Inject state DB, agent graph store (#20689)

## Why

We want the agent graph store to be passed down the stack as a real
dependency, the same way we already treat the thread store.

This will let us inject the agent graph store as a real dependency and
support implementations other than the local SQLite-backed one. Right
now most code instantiates a state DB and an agent graph store
just-in-time. Ideally, we would not depend on the state DB directly but
only read through the higher-level interfaces.

This change makes the dependency boundaries explicit and moves state DB
initialization to process bootstrap instead of hiding it inside local
store implementations.

## What changed

- `ThreadManager` now requires a `StateDbHandle` and an
`AgentGraphStore` at construction time instead of treating them as
optional internals.
- The local store constructors no longer lazily initialize SQLite.
Callers now initialize the state DB once per process and use that shared
handle to build:
  - `LocalThreadStore`
  - `LocalAgentGraphStore`
- App bootstraps (`app-server`, `mcp-server`, `prompt_debug`, and the
thread-manager sample) now initialize the state DB up front and inject
the resulting handle down the stack.
- `app-server` now consistently uses its process-scoped state DB handle
instead of reopening SQLite or trying to recover it from loaded threads.
- Device-key storage now reuses the shared state DB handle instead of
maintaining its own lazy opener.
- The thread archive / descendant traversal paths now use the injected
`AgentGraphStore` instead of reaching through local
thread-store-specific state.

## Verification

- `cargo check -p codex-core -p codex-thread-store -p codex-app-server
-p codex-mcp-server -p codex-thread-manager-sample --tests`
- `cargo test -p codex-thread-store`
- `cargo test -p codex-core
thread_manager_accepts_separate_agent_graph_store_and_thread_store --
--nocapture`
- `cargo test -p codex-app-server
thread_archive_archives_spawned_descendants -- --nocapture`

codex-rs/app-server/src/message_processor.rs

@@ -61,6 +61,7 @@ use codex_app_server_protocol::experimental_required_message;
 use codex_arg0::Arg0DispatchPaths;
 use codex_chatgpt::workspace_settings;
 use codex_core::ThreadManager;
+use codex_core::agent_graph_store_from_state_db;
 use codex_core::config::Config;
 use codex_core::thread_store_from_config;
 use codex_exec_server::EnvironmentManager;
@@ -254,7 +255,7 @@ pub(crate) struct MessageProcessorArgs {
     pub(crate) environment_manager: Arc<EnvironmentManager>,
     pub(crate) feedback: CodexFeedback,
     pub(crate) log_db: Option<LogDbLayer>,
-    pub(crate) state_db: Option<StateDbHandle>,
+    pub(crate) state_db: StateDbHandle,
     pub(crate) config_warnings: Vec<ConfigWarningNotification>,
     pub(crate) session_source: SessionSource,
     pub(crate) auth_manager: Arc<AuthManager>,
@@ -291,14 +292,16 @@ impl MessageProcessor {
         // affect per-thread behavior, but they must not move newly started,
         // resumed, or forked threads to a different persistence backend/root.
         let thread_store = thread_store_from_config(config.as_ref(), state_db.clone());
+        let agent_graph_store = agent_graph_store_from_state_db(state_db.clone());
         let thread_manager = Arc::new(ThreadManager::new(
             config.as_ref(),
             auth_manager.clone(),
             session_source,
             environment_manager,
             Some(analytics_events_client.clone()),
-            Arc::clone(&thread_store),
             state_db.clone(),
+            Arc::clone(&thread_store),
+            agent_graph_store.clone(),
         ));
         thread_manager
             .plugins_manager()
@@ -344,7 +347,7 @@ impl MessageProcessor {
             Arc::clone(&config),
             feedback,
             log_db,
-            state_db.clone(),
+            Some(state_db.clone()),
         );
         let git_processor = GitRequestProcessor::new();
         let initialize_processor = InitializeRequestProcessor::new(
@@ -395,7 +398,7 @@ impl MessageProcessor {
             thread_watch_manager.clone(),
             Arc::clone(&thread_list_state_permit),
             thread_goal_processor.clone(),
-            state_db.clone(),
+            Some(state_db.clone()),
         );
         let turn_processor = TurnRequestProcessor::new(
             auth_manager.clone(),