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/cli/src/main.rs

@@ -51,6 +51,7 @@ struct MultitoolCli {
     subcommand: Option<Subcommand>,
 }
 
+#[allow(clippy::large_enum_variant)]
 #[derive(Debug, clap::Subcommand)]
 enum Subcommand {
     /// Run Codex non-interactively.
@@ -255,7 +256,7 @@ async fn cli_main(codex_linux_sandbox_exe: Option<PathBuf>) -> anyhow::Result<()
         }
         Some(Subcommand::Exec(mut exec_cli)) => {
             prepend_config_flags(
-                &mut exec_cli.config_overrides,
+                &mut exec_cli.shared.config_overrides,
                 root_config_overrides.clone(),
             );
             codex_exec::run_main(exec_cli, codex_linux_sandbox_exe).await?;

codex-rs/exec/src/cli.rs

@@ -1,3 +1,4 @@
+use clap::Args;
 use clap::Parser;
 use clap::ValueEnum;
 use codex_common::CliConfigOverrides;
@@ -10,6 +11,33 @@ pub struct Cli {
     #[command(subcommand)]
     pub command: Option<Command>,
 
+    #[clap(flatten)]
+    pub shared: SharedExecArgs,
+}
+
+#[derive(Debug, clap::Subcommand)]
+pub enum Command {
+    /// Resume a previous session by id or pick the most recent with --last.
+    Resume(ResumeArgs),
+}
+
+#[derive(Parser, Debug)]
+pub struct ResumeArgs {
+    /// Conversation/session id (UUID). When provided, resumes this session.
+    /// If omitted, use --last to pick the most recent recorded session.
+    #[arg(value_name = "SESSION_ID")]
+    pub session_id: Option<String>,
+
+    /// Resume the most recent recorded session (newest) without specifying an id.
+    #[arg(long = "last", default_value_t = false, conflicts_with = "session_id")]
+    pub last: bool,
+
+    #[clap(flatten)]
+    pub shared: SharedExecArgs,
+}
+
+#[derive(Debug, Clone, Default, Args)]
+pub struct SharedExecArgs {
     /// Optional image(s) to attach to the initial prompt.
     #[arg(long = "image", short = 'i', value_name = "FILE", value_delimiter = ',', num_args = 1..)]
     pub images: Vec<PathBuf>,
@@ -56,9 +84,6 @@ pub struct Cli {
     #[arg(long = "output-schema", value_name = "FILE")]
     pub output_schema: Option<PathBuf>,
 
-    #[clap(skip)]
-    pub config_overrides: CliConfigOverrides,
-
     /// Specifies color settings for use in the output.
     #[arg(long = "color", value_enum, default_value_t = Color::Auto)]
     pub color: Color,
@@ -86,34 +111,15 @@ pub struct Cli {
     #[arg(long = "output-last-message")]
     pub last_message_file: Option<PathBuf>,
 
+    #[clap(skip)]
+    pub config_overrides: CliConfigOverrides,
+
     /// Initial instructions for the agent. If not provided as an argument (or
     /// if `-` is used), instructions are read from stdin.
     #[arg(value_name = "PROMPT")]
     pub prompt: Option<String>,
 }
 
-#[derive(Debug, clap::Subcommand)]
-pub enum Command {
-    /// Resume a previous session by id or pick the most recent with --last.
-    Resume(ResumeArgs),
-}
-
-#[derive(Parser, Debug)]
-pub struct ResumeArgs {
-    /// Conversation/session id (UUID). When provided, resumes this session.
-    /// If omitted, use --last to pick the most recent recorded session.
-    #[arg(value_name = "SESSION_ID")]
-    pub session_id: Option<String>,
-
-    /// Resume the most recent recorded session (newest) without specifying an id.
-    #[arg(long = "last", default_value_t = false, conflicts_with = "session_id")]
-    pub last: bool,
-
-    /// Prompt to send after resuming the session. If `-` is used, read from stdin.
-    #[arg(value_name = "PROMPT")]
-    pub prompt: Option<String>,
-}
-
 #[derive(Debug, Clone, Copy, Default, PartialEq, Eq, ValueEnum)]
 #[value(rename_all = "kebab-case")]
 pub enum Color {

codex-rs/exec/src/lib.rs

@@ -36,6 +36,7 @@ use tracing_subscriber::EnvFilter;
 use tracing_subscriber::prelude::*;
 
 use crate::cli::Command as ExecCommand;
+use crate::cli::SharedExecArgs;
 use crate::event_processor::CodexStatus;
 use crate::event_processor::EventProcessor;
 use codex_core::default_client::set_default_originator;
@@ -46,8 +47,19 @@ pub async fn run_main(cli: Cli, codex_linux_sandbox_exe: Option<PathBuf>) -> any
         tracing::warn!(?err, "Failed to set codex exec originator override {err:?}");
     }
 
-    let Cli {
-        command,
+    let Cli { command, shared } = cli;
+
+    // Merge overrides from root CLI.
+    let mut config_overrides = shared.config_overrides.clone();
+
+    let shared = command
+        .as_ref()
+        .map(|cmd| match cmd {
+            ExecCommand::Resume(args) => args.shared.clone(),
+        })
+        .unwrap_or(shared);
+
+    let SharedExecArgs {
         images,
         model: model_cli_arg,
         oss,
@@ -61,19 +73,15 @@ pub async fn run_main(cli: Cli, codex_linux_sandbox_exe: Option<PathBuf>) -> any
         json: json_mode,
         experimental_json,
         sandbox_mode: sandbox_mode_cli_arg,
-        prompt,
         output_schema: output_schema_path,
         include_plan_tool,
-        config_overrides,
-    } = cli;
+        prompt: prompt_arg,
+        ..
+    } = shared;
 
-    // Determine the prompt source (parent or subcommand) and read from stdin if needed.
-    let prompt_arg = match &command {
-        // Allow prompt before the subcommand by falling back to the parent-level prompt
-        // when the Resume subcommand did not provide its own prompt.
-        Some(ExecCommand::Resume(args)) => args.prompt.clone().or(prompt),
-        None => prompt,
-    };
+    config_overrides
+        .raw_overrides
+        .splice(0..0, shared.config_overrides.raw_overrides);
 
     let prompt = match prompt_arg {
         Some(p) if p != "-" => p,

codex-rs/exec/src/main.rs

@@ -30,6 +30,7 @@ fn main() -> anyhow::Result<()> {
         // Merge root-level overrides into inner CLI struct so downstream logic remains unchanged.
         let mut inner = top_cli.inner;
         inner
+            .shared
             .config_overrides
             .raw_overrides
             .splice(0..0, top_cli.config_overrides.raw_overrides);

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

@@ -0,0 +1,138 @@
+#![cfg(not(target_os = "windows"))]
+#![allow(clippy::expect_used, clippy::unwrap_used)]
+
+use core_test_support::responses;
+use core_test_support::test_codex_exec::test_codex_exec;
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn config_overrides_are_applied_resume() -> anyhow::Result<()> {
+    config_overrides_are_applied_resume_inner(
+        &["--model", "o3", "prompt text"],
+        &[
+            "resume",
+            "--skip-git-repo-check",
+            "fake id",
+            "--model",
+            "o3",
+            "resume prompt text",
+        ],
+    )
+    .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(())
+}
+
+async fn config_overrides_are_applied_resume_inner(
+    args: &[&str],
+    resume_args: &[&str],
+) -> anyhow::Result<()> {
+    let test = test_codex_exec();
+
+    let match_config_overrides_applied = |req: &wiremock::Request| {
+        let body = std::str::from_utf8(&req.body).unwrap_or("");
+        body.contains("prompt text") && body.contains("o3")
+    };
+
+    let server = responses::start_mock_server().await;
+    responses::mount_sse_once_match(
+        &server,
+        match_config_overrides_applied,
+        responses::sse(vec![
+            responses::ev_assistant_message("msg-1", "config overrides are applied."),
+            responses::ev_completed("resp-2"),
+        ]),
+    )
+    .await;
+
+    test.cmd_with_server(&server)
+        .arg("--skip-git-repo-check")
+        .arg("--experimental-json")
+        .args(args)
+        .assert()
+        .code(0);
+
+    let match_config_resume_overrides_applied = |req: &wiremock::Request| {
+        let body = std::str::from_utf8(&req.body).unwrap_or("");
+        body.contains("resume prompt text") && body.contains("o3")
+    };
+
+    responses::mount_sse_once_match(
+        &server,
+        match_config_resume_overrides_applied,
+        responses::sse(vec![
+            responses::ev_assistant_message("msg-1", "config overrides are applied resume."),
+            responses::ev_completed("resp-2"),
+        ]),
+    )
+    .await;
+
+    test.cmd_with_server(&server)
+        .args(resume_args)
+        .assert()
+        .code(0);
+
+    Ok(())
+}
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn config_overrides_are_applied() -> anyhow::Result<()> {
+    config_overrides_are_applied_inner(&["-c", "model=o3", "prompt text"]).await?;
+    config_overrides_are_applied_inner(&["prompt text", "-c", "model=o3"]).await?;
+    config_overrides_are_applied_inner(&["--model", "o3", "prompt text"]).await?;
+
+    Ok(())
+}
+
+async fn config_overrides_are_applied_inner(args: &[&str]) -> anyhow::Result<()> {
+    let test = test_codex_exec();
+
+    let match_config_overrides_applied = |req: &wiremock::Request| {
+        let body = std::str::from_utf8(&req.body).unwrap_or("");
+        body.contains("prompt text") && body.contains("o3")
+    };
+
+    let server = responses::start_mock_server().await;
+    responses::mount_sse_once_match(
+        &server,
+        match_config_overrides_applied,
+        responses::sse(vec![
+            responses::ev_assistant_message("msg-1", "config overrides are applied."),
+            responses::ev_completed("resp-2"),
+        ]),
+    )
+    .await;
+
+    test.cmd_with_server(&server)
+        .arg("--skip-git-repo-check")
+        .args(args)
+        .assert()
+        .code(0);
+
+    Ok(())
+}

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

@@ -1,5 +1,6 @@
 // Aggregates all former standalone integration tests as modules.
 mod apply_patch;
+mod config_overrides;
 mod output_schema;
 mod resume;
 mod sandbox;