[codex] Inject agent graph store into ThreadManager (#29736)

Pick up the AgentGraphStore migration.

- Inject an explicit optional agent graph store into `ThreadManager` 
- Move all calls to spawn, close, recursive resume, and
subtree/archive/delete/feedback traversal through it
- Keep using  `LocalAgentGraphStore` when SQLite is available

This required some changes to the interface to deal with futures:

- The interface now matches `ThreadStore`'s object-safe pattern by
returning a boxed `AgentGraphStoreFuture` directly, allowing
`ThreadManager` to hold `Arc<dyn AgentGraphStore>`

*Slight behavior change!* Unfiltered subtree enumeration now performs a
single all-status breadth-first traversal, so a closed grandchild
beneath an open edge is included; the previous Open-then-Closed
traversals could not cross mixed-status paths and silently omitted it.

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

@@ -247,7 +247,7 @@ mod tests {
                 )),
                 /*analytics_events_client*/ None,
                 Arc::clone(&thread_store),
-                Some(state_db.clone()),
+                codex_core::local_agent_graph_store_from_state_db(Some(&state_db)),
                 "11111111-1111-4111-8111-111111111111".to_string(),
                 /*attestation_provider*/ None,
                 /*external_time_provider*/ None,

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

@@ -373,7 +373,7 @@ impl MessageProcessor {
                 )),
                 Some(analytics_events_client.clone()),
                 Arc::clone(&thread_store),
-                state_db.clone(),
+                codex_core::local_agent_graph_store_from_state_db(state_db.as_ref()),
                 installation_id,
                 Some(app_server_attestation_provider(
                     outgoing.clone(),

codex-rs/app-server/src/request_processors/feedback_processor.rs

@@ -102,27 +102,7 @@ impl FeedbackRequestProcessor {
                         warn!(
                             "failed to list feedback subtree for thread_id={conversation_id}: {err}"
                         );
-                        let mut thread_ids = vec![conversation_id];
-                        if let Some(state_db_ctx) = state_db_ctx.as_ref() {
-                            for status in [
-                                codex_state::DirectionalThreadSpawnEdgeStatus::Open,
-                                codex_state::DirectionalThreadSpawnEdgeStatus::Closed,
-                            ] {
-                                match state_db_ctx
-                                    .list_thread_spawn_descendants_with_status(
-                                        conversation_id,
-                                        status,
-                                    )
-                                    .await
-                                {
-                                    Ok(descendant_ids) => thread_ids.extend(descendant_ids),
-                                    Err(err) => warn!(
-                                        "failed to list persisted feedback subtree for thread_id={conversation_id}: {err}"
-                                    ),
-                                }
-                            }
-                        }
-                        thread_ids
+                        vec![conversation_id]
                     }
                 },
                 None => Vec::new(),

codex-rs/app-server/src/request_processors/thread_delete.rs

@@ -1,6 +1,5 @@
 //! `thread/delete` request handling.
 
-use super::thread_processor::core_thread_write_error;
 use super::thread_processor::unsupported_thread_store_operation;
 use super::*;
 
@@ -37,23 +36,7 @@ impl ThreadRequestProcessor {
         let thread_id = ThreadId::from_string(&params.thread_id)
             .map_err(|err| invalid_request(format!("invalid thread id: {err}")))?;
 
-        let mut thread_ids = self.state_db_spawn_subtree_thread_ids(thread_id).await?;
-        let mut seen = thread_ids.iter().copied().collect::<HashSet<_>>();
-
-        match self
-            .thread_manager
-            .list_agent_subtree_thread_ids(thread_id)
-            .await
-        {
-            Ok(live_thread_ids) => {
-                for live_thread_id in live_thread_ids {
-                    if seen.insert(live_thread_id) {
-                        thread_ids.push(live_thread_id);
-                    }
-                }
-            }
-            Err(err) => return Err(core_thread_write_error("delete thread", err)),
-        }
+        let thread_ids = self.state_db_spawn_subtree_thread_ids(thread_id).await?;
 
         self.validate_root_thread_delete(thread_id, thread_ids.len() > 1)
             .await?;

codex-rs/app-server/src/request_processors/thread_processor.rs

@@ -1431,25 +1431,14 @@ impl ThreadRequestProcessor {
         &self,
         thread_id: ThreadId,
     ) -> Result<Vec<ThreadId>, JSONRPCErrorError> {
-        let mut thread_ids = vec![thread_id];
-        let Some(state_db_ctx) = self.state_db.as_ref() else {
-            return Ok(thread_ids);
-        };
-        let mut seen = HashSet::from([thread_id]);
-        let descendants = state_db_ctx
-            .list_thread_spawn_descendants(thread_id)
+        self.thread_manager
+            .list_agent_subtree_thread_ids(thread_id)
             .await
             .map_err(|err| {
                 internal_error(format!(
                     "failed to list spawned descendants for thread id {thread_id}: {err}"
                 ))
-            })?;
-        for descendant_id in descendants {
-            if seen.insert(descendant_id) {
-                thread_ids.push(descendant_id);
-            }
-        }
-        Ok(thread_ids)
+            })
     }
 
     async fn thread_increment_elicitation_inner(