diff --git a/src/google/adk/cli/utils/agent_loader.py b/src/google/adk/cli/utils/agent_loader.py
index 6ea3fc36..b4330681 100644
--- a/src/google/adk/cli/utils/agent_loader.py
+++ b/src/google/adk/cli/utils/agent_loader.py
@@ -15,6 +15,7 @@
 from __future__ import annotations
 
 import importlib
+import importlib.util
 import logging
 import os
 from pathlib import Path
@@ -205,22 +206,30 @@ class AgentLoader(BaseAgentLoader):
     envs.load_dotenv_for_agent(actual_agent_name, str(agents_dir))
 
     if root_agent := self._load_from_module_or_package(actual_agent_name):
-      self._ensure_app_name_matches(
-          maybe_app=root_agent,
+      self._record_origin_metadata(
+          loaded=root_agent,
           expected_app_name=actual_agent_name,
+          module_name=actual_agent_name,
           agents_dir=agents_dir,
       )
       return root_agent
 
     if root_agent := self._load_from_submodule(actual_agent_name):
-      self._ensure_app_name_matches(
-          maybe_app=root_agent,
+      self._record_origin_metadata(
+          loaded=root_agent,
           expected_app_name=actual_agent_name,
+          module_name=f"{actual_agent_name}.agent",
           agents_dir=agents_dir,
       )
       return root_agent
 
     if root_agent := self._load_from_yaml_config(actual_agent_name, agents_dir):
+      self._record_origin_metadata(
+          loaded=root_agent,
+          expected_app_name=actual_agent_name,
+          module_name=None,
+          agents_dir=agents_dir,
+      )
       return root_agent
 
     # If no root_agent was found by any pattern
@@ -250,32 +259,42 @@ class AgentLoader(BaseAgentLoader):
         f" root_agent is exposed.{hint}"
     )
 
-  def _ensure_app_name_matches(
+  def _record_origin_metadata(
       self,
       *,
-      maybe_app: Union[BaseAgent, App],
+      loaded: Union[BaseAgent, App],
       expected_app_name: str,
+      module_name: Optional[str],
       agents_dir: str,
   ) -> None:
-    """Raises a detailed error when App.name does not match its directory."""
+    """Annotates loaded agent/App with its origin for later diagnostics."""
 
-    if not isinstance(maybe_app, App):
-      return
-
-    # Built-in apps live under double-underscore directories.
+    # Do not attach metadata for built-in agents (double underscore names).
     if expected_app_name.startswith("__"):
       return
 
-    if maybe_app.name == expected_app_name:
-      return
+    origin_path: Optional[Path] = None
+    if module_name:
+      spec = importlib.util.find_spec(module_name)
+      if spec and spec.origin:
+        module_origin = Path(spec.origin).resolve()
+        origin_path = (
+            module_origin.parent if module_origin.is_file() else module_origin
+        )
 
-    raise ValueError(
-        "App name mismatch detected. The App defined at "
-        f"'{agents_dir}/{expected_app_name}' declares name "
-        f"'{maybe_app.name}', but ADK expects it to match the directory "
-        f"name '{expected_app_name}'. Rename the App or the folder so they "
-        "match, then reload."
-    )
+    if origin_path is None:
+      candidate = Path(agents_dir, expected_app_name)
+      origin_path = candidate if candidate.exists() else Path(agents_dir)
+
+    def _attach_metadata(target: Union[BaseAgent, App]) -> None:
+      setattr(target, "_adk_origin_app_name", expected_app_name)
+      setattr(target, "_adk_origin_path", origin_path)
+
+    if isinstance(loaded, App):
+      _attach_metadata(loaded)
+      _attach_metadata(loaded.root_agent)
+    else:
+      _attach_metadata(loaded)
 
   @override
   def load_agent(self, agent_name: str) -> Union[BaseAgent, App]:
diff --git a/src/google/adk/runners.py b/src/google/adk/runners.py
index f68008af..50197dda 100644
--- a/src/google/adk/runners.py
+++ b/src/google/adk/runners.py
@@ -155,6 +155,7 @@ class Runner:
         self._agent_origin_app_name,
         self._agent_origin_dir,
     ) = self._infer_agent_origin(self.agent)
+    self._app_name_alignment_hint: Optional[str] = None
     self._enforce_app_name_alignment()
 
   def _validate_runner_params(
@@ -230,35 +231,47 @@ class Runner:
     module_path = Path(module_file).resolve()
     project_root = Path.cwd()
     try:
-      module_path.relative_to(project_root)
+      relative_path = module_path.relative_to(project_root)
     except ValueError:
       return None, module_path.parent
-
-    current = module_path.parent
-    while current != project_root and current.parent != current:
-      parent = current.parent
-      if parent.name == 'agents':
-        return current.name, current
-      current = parent
-
-    return None, module_path.parent
+    origin_dir = module_path.parent
+    if 'agents' not in relative_path.parts:
+      return None, origin_dir
+    origin_name = origin_dir.name
+    if origin_name.startswith('.'):
+      return None, origin_dir
+    return origin_name, origin_dir
 
   def _enforce_app_name_alignment(self) -> None:
     origin_name = self._agent_origin_app_name
     origin_dir = self._agent_origin_dir
     if not origin_name or origin_name.startswith('__'):
+      self._app_name_alignment_hint = None
       return
     if origin_name == self.app_name:
+      self._app_name_alignment_hint = None
       return
     origin_location = str(origin_dir) if origin_dir else origin_name
-    message = (
-        'App name mismatch detected. The runner is configured with '
-        f'app name "{self.app_name}", but the root agent was loaded from '
-        f'"{origin_location}", which implies app name "{origin_name}". '
-        'Rename the App or its directory so the names match before running '
-        'the agent.'
+    mismatch_details = (
+        'The runner is configured with app name '
+        f'"{self.app_name}", but the root agent was loaded from '
+        f'"{origin_location}", which implies app name "{origin_name}".'
+    )
+    resolution = (
+        'Ensure the runner app_name matches that directory or pass app_name '
+        'explicitly when constructing the runner.'
+    )
+    self._app_name_alignment_hint = f'{mismatch_details} {resolution}'
+    logger.warning('App name mismatch detected. %s', mismatch_details)
+
+  def _format_session_not_found_message(self, session_id: str) -> str:
+    message = f'Session not found: {session_id}'
+    if not self._app_name_alignment_hint:
+      return message
+    return (
+        f'{message}. {self._app_name_alignment_hint} '
+        'The mismatch prevents the runner from locating the session.'
     )
-    raise ValueError(message)
 
   def run(
       self,
@@ -362,7 +375,8 @@ class Runner:
             app_name=self.app_name, user_id=user_id, session_id=session_id
         )
         if not session:
-          raise ValueError(f'Session not found: {session_id}')
+          message = self._format_session_not_found_message(session_id)
+          raise ValueError(message)
         if not invocation_id and not new_message:
           raise ValueError('Both invocation_id and new_message are None.')
 
diff --git a/src/google/adk/tools/agent_tool.py b/src/google/adk/tools/agent_tool.py
index 9f276fa4..43c2d2be 100644
--- a/src/google/adk/tools/agent_tool.py
+++ b/src/google/adk/tools/agent_tool.py
@@ -125,8 +125,13 @@ class AgentTool(BaseTool):
           role='user',
           parts=[types.Part.from_text(text=args['request'])],
       )
+    invocation_context = tool_context._invocation_context
+    parent_app_name = (
+        invocation_context.app_name if invocation_context else None
+    )
+    child_app_name = parent_app_name or self.agent.name
     runner = Runner(
-        app_name=self.agent.name,
+        app_name=child_app_name,
         agent=self.agent,
         artifact_service=ForwardingArtifactService(tool_context),
         session_service=InMemorySessionService(),
@@ -141,7 +146,7 @@ class AgentTool(BaseTool):
         if not k.startswith('_adk')  # Filter out adk internal states
     }
     session = await runner.session_service.create_session(
-        app_name=self.agent.name,
+        app_name=child_app_name,
         user_id=tool_context._invocation_context.user_id,
         state=state_dict,
     )
diff --git a/tests/unittests/test_runners.py b/tests/unittests/test_runners.py
index e6578aab..d78061dd 100644
--- a/tests/unittests/test_runners.py
+++ b/tests/unittests/test_runners.py
@@ -12,6 +12,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from pathlib import Path
+import textwrap
 from typing import Optional
 
 from google.adk.agents.base_agent import BaseAgent
@@ -21,6 +23,7 @@ from google.adk.agents.llm_agent import LlmAgent
 from google.adk.apps.app import App
 from google.adk.apps.app import ResumabilityConfig
 from google.adk.artifacts.in_memory_artifact_service import InMemoryArtifactService
+from google.adk.cli.utils.agent_loader import AgentLoader
 from google.adk.events.event import Event
 from google.adk.plugins.base_plugin import BasePlugin
 from google.adk.runners import Runner
@@ -158,6 +161,120 @@ class TestRunnerFindAgentToRun:
         artifact_service=self.artifact_service,
     )
 
+
+@pytest.mark.asyncio
+async def test_session_not_found_message_includes_alignment_hint():
+
+  class RunnerWithMismatch(Runner):
+
+    def _infer_agent_origin(
+        self, agent: BaseAgent
+    ) -> tuple[Optional[str], Optional[Path]]:
+      del agent
+      return "expected_app", Path("/workspace/agents/expected_app")
+
+  session_service = InMemorySessionService()
+  runner = RunnerWithMismatch(
+      app_name="configured_app",
+      agent=MockLlmAgent("root_agent"),
+      session_service=session_service,
+      artifact_service=InMemoryArtifactService(),
+  )
+
+  agen = runner.run_async(
+      user_id="user",
+      session_id="missing",
+      new_message=types.Content(role="user", parts=[]),
+  )
+
+  with pytest.raises(ValueError) as excinfo:
+    await agen.__anext__()
+
+  await agen.aclose()
+
+  message = str(excinfo.value)
+  assert "Session not found" in message
+  assert "configured_app" in message
+  assert "expected_app" in message
+  assert "Ensure the runner app_name matches" in message
+
+
+@pytest.mark.asyncio
+async def test_runner_allows_nested_agent_directories(tmp_path, monkeypatch):
+  project_root = tmp_path / "workspace"
+  agent_dir = project_root / "agents" / "examples" / "001_hello_world"
+  agent_dir.mkdir(parents=True)
+  # Make package structure importable.
+  for pkg_dir in [
+      project_root / "agents",
+      project_root / "agents" / "examples",
+      agent_dir,
+  ]:
+    (pkg_dir / "__init__.py").write_text("", encoding="utf-8")
+  # Extra directories that previously confused origin inference, e.g. virtualenv.
+  (project_root / "agents" / ".venv").mkdir()
+
+  agent_source = textwrap.dedent("""\
+      from google.adk.events.event import Event
+      from google.adk.agents.base_agent import BaseAgent
+      from google.genai import types
+
+
+      class SimpleAgent(BaseAgent):
+
+        def __init__(self):
+          super().__init__(name='simplest_agent', sub_agents=[])
+
+        async def _run_async_impl(self, invocation_context):
+          yield Event(
+              invocation_id=invocation_context.invocation_id,
+              author=self.name,
+              content=types.Content(
+                  role='model',
+                  parts=[types.Part(text='hello from nested')],
+              ),
+          )
+
+
+      root_agent = SimpleAgent()
+      """)
+  (agent_dir / "agent.py").write_text(agent_source, encoding="utf-8")
+
+  monkeypatch.chdir(project_root)
+  loader = AgentLoader(agents_dir="agents/examples")
+  loaded_agent = loader.load_agent("001_hello_world")
+
+  assert isinstance(loaded_agent, BaseAgent)
+  session_service = InMemorySessionService()
+  artifact_service = InMemoryArtifactService()
+  runner = Runner(
+      app_name="001_hello_world",
+      agent=loaded_agent,
+      session_service=session_service,
+      artifact_service=artifact_service,
+  )
+  assert runner._app_name_alignment_hint is None
+
+  session = await session_service.create_session(
+      app_name="001_hello_world",
+      user_id="user",
+  )
+  agen = runner.run_async(
+      user_id=session.user_id,
+      session_id=session.id,
+      new_message=types.Content(
+          role="user",
+          parts=[types.Part(text="hi")],
+      ),
+  )
+  event = await agen.__anext__()
+  await agen.aclose()
+
+  assert event.author == "simplest_agent"
+  assert event.content
+  assert event.content.parts
+  assert event.content.parts[0].text == "hello from nested"
+
   def test_find_agent_to_run_with_function_response_scenario(self):
     """Test finding agent when last event is function response."""
     # Create a function call from sub_agent1
diff --git a/tests/unittests/tools/test_agent_tool.py b/tests/unittests/tools/test_agent_tool.py
index 1743a30f..d38d53db 100644
--- a/tests/unittests/tools/test_agent_tool.py
+++ b/tests/unittests/tools/test_agent_tool.py
@@ -12,15 +12,23 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from typing import Any
 from typing import Optional
 
 from google.adk.agents.callback_context import CallbackContext
+from google.adk.agents.invocation_context import InvocationContext
 from google.adk.agents.llm_agent import Agent
+from google.adk.agents.run_config import RunConfig
 from google.adk.agents.sequential_agent import SequentialAgent
+from google.adk.artifacts.in_memory_artifact_service import InMemoryArtifactService
+from google.adk.memory.in_memory_memory_service import InMemoryMemoryService
 from google.adk.models.llm_request import LlmRequest
 from google.adk.models.llm_response import LlmResponse
 from google.adk.plugins.base_plugin import BasePlugin
+from google.adk.plugins.plugin_manager import PluginManager
+from google.adk.sessions.in_memory_session_service import InMemorySessionService
 from google.adk.tools.agent_tool import AgentTool
+from google.adk.tools.tool_context import ToolContext
 from google.adk.utils.variant_utils import GoogleLLMVariant
 from google.genai import types
 from google.genai.types import Part
@@ -51,6 +59,120 @@ def change_state_callback(callback_context: CallbackContext):
   print('change_state_callback: ', callback_context.state)
 
 
+@mark.asyncio
+async def test_agent_tool_inherits_parent_app_name(monkeypatch):
+  parent_app_name = 'parent_app'
+  captured: dict[str, str] = {}
+
+  class RecordingSessionService(InMemorySessionService):
+
+    async def create_session(
+        self,
+        *,
+        app_name: str,
+        user_id: str,
+        state: Optional[dict[str, Any]] = None,
+        session_id: Optional[str] = None,
+    ):
+      captured['session_app_name'] = app_name
+      return await super().create_session(
+          app_name=app_name,
+          user_id=user_id,
+          state=state,
+          session_id=session_id,
+      )
+
+  monkeypatch.setattr(
+      'google.adk.sessions.in_memory_session_service.InMemorySessionService',
+      RecordingSessionService,
+  )
+
+  async def _empty_async_generator():
+    if False:
+      yield None
+
+  class StubRunner:
+
+    def __init__(
+        self,
+        *,
+        app_name: str,
+        agent: Agent,
+        artifact_service,
+        session_service,
+        memory_service,
+        credential_service,
+        plugins,
+    ):
+      del artifact_service, memory_service, credential_service
+      captured['runner_app_name'] = app_name
+      self.agent = agent
+      self.session_service = session_service
+      self.plugin_manager = PluginManager(plugins=plugins)
+      self.app_name = app_name
+
+    def run_async(
+        self,
+        *,
+        user_id: str,
+        session_id: str,
+        invocation_id: Optional[str] = None,
+        new_message: Optional[types.Content] = None,
+        state_delta: Optional[dict[str, Any]] = None,
+        run_config: Optional[RunConfig] = None,
+    ):
+      del (
+          user_id,
+          session_id,
+          invocation_id,
+          new_message,
+          state_delta,
+          run_config,
+      )
+      return _empty_async_generator()
+
+  monkeypatch.setattr('google.adk.runners.Runner', StubRunner)
+
+  tool_agent = Agent(
+      name='tool_agent',
+      model='test-model',
+  )
+  agent_tool = AgentTool(agent=tool_agent)
+  root_agent = Agent(
+      name='root_agent',
+      model='test-model',
+      tools=[agent_tool],
+  )
+
+  artifact_service = InMemoryArtifactService()
+  parent_session_service = InMemorySessionService()
+  parent_session = await parent_session_service.create_session(
+      app_name=parent_app_name,
+      user_id='user',
+  )
+  invocation_context = InvocationContext(
+      artifact_service=artifact_service,
+      session_service=parent_session_service,
+      memory_service=InMemoryMemoryService(),
+      plugin_manager=PluginManager(),
+      invocation_id='invocation-id',
+      agent=root_agent,
+      session=parent_session,
+      run_config=RunConfig(),
+  )
+  tool_context = ToolContext(invocation_context)
+
+  assert tool_context._invocation_context.app_name == parent_app_name
+
+  await agent_tool.run_async(
+      args={'request': 'hello'},
+      tool_context=tool_context,
+  )
+
+  assert captured['runner_app_name'] == parent_app_name
+  assert captured['session_app_name'] == parent_app_name
+
+
 def test_no_schema():
   mock_model = testing_utils.MockModel.create(
       responses=[