Revert state DB injection and agent graph store (#21481)

## Why

Reverts #20689 to restore the previous optional state DB plumbing. The
conflict resolution keeps the newer installation ID and session/thread
identity changes that landed after #20689, while removing the mandatory
state DB and agent graph store dependency from ThreadManager
construction.

## What changed

- Restored `Option<StateDbHandle>` through app-server, MCP server,
prompt debug, and test entry points.
- Removed the `codex-core` dependency on `codex-agent-graph-store` and
reverted descendant lookup back to the existing state DB path when
available.
- Kept newer `installation_id` forwarding by passing it beside the
optional DB handle.
- Kept local thread-name updates working when the optional state DB
handle is absent.

## Validation

- `git diff --check`
- `cargo test -p codex-thread-store`
- `cargo test -p codex-state -p codex-rollout -p
codex-app-server-protocol`
- Attempted `env CARGO_INCREMENTAL=0 cargo test -p codex-core -p
codex-app-server -p codex-app-server-client -p codex-mcp-server -p
codex-thread-manager-sample -p codex-tui`; blocked locally by a rustc
ICE while compiling `v8 v146.4.0` with `rustc 1.93.0 (254b59607
2026-01-19)` on `aarch64-apple-darwin`.

codex-rs/thread-manager-sample/src/main.rs

@@ -52,11 +52,10 @@ use codex_core_api::TuiNotificationSettings;
 use codex_core_api::UriBasedFileOpener;
 use codex_core_api::UserInput;
 use codex_core_api::WebSearchMode;
-use codex_core_api::agent_graph_store_from_state_db;
 use codex_core_api::arg0_dispatch_or_else;
 use codex_core_api::built_in_model_providers;
 use codex_core_api::find_codex_home;
-use codex_core_api::init_state_db_from_config;
+use codex_core_api::init_state_db;
 use codex_core_api::item_event_to_server_notification;
 use codex_core_api::resolve_installation_id;
 use codex_core_api::set_default_originator;
@@ -106,6 +105,7 @@ async fn run_main(arg0_paths: Arg0DispatchPaths) -> anyhow::Result<()> {
     };
 
     let config = new_config(args.model, arg0_paths)?;
+    let state_db = init_state_db(&config).await;
 
     let auth_manager =
         AuthManager::shared_from_config(&config, /*enable_codex_api_key_env*/ false).await;
@@ -113,11 +113,7 @@ async fn run_main(arg0_paths: Arg0DispatchPaths) -> anyhow::Result<()> {
         config.codex_self_exe.clone(),
         config.codex_linux_sandbox_exe.clone(),
     )?;
-    let Some(state_db) = init_state_db_from_config(&config).await else {
-        bail!("thread manager sample requires state db");
-    };
     let thread_store = thread_store_from_config(&config, state_db.clone());
-    let agent_graph_store = agent_graph_store_from_state_db(state_db.clone());
     let environment_manager =
         Arc::new(EnvironmentManager::new(EnvironmentManagerArgs::new(local_runtime_paths)).await);
     let installation_id = resolve_installation_id(&config.codex_home).await?;
@@ -127,9 +123,8 @@ async fn run_main(arg0_paths: Arg0DispatchPaths) -> anyhow::Result<()> {
         SessionSource::Exec,
         environment_manager,
         /*analytics_events_client*/ None,
-        state_db,
         Arc::clone(&thread_store),
-        agent_graph_store,
+        state_db,
         installation_id,
     );