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());