fix(agent): prevent duplicate responses when sub-agents complete concurrently

When the main agent spawns multiple sub-agents, each completion
independently triggered a new _dispatch, causing 3-4 user-visible
responses instead of a single comprehensive report.

- Extend _drain_pending to block-wait on pending_queue when sub-agents
  are still running, keeping the runner loop alive for in-order injection
- Pass pending_queue in the system message path so subsequent sub-agent
  results can still be injected mid-turn via a new dispatch

nanobot/agent/loop.py

@@ -423,15 +423,18 @@ class AgentLoop:
             self._set_runtime_checkpoint(session, payload)
 
         async def _drain_pending(*, limit: int = _MAX_INJECTIONS_PER_TURN) -> list[dict[str, Any]]:
-            """Non-blocking drain of follow-up messages from the pending queue."""
+            """Drain follow-up messages from the pending queue.
+
+            When no messages are immediately available but sub-agents
+            spawned in this dispatch are still running, blocks until at
+            least one result arrives (or timeout).  This keeps the runner
+            loop alive so subsequent sub-agent completions are consumed
+            in-order rather than dispatched separately.
+            """
             if pending_queue is None:
                 return []
-            items: list[dict[str, Any]] = []
-            while len(items) < limit:
-                try:
-                    pending_msg = pending_queue.get_nowait()
-                except asyncio.QueueEmpty:
-                    break
+
+            def _to_user_message(pending_msg: InboundMessage) -> dict[str, Any]:
                 content = pending_msg.content
                 media = pending_msg.media if pending_msg.media else None
                 if media:
@@ -447,7 +450,36 @@ class AgentLoop:
                     merged: str | list[dict[str, Any]] = f"{runtime_ctx}\n\n{user_content}"
                 else:
                     merged = [{"type": "text", "text": runtime_ctx}] + user_content
-                items.append({"role": "user", "content": merged})
+                return {"role": "user", "content": merged}
+
+            items: list[dict[str, Any]] = []
+            while len(items) < limit:
+                try:
+                    items.append(_to_user_message(pending_queue.get_nowait()))
+                except asyncio.QueueEmpty:
+                    break
+
+            # Block if nothing drained but sub-agents spawned in this dispatch
+            # are still running.  Keeps the runner loop alive so subsequent
+            # completions are injected in-order rather than dispatched separately.
+            if (not items
+                    and session is not None
+                    and self.subagents.get_running_count_by_session(session.key) > 0):
+                try:
+                    msg = await asyncio.wait_for(pending_queue.get(), timeout=300)
+                except asyncio.TimeoutError:
+                    logger.warning(
+                        "Timeout waiting for sub-agent completion in session {}",
+                        session.key,
+                    )
+                    return items
+                items.append(_to_user_message(msg))
+                while len(items) < limit:
+                    try:
+                        items.append(_to_user_message(pending_queue.get_nowait()))
+                    except asyncio.QueueEmpty:
+                        break
+
             return items
 
         result = await self.runner.run(AgentRunSpec(
@@ -744,6 +776,7 @@ class AgentLoop:
             final_content, _, all_msgs, _, _ = await self._run_agent_loop(
                 messages, session=session, channel=channel, chat_id=chat_id,
                 message_id=msg.metadata.get("message_id"),
+                pending_queue=pending_queue,
             )
             self._save_turn(session, all_msgs, 1 + len(history))
             self._clear_runtime_checkpoint(session)

tests/agent/tools/test_subagent_tools.py

@@ -1,8 +1,9 @@
 """Tests for subagent tool registration and wiring."""
 
+import asyncio
 import time
 from types import SimpleNamespace
-from unittest.mock import AsyncMock, MagicMock
+from unittest.mock import AsyncMock, MagicMock, patch
 
 import pytest
 
@@ -51,3 +52,209 @@ async def test_subagent_exec_tool_receives_allowed_env_keys(tmp_path):
     )
 
     mgr.runner.run.assert_awaited_once()
+
+
+@pytest.mark.asyncio
+async def test_drain_pending_blocks_while_subagents_running(tmp_path):
+    """_drain_pending should block when no messages are available but sub-agents are still running."""
+    from nanobot.agent.loop import AgentLoop
+    from nanobot.agent.subagent import SubagentManager
+    from nanobot.bus.events import InboundMessage
+    from nanobot.bus.queue import MessageBus
+    from nanobot.session.manager import Session
+
+    bus = MessageBus()
+    provider = MagicMock()
+    provider.get_default_model.return_value = "test-model"
+
+    loop = AgentLoop(bus=bus, provider=provider, workspace=tmp_path, model="test-model")
+
+    pending_queue: asyncio.Queue[InboundMessage] = asyncio.Queue()
+    session = Session(key="test:drain-block")
+    injection_callback = None
+
+    # Capture the injection_callback that _run_agent_loop creates
+    original_run = loop.runner.run
+
+    async def fake_runner_run(spec):
+        nonlocal injection_callback
+        injection_callback = spec.injection_callback
+
+        # Simulate: first call to injection_callback should block because
+        # sub-agents are running and no messages are in the queue yet.
+        # We'll resolve this from a concurrent task.
+        return SimpleNamespace(
+            stop_reason="done",
+            final_content="done",
+            error=None,
+            tool_events=[],
+            messages=[],
+            usage={},
+            had_injections=False,
+            tools_used=[],
+        )
+
+    loop.runner.run = AsyncMock(side_effect=fake_runner_run)
+
+    # Register a running sub-agent in the SubagentManager for this session
+    async def _hang_forever():
+        await asyncio.Event().wait()
+
+    hang_task = asyncio.create_task(_hang_forever())
+    loop.subagents._session_tasks.setdefault(session.key, set()).add("sub-drain-1")
+    loop.subagents._running_tasks["sub-drain-1"] = hang_task
+
+    # Run _run_agent_loop — this defines the _drain_pending closure
+    await loop._run_agent_loop(
+        [{"role": "user", "content": "test"}],
+        session=session,
+        channel="test",
+        chat_id="c1",
+        pending_queue=pending_queue,
+    )
+
+    assert injection_callback is not None
+
+    # Now test the callback directly
+    # With sub-agents running and an empty queue, it should block
+    drain_task = asyncio.create_task(injection_callback())
+
+    # Give it a moment to enter the blocking wait
+    await asyncio.sleep(0.05)
+
+    # Should still be running (blocked on pending_queue.get())
+    assert not drain_task.done(), "drain should block while sub-agents are running"
+
+    # Now put a message in the queue (simulating sub-agent completion)
+    await pending_queue.put(InboundMessage(
+        sender_id="subagent",
+        channel="test",
+        chat_id="c1",
+        content="Sub-agent result",
+        media=None,
+        metadata={},
+    ))
+
+    # Should unblock and return results
+    results = await asyncio.wait_for(drain_task, timeout=2.0)
+    assert len(results) >= 1
+    assert results[0]["role"] == "user"
+    assert "Sub-agent result" in str(results[0]["content"])
+
+    # Cleanup
+    hang_task.cancel()
+    try:
+        await hang_task
+    except asyncio.CancelledError:
+        pass
+
+
+@pytest.mark.asyncio
+async def test_drain_pending_no_block_when_no_subagents(tmp_path):
+    """_drain_pending should not block when no sub-agents are running."""
+    from nanobot.agent.loop import AgentLoop
+    from nanobot.bus.queue import MessageBus
+
+    bus = MessageBus()
+    provider = MagicMock()
+    provider.get_default_model.return_value = "test-model"
+
+    loop = AgentLoop(bus=bus, provider=provider, workspace=tmp_path, model="test-model")
+
+    pending_queue: asyncio.Queue = asyncio.Queue()
+    injection_callback = None
+
+    async def fake_runner_run(spec):
+        nonlocal injection_callback
+        injection_callback = spec.injection_callback
+        return SimpleNamespace(
+            stop_reason="done",
+            final_content="done",
+            error=None,
+            tool_events=[],
+            messages=[],
+            usage={},
+            had_injections=False,
+            tools_used=[],
+        )
+
+    loop.runner.run = AsyncMock(side_effect=fake_runner_run)
+
+    await loop._run_agent_loop(
+        [{"role": "user", "content": "test"}],
+        session=None,
+        channel="test",
+        chat_id="c1",
+        pending_queue=pending_queue,
+    )
+
+    assert injection_callback is not None
+
+    # With no sub-agents and empty queue, should return immediately
+    results = await asyncio.wait_for(injection_callback(), timeout=1.0)
+    assert results == []
+
+
+@pytest.mark.asyncio
+async def test_drain_pending_timeout(tmp_path):
+    """_drain_pending should return empty after timeout when sub-agents hang."""
+    from nanobot.agent.loop import AgentLoop
+    from nanobot.bus.queue import MessageBus
+    from nanobot.session.manager import Session
+
+    bus = MessageBus()
+    provider = MagicMock()
+    provider.get_default_model.return_value = "test-model"
+
+    loop = AgentLoop(bus=bus, provider=provider, workspace=tmp_path, model="test-model")
+
+    pending_queue: asyncio.Queue = asyncio.Queue()
+    session = Session(key="test:drain-timeout")
+    injection_callback = None
+
+    async def fake_runner_run(spec):
+        nonlocal injection_callback
+        injection_callback = spec.injection_callback
+        return SimpleNamespace(
+            stop_reason="done",
+            final_content="done",
+            error=None,
+            tool_events=[],
+            messages=[],
+            usage={},
+            had_injections=False,
+            tools_used=[],
+        )
+
+    loop.runner.run = AsyncMock(side_effect=fake_runner_run)
+
+    # Register a "running" sub-agent that will never complete
+    async def _hang_forever():
+        await asyncio.Event().wait()
+
+    hang_task = asyncio.create_task(_hang_forever())
+    loop.subagents._session_tasks.setdefault(session.key, set()).add("sub-timeout-1")
+    loop.subagents._running_tasks["sub-timeout-1"] = hang_task
+
+    await loop._run_agent_loop(
+        [{"role": "user", "content": "test"}],
+        session=session,
+        channel="test",
+        chat_id="c1",
+        pending_queue=pending_queue,
+    )
+
+    assert injection_callback is not None
+
+    # Patch the timeout to be very short for testing
+    with patch("nanobot.agent.loop.asyncio.wait_for") as mock_wait:
+        mock_wait.side_effect = asyncio.TimeoutError
+        results = await injection_callback()
+        assert results == []
+
+    # Cleanup
+    hang_task.cancel()
+    try:
+        await hang_task
+    except asyncio.CancelledError:
+        pass