Add layered config.toml support to app server (#9510)

This PR adds support for chained (layered) config.toml file merging for
clients that use the app server interface. This feature already exists
for the TUI, but it does not work for GUI clients.

It does the following:
* Changes code paths for new thread, resume thread, and fork thread to
use the effective config based on the cwd.
* Updates the `config/read` API to accept an optional `cwd` parameter.
If specified, the API returns the effective config based on that cwd
path. Also optionally includes all layers including project config
files. If cwd is not specified, the API falls back on its older behavior
where it considers only the global (non-project) config files when
computing the effective config.

The changes in codex_message_processor.rs look deceptively large. They
mostly just involve moving existing blocks of code to a later point in
some functions so it can use the cwd to calculate the config.

This PR builds upon #9509 and should be reviewed and merged after that
PR.

Tested:
* Verified change with (dependent, as-yet-uncommitted) changes to IDE
Extension and confirmed correct behavior

The full fix requires additional changes in the IDE Extension code base,
but they depend on this PR.

codex-rs/app-server/tests/suite/v2/thread_start.rs

@@ -8,6 +8,9 @@ use codex_app_server_protocol::RequestId;
 use codex_app_server_protocol::ThreadStartParams;
 use codex_app_server_protocol::ThreadStartResponse;
 use codex_app_server_protocol::ThreadStartedNotification;
+use codex_core::config::set_project_trust_level;
+use codex_protocol::config_types::TrustLevel;
+use codex_protocol::openai_models::ReasoningEffort;
 use std::path::Path;
 use tempfile::TempDir;
 use tokio::time::timeout;
@@ -69,6 +72,47 @@ async fn thread_start_creates_thread_and_emits_started() -> Result<()> {
     Ok(())
 }
 
+#[tokio::test]
+async fn thread_start_respects_project_config_from_cwd() -> Result<()> {
+    let server = create_mock_responses_server_repeating_assistant("Done").await;
+
+    let codex_home = TempDir::new()?;
+    create_config_toml(codex_home.path(), &server.uri())?;
+
+    let workspace = TempDir::new()?;
+    let project_config_dir = workspace.path().join(".codex");
+    std::fs::create_dir_all(&project_config_dir)?;
+    std::fs::write(
+        project_config_dir.join("config.toml"),
+        r#"
+model_reasoning_effort = "high"
+"#,
+    )?;
+    set_project_trust_level(codex_home.path(), workspace.path(), TrustLevel::Trusted)?;
+
+    let mut mcp = McpProcess::new(codex_home.path()).await?;
+    timeout(DEFAULT_READ_TIMEOUT, mcp.initialize()).await??;
+
+    let req_id = mcp
+        .send_thread_start_request(ThreadStartParams {
+            cwd: Some(workspace.path().to_string_lossy().into_owned()),
+            ..Default::default()
+        })
+        .await?;
+
+    let resp: JSONRPCResponse = timeout(
+        DEFAULT_READ_TIMEOUT,
+        mcp.read_stream_until_response_message(RequestId::Integer(req_id)),
+    )
+    .await??;
+    let ThreadStartResponse {
+        reasoning_effort, ..
+    } = to_response::<ThreadStartResponse>(resp)?;
+
+    assert_eq!(reasoning_effort, Some(ReasoningEffort::High));
+    Ok(())
+}
+
 // Helper to create a config.toml pointing at the mock model server.
 fn create_config_toml(codex_home: &Path, server_uri: &str) -> std::io::Result<()> {
     let config_toml = codex_home.join("config.toml");