fix: improve uploaded document retrieval and deep research reuse (#4784)

* fix: improve uploaded document retrieval and deep research reuse

* test: add coverage for upload manifest and document pagination

* chore: rerun CI

* fix: restore _insert_before_latest_user helper

* fix(agent_loop): restore missing upload context helper

tests/test_agent_loop.py

@@ -39,6 +39,7 @@ try:
         _classify_agent_request,
         _compute_final_metrics,
         _append_tool_results,
+        _insert_before_latest_user,
         _MCP_KEYWORDS,
     )
     _IMPORTED_AGENT_LOOP = sys.modules.get("src.agent_loop")
@@ -73,6 +74,36 @@ def test_polish_internet_search_request_classifies_as_web():
     assert "web" in intent["domains"]
 
 
+def test_insert_before_latest_user_places_context_before_last_user_turn():
+    messages = [
+        {"role": "user", "content": "first"},
+        {"role": "assistant", "content": "reply"},
+        {"role": "user", "content": "latest"},
+    ]
+    context = {"role": "system", "content": "context"}
+
+    out = _insert_before_latest_user(messages, context)
+
+    assert out == [
+        {"role": "user", "content": "first"},
+        {"role": "assistant", "content": "reply"},
+        context,
+        {"role": "user", "content": "latest"},
+    ]
+    assert messages == [
+        {"role": "user", "content": "first"},
+        {"role": "assistant", "content": "reply"},
+        {"role": "user", "content": "latest"},
+    ]
+
+
+def test_insert_before_latest_user_appends_when_no_user_message_exists():
+    messages = [{"role": "assistant", "content": "reply"}]
+    context = {"role": "system", "content": "context"}
+
+    assert _insert_before_latest_user(messages, context) == [messages[0], context]
+
+
 # ---------------------------------------------------------------------------
 # _detect_admin_intent
 # ---------------------------------------------------------------------------