fix: apply_patch shell_serialization tests (#4786)

## Summary
Adds additional shell_serialization tests specifically for apply_patch
and other cases.

## Test Plan
- [x] These are all tests

codex-rs/core/tests/suite/shell_serialization.rs

@@ -10,9 +10,12 @@ use codex_core::protocol::Op;
 use codex_core::protocol::SandboxPolicy;
 use codex_protocol::config_types::ReasoningSummary;
 use core_test_support::assert_regex_match;
+use core_test_support::responses::ev_apply_patch_function_call;
 use core_test_support::responses::ev_assistant_message;
 use core_test_support::responses::ev_completed;
+use core_test_support::responses::ev_custom_tool_call;
 use core_test_support::responses::ev_function_call;
+use core_test_support::responses::ev_local_shell_call;
 use core_test_support::responses::ev_response_created;
 use core_test_support::responses::mount_sse_sequence;
 use core_test_support::responses::sse;
@@ -21,8 +24,11 @@ use core_test_support::skip_if_no_network;
 use core_test_support::test_codex::TestCodex;
 use core_test_support::test_codex::test_codex;
 use core_test_support::wait_for_event;
+use pretty_assertions::assert_eq;
+use regex_lite::Regex;
 use serde_json::Value;
 use serde_json::json;
+use std::fs;
 
 async fn submit_turn(test: &TestCodex, prompt: &str, sandbox_policy: SandboxPolicy) -> Result<()> {
     let session_model = test.session_configured.model.clone();
@@ -72,6 +78,21 @@ fn find_function_call_output<'a>(bodies: &'a [Value], call_id: &str) -> Option<&
     None
 }
 
+fn find_custom_tool_call_output<'a>(bodies: &'a [Value], call_id: &str) -> Option<&'a Value> {
+    for body in bodies {
+        if let Some(items) = body.get("input").and_then(Value::as_array) {
+            for item in items {
+                if item.get("type").and_then(Value::as_str) == Some("custom_tool_call_output")
+                    && item.get("call_id").and_then(Value::as_str) == Some(call_id)
+                {
+                    return Some(item);
+                }
+            }
+        }
+    }
+    None
+}
+
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
 async fn shell_output_stays_json_without_freeform_apply_patch() -> Result<()> {
     skip_if_no_network!(Ok(()));
@@ -120,7 +141,12 @@ async fn shell_output_stays_json_without_freeform_apply_patch() -> Result<()> {
         .and_then(Value::as_str)
         .expect("shell output string");
 
-    let parsed: Value = serde_json::from_str(output)?;
+    let mut parsed: Value = serde_json::from_str(output)?;
+    if let Some(metadata) = parsed.get_mut("metadata").and_then(Value::as_object_mut) {
+        // duration_seconds is non-deterministic; remove it for deep equality
+        let _ = metadata.remove("duration_seconds");
+    }
+
     assert_eq!(
         parsed
             .get("metadata")
@@ -199,6 +225,83 @@ freeform shell
     Ok(())
 }
 
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn shell_output_for_freeform_tool_records_duration() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = start_mock_server().await;
+    let mut builder = test_codex().with_config(|config| {
+        config.include_apply_patch_tool = true;
+    });
+    let test = builder.build(&server).await?;
+
+    #[cfg(target_os = "linux")]
+    let sleep_cmd = vec!["/bin/bash", "-c", "sleep 1"];
+
+    #[cfg(target_os = "macos")]
+    let sleep_cmd = vec!["/bin/bash", "-c", "sleep 1"];
+
+    #[cfg(windows)]
+    let sleep_cmd = "timeout 1";
+
+    let call_id = "shell-structured";
+    let args = json!({
+        "command": sleep_cmd,
+        "timeout_ms": 2_000,
+    });
+    let responses = vec![
+        sse(vec![
+            json!({"type": "response.created", "response": {"id": "resp-1"}}),
+            ev_function_call(call_id, "shell", &serde_json::to_string(&args)?),
+            ev_completed("resp-1"),
+        ]),
+        sse(vec![
+            ev_assistant_message("msg-1", "done"),
+            ev_completed("resp-2"),
+        ]),
+    ];
+    mount_sse_sequence(&server, responses).await;
+
+    submit_turn(
+        &test,
+        "run the structured shell command",
+        SandboxPolicy::DangerFullAccess,
+    )
+    .await?;
+
+    let requests = server
+        .received_requests()
+        .await
+        .expect("recorded requests present");
+    let bodies = request_bodies(&requests)?;
+    let output_item =
+        find_function_call_output(&bodies, call_id).expect("structured output present");
+    let output = output_item
+        .get("output")
+        .and_then(Value::as_str)
+        .expect("structured output string");
+
+    let expected_pattern = r#"(?s)^Exit code: 0
+Wall time: [0-9]+(?:\.[0-9]+)? seconds
+Output:
+$"#;
+    assert_regex_match(expected_pattern, output);
+
+    let wall_time_regex = Regex::new(r"(?m)^Wall (?:time|Clock): ([0-9]+(?:\.[0-9]+)?) seconds$")
+        .expect("compile wall time regex");
+    let wall_time_seconds = wall_time_regex
+        .captures(output)
+        .and_then(|caps| caps.get(1))
+        .and_then(|value| value.as_str().parse::<f32>().ok())
+        .expect("expected structured shell output to contain wall time seconds");
+    assert!(
+        wall_time_seconds > 0.5,
+        "expected wall time to be greater than zero seconds, got {wall_time_seconds}"
+    );
+
+    Ok(())
+}
+
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
 async fn shell_output_reserializes_truncated_content() -> Result<()> {
     skip_if_no_network!(Ok(()));
@@ -276,3 +379,446 @@ $"#;
 
     Ok(())
 }
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn apply_patch_custom_tool_output_is_structured() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = start_mock_server().await;
+    let mut builder = test_codex().with_config(|config| {
+        config.include_apply_patch_tool = true;
+    });
+    let test = builder.build(&server).await?;
+
+    let call_id = "apply-patch-structured";
+    let file_name = "structured.txt";
+    let patch = format!(
+        r#"*** Begin Patch
+*** Add File: {file_name}
++from custom tool
+*** End Patch
+"#
+    );
+    let responses = vec![
+        sse(vec![
+            json!({"type": "response.created", "response": {"id": "resp-1"}}),
+            ev_custom_tool_call(call_id, "apply_patch", &patch),
+            ev_completed("resp-1"),
+        ]),
+        sse(vec![
+            ev_assistant_message("msg-1", "done"),
+            ev_completed("resp-2"),
+        ]),
+    ];
+    mount_sse_sequence(&server, responses).await;
+
+    submit_turn(
+        &test,
+        "apply the patch via custom tool",
+        SandboxPolicy::DangerFullAccess,
+    )
+    .await?;
+
+    let requests = server
+        .received_requests()
+        .await
+        .expect("recorded requests present");
+    let bodies = request_bodies(&requests)?;
+    let output_item =
+        find_custom_tool_call_output(&bodies, call_id).expect("apply_patch output present");
+    let output = output_item
+        .get("output")
+        .and_then(Value::as_str)
+        .expect("apply_patch output string");
+
+    let expected_pattern = format!(
+        r"(?s)^Exit code: 0
+Wall time: [0-9]+(?:\.[0-9]+)? seconds
+Output:
+Success. Updated the following files:
+A {file_name}
+?$"
+    );
+    assert_regex_match(&expected_pattern, output);
+
+    Ok(())
+}
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn apply_patch_custom_tool_call_creates_file() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = start_mock_server().await;
+    let mut builder = test_codex().with_config(|config| {
+        config.include_apply_patch_tool = true;
+    });
+    let test = builder.build(&server).await?;
+
+    let call_id = "apply-patch-add-file";
+    let file_name = "custom_tool_apply_patch.txt";
+    let patch = format!(
+        "*** Begin Patch\n*** Add File: {file_name}\n+custom tool content\n*** End Patch\n"
+    );
+    let responses = vec![
+        sse(vec![
+            json!({"type": "response.created", "response": {"id": "resp-1"}}),
+            ev_custom_tool_call(call_id, "apply_patch", &patch),
+            ev_completed("resp-1"),
+        ]),
+        sse(vec![
+            ev_assistant_message("msg-1", "apply_patch done"),
+            ev_completed("resp-2"),
+        ]),
+    ];
+    mount_sse_sequence(&server, responses).await;
+
+    submit_turn(
+        &test,
+        "apply the patch via custom tool to create a file",
+        SandboxPolicy::DangerFullAccess,
+    )
+    .await?;
+
+    let requests = server
+        .received_requests()
+        .await
+        .expect("recorded requests present");
+    let bodies = request_bodies(&requests)?;
+    let output_item =
+        find_custom_tool_call_output(&bodies, call_id).expect("apply_patch output present");
+    let output = output_item
+        .get("output")
+        .and_then(Value::as_str)
+        .expect("apply_patch output string");
+
+    let expected_pattern = format!(
+        r"(?s)^Exit code: 0
+Wall time: [0-9]+(?:\.[0-9]+)? seconds
+Output:
+Success. Updated the following files:
+A {file_name}
+?$"
+    );
+    assert_regex_match(&expected_pattern, output);
+
+    let new_file_path = test.cwd.path().join(file_name);
+    let created_contents = fs::read_to_string(&new_file_path)?;
+    assert_eq!(
+        created_contents, "custom tool content\n",
+        "expected file contents for {file_name}"
+    );
+
+    Ok(())
+}
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn apply_patch_custom_tool_call_updates_existing_file() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = start_mock_server().await;
+    let mut builder = test_codex().with_config(|config| {
+        config.include_apply_patch_tool = true;
+    });
+    let test = builder.build(&server).await?;
+
+    let call_id = "apply-patch-update-file";
+    let file_name = "custom_tool_apply_patch_existing.txt";
+    let file_path = test.cwd.path().join(file_name);
+    fs::write(&file_path, "before\n")?;
+    let patch = format!(
+        "*** Begin Patch\n*** Update File: {file_name}\n@@\n-before\n+after\n*** End Patch\n"
+    );
+    let responses = vec![
+        sse(vec![
+            json!({"type": "response.created", "response": {"id": "resp-1"}}),
+            ev_custom_tool_call(call_id, "apply_patch", &patch),
+            ev_completed("resp-1"),
+        ]),
+        sse(vec![
+            ev_assistant_message("msg-1", "apply_patch update done"),
+            ev_completed("resp-2"),
+        ]),
+    ];
+    mount_sse_sequence(&server, responses).await;
+
+    submit_turn(
+        &test,
+        "apply the patch via custom tool to update a file",
+        SandboxPolicy::DangerFullAccess,
+    )
+    .await?;
+
+    let requests = server
+        .received_requests()
+        .await
+        .expect("recorded requests present");
+    let bodies = request_bodies(&requests)?;
+    let output_item =
+        find_custom_tool_call_output(&bodies, call_id).expect("apply_patch output present");
+    let output = output_item
+        .get("output")
+        .and_then(Value::as_str)
+        .expect("apply_patch output string");
+
+    let expected_pattern = format!(
+        r"(?s)^Exit code: 0
+Wall time: [0-9]+(?:\.[0-9]+)? seconds
+Output:
+Success. Updated the following files:
+M {file_name}
+?$"
+    );
+    assert_regex_match(&expected_pattern, output);
+
+    let updated_contents = fs::read_to_string(file_path)?;
+    assert_eq!(updated_contents, "after\n", "expected updated file content");
+
+    Ok(())
+}
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn apply_patch_custom_tool_call_reports_failure_output() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = start_mock_server().await;
+    let mut builder = test_codex().with_config(|config| {
+        config.include_apply_patch_tool = true;
+    });
+    let test = builder.build(&server).await?;
+
+    let call_id = "apply-patch-failure";
+    let missing_file = "missing_custom_tool_apply_patch.txt";
+    let patch = format!(
+        "*** Begin Patch\n*** Update File: {missing_file}\n@@\n-before\n+after\n*** End Patch\n"
+    );
+    let responses = vec![
+        sse(vec![
+            json!({"type": "response.created", "response": {"id": "resp-1"}}),
+            ev_custom_tool_call(call_id, "apply_patch", &patch),
+            ev_completed("resp-1"),
+        ]),
+        sse(vec![
+            ev_assistant_message("msg-1", "apply_patch failure done"),
+            ev_completed("resp-2"),
+        ]),
+    ];
+    mount_sse_sequence(&server, responses).await;
+
+    submit_turn(
+        &test,
+        "attempt a failing apply_patch via custom tool",
+        SandboxPolicy::DangerFullAccess,
+    )
+    .await?;
+
+    let requests = server
+        .received_requests()
+        .await
+        .expect("recorded requests present");
+    let bodies = request_bodies(&requests)?;
+    let output_item =
+        find_custom_tool_call_output(&bodies, call_id).expect("apply_patch output present");
+    let output = output_item
+        .get("output")
+        .and_then(Value::as_str)
+        .expect("apply_patch output string");
+
+    let expected_output = format!(
+        "apply_patch verification failed: Failed to read file to update {}/{missing_file}: No such file or directory (os error 2)",
+        test.cwd.path().to_string_lossy()
+    );
+    assert_eq!(output, expected_output);
+
+    Ok(())
+}
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn apply_patch_function_call_output_is_structured() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = start_mock_server().await;
+    let mut builder = test_codex().with_config(|config| {
+        config.include_apply_patch_tool = true;
+    });
+    let test = builder.build(&server).await?;
+
+    let call_id = "apply-patch-function";
+    let file_name = "function_apply_patch.txt";
+    let patch =
+        format!("*** Begin Patch\n*** Add File: {file_name}\n+via function call\n*** End Patch\n");
+    let responses = vec![
+        sse(vec![
+            json!({"type": "response.created", "response": {"id": "resp-1"}}),
+            ev_apply_patch_function_call(call_id, &patch),
+            ev_completed("resp-1"),
+        ]),
+        sse(vec![
+            ev_assistant_message("msg-1", "apply_patch function done"),
+            ev_completed("resp-2"),
+        ]),
+    ];
+    mount_sse_sequence(&server, responses).await;
+
+    submit_turn(
+        &test,
+        "apply the patch via function-call apply_patch",
+        SandboxPolicy::DangerFullAccess,
+    )
+    .await?;
+
+    let requests = server
+        .received_requests()
+        .await
+        .expect("recorded requests present");
+    let bodies = request_bodies(&requests)?;
+    let output_item =
+        find_function_call_output(&bodies, call_id).expect("apply_patch function output present");
+    let output = output_item
+        .get("output")
+        .and_then(Value::as_str)
+        .expect("apply_patch output string");
+
+    let expected_pattern = format!(
+        r"(?s)^Exit code: 0
+Wall time: [0-9]+(?:\.[0-9]+)? seconds
+Output:
+Success. Updated the following files:
+A {file_name}
+?$"
+    );
+    assert_regex_match(&expected_pattern, output);
+
+    Ok(())
+}
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn shell_output_is_structured_for_nonzero_exit() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = start_mock_server().await;
+    let mut builder = test_codex().with_config(|config| {
+        config.model = "gpt-5-codex".to_string();
+        config.model_family =
+            find_family_for_model("gpt-5-codex").expect("gpt-5-codex is a model family");
+        config.include_apply_patch_tool = true;
+    });
+    let test = builder.build(&server).await?;
+
+    let call_id = "shell-nonzero-exit";
+    let args = json!({
+        "command": ["/bin/sh", "-c", "exit 42"],
+        "timeout_ms": 1_000,
+    });
+    let responses = vec![
+        sse(vec![
+            json!({"type": "response.created", "response": {"id": "resp-1"}}),
+            ev_function_call(call_id, "shell", &serde_json::to_string(&args)?),
+            ev_completed("resp-1"),
+        ]),
+        sse(vec![
+            ev_assistant_message("msg-1", "shell failure handled"),
+            ev_completed("resp-2"),
+        ]),
+    ];
+    mount_sse_sequence(&server, responses).await;
+
+    submit_turn(
+        &test,
+        "run the failing shell command",
+        SandboxPolicy::DangerFullAccess,
+    )
+    .await?;
+
+    let requests = server
+        .received_requests()
+        .await
+        .expect("recorded requests present");
+    let bodies = request_bodies(&requests)?;
+    let output_item = find_function_call_output(&bodies, call_id).expect("shell output present");
+    let output = output_item
+        .get("output")
+        .and_then(Value::as_str)
+        .expect("shell output string");
+
+    let expected_output = r"Exit code: 42
+Wall time: 0 seconds
+Output:
+";
+    assert_eq!(output, expected_output);
+    assert!(
+        serde_json::from_str::<Value>(output).is_err(),
+        "expected structured shell output to be plain text",
+    );
+    assert!(
+        output.starts_with("Exit code: 42\n"),
+        "expected non-zero exit code prefix, got {output:?}",
+    );
+    assert!(
+        output.contains("\nOutput:\n"),
+        "expected Output section, got {output:?}",
+    );
+
+    Ok(())
+}
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn local_shell_call_output_is_structured() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = start_mock_server().await;
+    let mut builder = test_codex().with_config(|config| {
+        config.model = "gpt-5-codex".to_string();
+        config.model_family =
+            find_family_for_model("gpt-5-codex").expect("gpt-5-codex is a model family");
+        config.include_apply_patch_tool = true;
+    });
+    let test = builder.build(&server).await?;
+
+    let call_id = "local-shell-call";
+    let responses = vec![
+        sse(vec![
+            json!({"type": "response.created", "response": {"id": "resp-1"}}),
+            ev_local_shell_call(call_id, "completed", vec!["/bin/echo", "local shell"]),
+            ev_completed("resp-1"),
+        ]),
+        sse(vec![
+            ev_assistant_message("msg-1", "local shell done"),
+            ev_completed("resp-2"),
+        ]),
+    ];
+    mount_sse_sequence(&server, responses).await;
+
+    submit_turn(
+        &test,
+        "run the local shell command",
+        SandboxPolicy::DangerFullAccess,
+    )
+    .await?;
+
+    let requests = server
+        .received_requests()
+        .await
+        .expect("recorded requests present");
+    let bodies = request_bodies(&requests)?;
+    let output_item =
+        find_function_call_output(&bodies, call_id).expect("local shell output present");
+    let output = output_item
+        .get("output")
+        .and_then(Value::as_str)
+        .expect("local shell output string");
+
+    assert!(
+        serde_json::from_str::<Value>(output).is_err(),
+        "expected structured local shell output to be plain text",
+    );
+    assert!(
+        output.starts_with("Exit code: 0\n"),
+        "expected zero exit code prefix, got {output:?}",
+    );
+    assert!(
+        output.contains("local shell"),
+        "expected command stdout to be present, got {output:?}",
+    );
+
+    Ok(())
+}