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/core/src/stream_events_utils.rs

@@ -138,8 +138,11 @@ pub(crate) async fn record_completed_response_item(
             .await;
     }
     mark_thread_memory_mode_polluted_if_external_context(sess, turn_context, item).await;
-    let has_memory_citation =
-        record_stage1_output_usage_and_detect_memory_citation(sess.state_db(), item).await;
+    let has_memory_citation = record_stage1_output_usage_and_detect_memory_citation(
+        sess.services.state_db.as_ref(),
+        item,
+    )
+    .await;
     if has_memory_citation {
         sess.record_memory_citation_for_turn(&turn_context.sub_id)
             .await;
@@ -174,7 +177,7 @@ pub(crate) async fn mark_thread_memory_mode_polluted_if_external_context(
 }
 
 async fn record_stage1_output_usage_and_detect_memory_citation(
-    state_db_ctx: Option<state_db::StateDbHandle>,
+    state_db_ctx: Option<&state_db::StateDbHandle>,
     item: &ResponseItem,
 ) -> bool {
     let Some(raw_text) = raw_assistant_output_text_from_item(item) else {