[feat] persist thread_dynamic_tools in db (#10252)

Persist thread_dynamic_tools in sqlite and read first from it. Fall back
to rollout files if it's not found. Persist dynamic tools to both sqlite
and rollout files.

Saw that new sessions get populated to db correctly & old sessions get
backfilled correctly at startup:
```
celia@com-92114 codex-rs % sqlite3 ~/.codex/state.sqlite \      "select thread_id, position,name,description,input_schema from thread_dynamic_tools;"
019c0cad-ec0d-74b2-a787-e8b33a349117|0|geo_lookup|lookup a city|{"properties":{"city":{"type":"string"}},"required":["city"],"type":"object"}
....
019c10ca-aa4b-7620-ae40-c0919fbd7ea7|0|geo_lookup|lookup a city|{"properties":{"city":{"type":"string"}},"required":["city"],"type":"object"}
```

codex-rs/core/src/state_db.rs

@@ -9,6 +9,7 @@ use chrono::Timelike;
 use chrono::Utc;
 use codex_otel::OtelManager;
 use codex_protocol::ThreadId;
+use codex_protocol::dynamic_tools::DynamicToolSpec;
 use codex_protocol::protocol::RolloutItem;
 use codex_protocol::protocol::SessionSource;
 use codex_state::DB_METRIC_COMPARE_ERROR;
@@ -196,6 +197,37 @@ pub async fn find_rollout_path_by_id(
         })
 }
 
+/// Get dynamic tools for a thread id using SQLite.
+pub async fn get_dynamic_tools(
+    context: Option<&codex_state::StateRuntime>,
+    thread_id: ThreadId,
+    stage: &str,
+) -> Option<Vec<DynamicToolSpec>> {
+    let ctx = context?;
+    match ctx.get_dynamic_tools(thread_id).await {
+        Ok(tools) => tools,
+        Err(err) => {
+            warn!("state db get_dynamic_tools failed during {stage}: {err}");
+            None
+        }
+    }
+}
+
+/// Persist dynamic tools for a thread id using SQLite, if none exist yet.
+pub async fn persist_dynamic_tools(
+    context: Option<&codex_state::StateRuntime>,
+    thread_id: ThreadId,
+    tools: Option<&[DynamicToolSpec]>,
+    stage: &str,
+) {
+    let Some(ctx) = context else {
+        return;
+    };
+    if let Err(err) = ctx.persist_dynamic_tools(thread_id, tools).await {
+        warn!("state db persist_dynamic_tools failed during {stage}: {err}");
+    }
+}
+
 /// Reconcile rollout items into SQLite, falling back to scanning the rollout file.
 pub async fn reconcile_rollout(
     context: Option<&codex_state::StateRuntime>,
@@ -235,6 +267,21 @@ pub async fn reconcile_rollout(
             "state db reconcile_rollout upsert failed {}: {err}",
             rollout_path.display()
         );
+        return;
+    }
+    if let Ok(meta_line) = crate::rollout::list::read_session_meta_line(rollout_path).await {
+        persist_dynamic_tools(
+            Some(ctx),
+            meta_line.meta.id,
+            meta_line.meta.dynamic_tools.as_deref(),
+            "reconcile_rollout",
+        )
+        .await;
+    } else {
+        warn!(
+            "state db reconcile_rollout missing session meta {}",
+            rollout_path.display()
+        );
     }
 }