fix local codex review comment

  - [P1] Preserve new session items when callback mutates history — packages/agents-core/src/runImplementation.ts:1651-1688
    If a sessionInputCallback mutates the history array (e.g. the natural pattern history.push(...newItems.map(item => ({ ...item }))); return history; to annotate new rows) the
  logic here misclassifies those freshly added items as existing history. Because we build historyCounts/historyRefs after the callback, the cloned entries land in historyRefs
  and the loop then skips them, leaving appended empty. Downstream we persist sessionItems: appended.length > 0 ? appended : [], so the turn’s new input never gets written to the
  session. That silently drops user input for any in-place merge strategy, which is a severe regression for the new memory feature.

Author: seratch

packages/agents-core/src/runImplementation.ts

@@ -1656,6 +1656,11 @@ export async function prepareInputItemsWithSession(
     };
   }
 
+  // Capture snapshots before invoking the callback so we can reason about the original state even
+  // if the callback mutates the history array in-place.
+  const historySnapshot = history.slice();
+  const newInputSnapshot = newInputItems.slice();
+
   // Delegate history reconciliation to the user-supplied callback. It must return a concrete list
   // to keep downstream model requests well-typed.
   const combined = await sessionInputCallback(history, newInputItems);
@@ -1665,10 +1670,10 @@ export async function prepareInputItemsWithSession(
     );
   }
 
-  const historyCounts = buildItemFrequencyMap(history);
-  const newInputCounts = buildItemFrequencyMap(newInputItems);
-  const historyRefs = buildItemReferenceMap(history);
-  const newInputRefs = buildItemReferenceMap(newInputItems);
+  const historyCounts = buildItemFrequencyMap(historySnapshot);
+  const newInputCounts = buildItemFrequencyMap(newInputSnapshot);
+  const historyRefs = buildItemReferenceMap(historySnapshot);
+  const newInputRefs = buildItemReferenceMap(newInputSnapshot);
 
   const appended: AgentInputItem[] = [];
   for (const item of combined) {
@@ -1707,7 +1712,7 @@ export async function prepareInputItemsWithSession(
       ? combined
       : appended.length > 0
         ? appended
-        : newInputItems,
+        : newInputSnapshot,
     sessionItems: appended.length > 0 ? appended : [],
   };
 }

packages/agents-core/test/runImplementation.test.ts

@@ -347,6 +347,46 @@ describe('prepareInputItemsWithSession', () => {
     expect(sessionItems[0]).toBe(newItem);
   });
 
+  it('persists appended copies when callbacks mutate history in place', async () => {
+    const historyItem: AgentInputItem = {
+      type: 'message',
+      role: 'user',
+      content: 'past',
+      id: 'history-1',
+    };
+    const newItem: AgentInputItem = {
+      type: 'message',
+      role: 'user',
+      content: 'fresh',
+      id: 'new-1',
+    };
+    const session = new StubSession([historyItem]);
+
+    let appendedItems: AgentInputItem[] = [];
+    const result = await prepareInputItemsWithSession(
+      [newItem],
+      session,
+      (history, newItems) => {
+        appendedItems = newItems.map((item) => ({
+          ...item,
+          providerData: { annotated: true },
+        }));
+        history.push(...appendedItems);
+        return history;
+      },
+    );
+
+    expect(appendedItems).toHaveLength(1);
+    expect(result.preparedInput).toEqual([historyItem, ...appendedItems]);
+    const sessionItems = result.sessionItems;
+    if (!sessionItems) {
+      throw new Error('Expected sessionItems to be defined.');
+    }
+    expect(sessionItems).toEqual(appendedItems);
+    expect(sessionItems[0]).toBe(appendedItems[0]);
+    expect(sessionItems[0]).not.toBe(newItem);
+  });
+
   it('omits session history from prepared input when includeHistoryInPreparedInput is false', async () => {
     const historyItem: AgentInputItem = {
       type: 'message',