMode;
     use crate::tasks::UserShellCommandTask;
     use crate::tasks::execute_user_shell_command;
+    use codex_mcp::mcp::auth::compute_auth_statuses;
+    use codex_mcp::mcp::collect_mcp_snapshot_from_manager;
     use codex_protocol::protocol::CodexErrorInfo;
     use codex_protocol::protocol::ErrorEvent;
     use codex_protocol::protocol::Event;