[codex] Surface runtime warnings in codex exec (#27415)

## Why

`codex exec` drops thread-scoped warning notifications. Warnings
discovered while a thread starts, including unreadable or invalid UTF-8
project `AGENTS.md` files, therefore become silent.

## What changed

- Process global and primary-thread warning notifications while
continuing to ignore warnings from unrelated threads.
- Render runtime warnings in human output and expose them through the
existing non-fatal error item in JSONL output.
- Add focused routing, rendering, and malformed project-instruction
coverage.

codex-rs/exec/src/lib_tests.rs

@@ -267,6 +267,35 @@ fn lagged_event_warning_message_is_explicit() {
     );
 }
 
+#[test]
+fn runtime_warnings_are_filtered_to_the_primary_thread() {
+    let primary_thread_id = "thread-1";
+    let turn_id = "turn-1";
+    let outcomes = [
+        codex_app_server_protocol::WarningNotification {
+            thread_id: None,
+            message: "global warning".to_string(),
+        },
+        codex_app_server_protocol::WarningNotification {
+            thread_id: Some(primary_thread_id.to_string()),
+            message: "primary warning".to_string(),
+        },
+        codex_app_server_protocol::WarningNotification {
+            thread_id: Some("thread-2".to_string()),
+            message: "other warning".to_string(),
+        },
+    ]
+    .map(|warning| {
+        should_process_notification(
+            &ServerNotification::Warning(warning),
+            primary_thread_id,
+            turn_id,
+        )
+    });
+
+    assert_eq!(outcomes, [true, true, false]);
+}
+
 #[tokio::test]
 async fn resume_lookup_model_providers_filters_only_last_lookup() {
     let codex_home = tempdir().expect("create temp codex home");