Fix project trust config parsing so CLI overrides work (#13090)

Fixes #13076

This PR fixes a bug that causes command-line config overrides for MCP
subtables to not be merged correctly.

Summary
- make project trust loading go through the dedicated struct so CLI
overrides can update trusted project-local MCP transports

---------

Co-authored-by: jif-oai <jif@openai.com>

codex-rs/core/src/config_loader/mod.rs

@@ -6,7 +6,6 @@ mod macos;
 mod tests;
 
 use crate::config::ConfigToml;
-use crate::config::deserialize_config_toml_with_base;
 use crate::config_loader::layer_io::LoadedConfigLayers;
 use crate::git_info::resolve_root_git_project_for_trust;
 use codex_app_server_protocol::ConfigLayerSource;
@@ -576,6 +575,11 @@ struct ProjectTrustContext {
     user_config_file: AbsolutePathBuf,
 }
 
+#[derive(Deserialize)]
+struct ProjectTrustConfigToml {
+    projects: Option<std::collections::HashMap<String, crate::config::ProjectConfig>>,
+}
+
 struct ProjectTrustDecision {
     trust_level: Option<TrustLevel>,
     trust_key: String,
@@ -666,10 +670,16 @@ async fn project_trust_context(
     config_base_dir: &Path,
     user_config_file: &AbsolutePathBuf,
 ) -> io::Result<ProjectTrustContext> {
-    let config_toml = deserialize_config_toml_with_base(merged_config.clone(), config_base_dir)?;
+    let project_trust_config: ProjectTrustConfigToml = {
+        let _guard = AbsolutePathBufGuard::new(config_base_dir);
+        merged_config
+            .clone()
+            .try_into()
+            .map_err(|err| std::io::Error::new(std::io::ErrorKind::InvalidData, err))?
+    };
 
     let project_root = find_project_root(cwd, project_root_markers).await?;
-    let projects = config_toml.projects.unwrap_or_default();
+    let projects = project_trust_config.projects.unwrap_or_default();
 
     let project_root_key = project_root.as_path().to_string_lossy().to_string();
     let repo_root = resolve_root_git_project_for_trust(cwd.as_path());

codex-rs/core/src/config_loader/tests.rs

@@ -1114,6 +1114,91 @@ async fn project_layers_disabled_when_untrusted_or_unknown() -> std::io::Result<
     Ok(())
 }
 
+#[tokio::test]
+async fn cli_override_can_update_project_local_mcp_server_when_project_is_trusted()
+-> std::io::Result<()> {
+    let tmp = tempdir()?;
+    let project_root = tmp.path().join("project");
+    let nested = project_root.join("child");
+    let dot_codex = project_root.join(".codex");
+    let codex_home = tmp.path().join("home");
+    tokio::fs::create_dir_all(&nested).await?;
+    tokio::fs::create_dir_all(&dot_codex).await?;
+    tokio::fs::create_dir_all(&codex_home).await?;
+    tokio::fs::write(project_root.join(".git"), "gitdir: here").await?;
+    tokio::fs::write(
+        dot_codex.join(CONFIG_TOML_FILE),
+        r#"
+[mcp_servers.sentry]
+url = "https://mcp.sentry.dev/mcp"
+enabled = false
+"#,
+    )
+    .await?;
+    make_config_for_test(&codex_home, &project_root, TrustLevel::Trusted, None).await?;
+
+    let config = ConfigBuilder::default()
+        .codex_home(codex_home)
+        .cli_overrides(vec![(
+            "mcp_servers.sentry.enabled".to_string(),
+            TomlValue::Boolean(true),
+        )])
+        .fallback_cwd(Some(nested))
+        .build()
+        .await?;
+
+    let server = config
+        .mcp_servers
+        .get()
+        .get("sentry")
+        .expect("trusted project MCP server should load");
+    assert!(server.enabled);
+
+    Ok(())
+}
+
+#[tokio::test]
+async fn cli_override_for_disabled_project_local_mcp_server_returns_invalid_transport()
+-> std::io::Result<()> {
+    let tmp = tempdir()?;
+    let project_root = tmp.path().join("project");
+    let nested = project_root.join("child");
+    let dot_codex = project_root.join(".codex");
+    let codex_home = tmp.path().join("home");
+    tokio::fs::create_dir_all(&nested).await?;
+    tokio::fs::create_dir_all(&dot_codex).await?;
+    tokio::fs::create_dir_all(&codex_home).await?;
+    tokio::fs::write(project_root.join(".git"), "gitdir: here").await?;
+    tokio::fs::write(
+        dot_codex.join(CONFIG_TOML_FILE),
+        r#"
+[mcp_servers.sentry]
+url = "https://mcp.sentry.dev/mcp"
+enabled = false
+"#,
+    )
+    .await?;
+
+    let err = ConfigBuilder::default()
+        .codex_home(codex_home)
+        .cli_overrides(vec![(
+            "mcp_servers.sentry.enabled".to_string(),
+            TomlValue::Boolean(true),
+        )])
+        .fallback_cwd(Some(nested))
+        .build()
+        .await
+        .expect_err("untrusted project layer should not provide MCP transport");
+
+    assert!(
+        err.to_string().contains("invalid transport")
+            && err.to_string().contains("mcp_servers.sentry"),
+        "unexpected error: {err}"
+    );
+
+    Ok(())
+}
+
 #[tokio::test]
 async fn invalid_project_config_ignored_when_untrusted_or_unknown() -> std::io::Result<()> {
     let tmp = tempdir()?;