[codex] add latency tracing spans (#27710)

## Why

We have some large gaps in our thread start, resume, and pre-sampling
traces that make it hard to tell where latency is coming from.

## What Changed

- Added coarse spans around thread start/resume, turn context
construction, rollout reconstruction, skill/plugin loading, and tool
preparation.
- Added a breakdown of discoverable-tool preparation across connector
loading, plugin discovery, and local plugin details.

## Testing

- `cargo check -p codex-app-server -p codex-core -p codex-core-skills -p
codex-core-plugins`
- Built the app-server locally and exercised thread start, first turn,
follow-up turn, server restart, thread resume, and a resumed turn.

codex-rs/core-plugins/src/loader.rs

@@ -46,6 +46,7 @@ use std::path::Path;
 use std::process::Command;
 use std::sync::Arc;
 use tempfile::TempDir;
+use tracing::instrument;
 use tracing::warn;
 
 const DEFAULT_SKILLS_DIR_NAME: &str = "skills";
@@ -111,6 +112,7 @@ struct PluginAppConfig {
     category: Option<String>,
 }
 
+#[instrument(level = "trace", skip_all)]
 pub async fn load_plugins_from_layer_stack(
     config_layer_stack: &ConfigLayerStack,
     extra_plugins: HashMap<String, PluginConfig>,