exec: fix config_overrides merging to ensure root flags are applied to subcommands

- Merge config_overrides from the root CLI into subcommands in run_main.
- Extend tests for config_overrides arguments ordering in config_overrides_are_applied_resume.

codex-rs/exec/tests/suite/config_overrides.rs

@@ -19,6 +19,32 @@ async fn config_overrides_are_applied_resume() -> anyhow::Result<()> {
     )
     .await?;
 
+    config_overrides_are_applied_resume_inner(
+        &["-c", "model=o3", "prompt text"],
+        &[
+            "resume",
+            "--skip-git-repo-check",
+            "fake id",
+            "-c",
+            "model=o3",
+            "resume prompt text",
+        ],
+    )
+    .await?;
+
+    config_overrides_are_applied_resume_inner(
+        &["-c", "model=o3", "prompt text"],
+        &[
+            "-c",
+            "model=o3",
+            "resume",
+            "--skip-git-repo-check",
+            "fake id",
+            "resume prompt text",
+        ],
+    )
+    .await?;
+
     Ok(())
 }