diff --git a/src/langbot/pkg/box/connector.py b/src/langbot/pkg/box/connector.py
index deda0b89..2257910d 100644
--- a/src/langbot/pkg/box/connector.py
+++ b/src/langbot/pkg/box/connector.py
@@ -120,13 +120,19 @@ class BoxRuntimeConnector(ManagedRuntimeConnector):
         self._relay_port = parsed.port or _DEFAULT_PORT
         self._filtered_box_config = _filter_config_for_runtime(_get_box_config(ap))
 
-    def _uses_websocket(self) -> bool:
+    def uses_websocket(self) -> bool:
         """Whether the connector should use WebSocket to reach the Box runtime.
 
         True when:
           - Running inside Docker (Box runtime is a separate container)
           - The ``--standalone-box`` CLI flag was passed
           - An explicit ``runtime.endpoint`` was configured
+
+        When this is True the Box runtime lives in a separate process with its
+        own filesystem view (container, pod sidecar, or remote host), so paths
+        it reports (e.g. skill ``package_root``) are NOT resolvable on the
+        LangBot side. When False, Box runs as a stdio child process that shares
+        LangBot's filesystem.
         """
         return bool(
             self.configured_runtime_endpoint
@@ -134,6 +140,10 @@ class BoxRuntimeConnector(ManagedRuntimeConnector):
             or platform.use_websocket_to_connect_box_runtime()
         )
 
+    # Backwards-compatible private alias.
+    def _uses_websocket(self) -> bool:
+        return self.uses_websocket()
+
     async def initialize(self) -> None:
         if self._uses_websocket():
             if platform.get_platform() == 'win32' and not self.configured_runtime_endpoint:
diff --git a/src/langbot/pkg/box/service.py b/src/langbot/pkg/box/service.py
index 6c8e8299..a4ef0dd3 100644
--- a/src/langbot/pkg/box/service.py
+++ b/src/langbot/pkg/box/service.py
@@ -67,6 +67,10 @@ class BoxService:
         self._available = False
         self._connector_error: str = ''
         self._reconnecting = False
+        # Optional explicit override for shares_filesystem_with_box. None means
+        # "derive from the connector transport". Set by tests / embedders that
+        # know the real LangBot<->Box filesystem topology.
+        self._shares_filesystem_with_box_override: bool | None = None
 
     @property
     def enabled(self) -> bool:
@@ -148,6 +152,32 @@ class BoxService:
     def available(self) -> bool:
         return self._available
 
+    @property
+    def shares_filesystem_with_box(self) -> bool:
+        """Whether LangBot and the Box runtime share a filesystem view.
+
+        This is True only when Box runs as a local stdio child process of
+        LangBot (same container/host). In that case paths the Box runtime
+        reports — notably skill ``package_root`` — resolve identically on the
+        LangBot side, so LangBot may validate them against its own filesystem.
+
+        It is False for every separated deployment (Docker Compose, k8s
+        sidecar, ``--standalone-box``, or an explicit ``runtime.endpoint``),
+        where the Box runtime owns its own filesystem and LangBot must trust
+        the paths it reports rather than checking them locally.
+
+        When Box is wired up with an injected client (tests, custom embeds)
+        there is no connector to introspect; we conservatively report False so
+        LangBot never wrongly drops Box-reported skills. An explicit override
+        can be set via ``_shares_filesystem_with_box`` (used by tests and any
+        embedder that knows the real topology).
+        """
+        if self._shares_filesystem_with_box_override is not None:
+            return self._shares_filesystem_with_box_override
+        if self._runtime_connector is None:
+            return False
+        return not self._runtime_connector.uses_websocket()
+
     async def execute_spec_payload(
         self,
         spec_payload: dict,
@@ -220,14 +250,24 @@ class BoxService:
         all skill packages mounted, regardless of which skill is currently
         activated.
 
-        Skills whose ``package_root`` is missing or no longer a directory on
-        the LangBot-visible filesystem are skipped with a warning instead of
-        being passed through to the backend. Without this guard the three
-        backends behave inconsistently on a stale mount: nsjail refuses to
-        start the sandbox (failing every exec in the session), Docker
-        silently auto-creates a root-owned empty directory on the host, and
-        E2B silently skips the upload — none of which surfaces an
-        actionable error to the agent or operator.
+        Path validation is filesystem-topology dependent. When LangBot and the
+        Box runtime share a filesystem (local stdio mode), a skill whose
+        ``package_root`` is missing or no longer a directory is skipped with a
+        warning instead of being passed through to the backend. Without that
+        guard the three backends behave inconsistently on a stale mount: nsjail
+        refuses to start the sandbox (failing every exec in the session),
+        Docker silently auto-creates a root-owned empty directory on the host,
+        and E2B silently skips the upload — none of which surfaces an
+        actionable error.
+
+        When Box runs as a separate process (Docker Compose, k8s sidecar,
+        ``--standalone-box``, or a remote ``runtime.endpoint``), the
+        ``package_root`` reported by ``list_skills`` is the Box runtime's own
+        filesystem path and is NOT resolvable on the LangBot side. Validating
+        it locally would wrongly drop every skill, so LangBot trusts the path
+        and lets the Box runtime resolve it. The Box runtime only ever reports
+        skills it discovered on its own filesystem, so the path is valid there
+        by construction.
         """
         skill_mgr = getattr(self.ap, 'skill_mgr', None)
         if skill_mgr is None:
@@ -235,13 +275,15 @@ class BoxService:
 
         from ..provider.tools.loaders import skill as skill_loader
 
+        validate_locally = self.shares_filesystem_with_box
+
         visible_skills = skill_loader.get_visible_skills(self.ap, query)
         mounts: list[dict] = []
         for skill_name, skill_data in visible_skills.items():
             package_root = str(skill_data.get('package_root', '') or '').strip()
             if not package_root:
                 continue
-            if not os.path.isdir(package_root):
+            if validate_locally and not os.path.isdir(package_root):
                 self.ap.logger.warning(
                     f'Skill "{skill_name}" package_root missing on filesystem '
                     f'({package_root}); skipping mount to prevent sandbox failures. '
diff --git a/src/langbot/pkg/skill/manager.py b/src/langbot/pkg/skill/manager.py
index a053697f..ddb2125c 100644
--- a/src/langbot/pkg/skill/manager.py
+++ b/src/langbot/pkg/skill/manager.py
@@ -46,6 +46,13 @@ class SkillManager:
             self.ap.logger.info('Box runtime unavailable; skill cache is empty.')
             return
 
+        # LangBot may only validate Box-reported paths against its own
+        # filesystem when the two share one (local stdio mode). In separated
+        # deployments (Docker Compose, k8s sidecar, --standalone-box, remote
+        # endpoint) the package_root lives on the Box runtime's filesystem and
+        # is not resolvable here, so we trust what Box reports.
+        validate_locally = bool(getattr(box_service, 'shares_filesystem_with_box', False))
+
         try:
             dropped = 0
             for skill_data in await box_service.list_skills():
@@ -53,7 +60,7 @@ class SkillManager:
                 if not skill_name:
                     continue
                 package_root = str(skill_data.get('package_root', '') or '').strip()
-                if package_root and not os.path.isdir(package_root):
+                if validate_locally and package_root and not os.path.isdir(package_root):
                     self.ap.logger.warning(
                         f'Skill "{skill_name}" reported by Box runtime but '
                         f'package_root missing on LangBot filesystem '
diff --git a/tests/unit_tests/box/test_box_service.py b/tests/unit_tests/box/test_box_service.py
index 44f42ec1..c7fe7c61 100644
--- a/tests/unit_tests/box/test_box_service.py
+++ b/tests/unit_tests/box/test_box_service.py
@@ -190,6 +190,66 @@ async def test_box_service_without_explicit_client_initializes_internal_connecto
     connector.initialize.assert_awaited_once()
 
 
+class TestSharesFilesystemWithBox:
+    """``shares_filesystem_with_box`` must reflect the real LangBot<->Box
+    filesystem topology, which is derived from the connector transport:
+
+    - stdio (local child process) → shared filesystem → True
+    - WebSocket (Docker / sidecar / --standalone-box / remote) → separated → False
+
+    This drives whether LangBot validates Box-reported skill paths locally.
+    Getting it wrong silently drops every skill in separated deployments.
+    """
+
+    def test_true_for_stdio_connector(self, monkeypatch: pytest.MonkeyPatch):
+        # Non-Docker Unix, no endpoint, not standalone → stdio transport.
+        monkeypatch.setattr('langbot.pkg.utils.platform.get_platform', lambda: 'linux')
+        monkeypatch.setattr('langbot.pkg.utils.platform.standalone_box', False)
+
+        service = BoxService(make_app(Mock()))
+
+        assert service._runtime_connector is not None
+        assert service._runtime_connector.uses_websocket() is False
+        assert service.shares_filesystem_with_box is True
+
+    def test_false_for_websocket_connector_via_endpoint(self, monkeypatch: pytest.MonkeyPatch):
+        monkeypatch.setattr('langbot.pkg.utils.platform.get_platform', lambda: 'linux')
+        monkeypatch.setattr('langbot.pkg.utils.platform.standalone_box', False)
+        app = make_app(Mock())
+        app.instance_config.data['box']['runtime']['endpoint'] = 'ws://pod-x-box:5410'
+
+        service = BoxService(app)
+
+        assert service._runtime_connector is not None
+        assert service._runtime_connector.uses_websocket() is True
+        assert service.shares_filesystem_with_box is False
+
+    def test_false_for_websocket_connector_in_docker(self, monkeypatch: pytest.MonkeyPatch):
+        monkeypatch.setattr('langbot.pkg.utils.platform.get_platform', lambda: 'docker')
+        monkeypatch.setattr('langbot.pkg.utils.platform.standalone_box', False)
+
+        service = BoxService(make_app(Mock()))
+
+        assert service.shares_filesystem_with_box is False
+
+    def test_false_when_client_injected_without_connector(self):
+        # Injected client (no connector) → unknown topology → conservative False
+        # so LangBot never wrongly drops Box-reported skills.
+        service = BoxService(make_app(Mock()), client=Mock(spec=BoxRuntimeClient))
+
+        assert service._runtime_connector is None
+        assert service.shares_filesystem_with_box is False
+
+    def test_explicit_override_wins(self):
+        service = BoxService(make_app(Mock()), client=Mock(spec=BoxRuntimeClient))
+
+        service._shares_filesystem_with_box_override = True
+        assert service.shares_filesystem_with_box is True
+
+        service._shares_filesystem_with_box_override = False
+        assert service.shares_filesystem_with_box is False
+
+
 @pytest.mark.asyncio
 async def test_box_service_get_sessions_delegates_to_client():
     client = Mock()
@@ -1342,11 +1402,16 @@ class TestBuildSkillExtraMounts:
     the backend never sees a bad mount.
     """
 
-    def _make_service(self, logger, skills):
+    def _make_service(self, logger, skills, *, shares_filesystem=True):
         app = make_app(logger)
         app.skill_mgr = SimpleNamespace(skills=skills)
         client = Mock(spec=BoxRuntimeClient)
-        return BoxService(app, client=client)
+        service = BoxService(app, client=client)
+        # Tests construct BoxService with an injected client (no connector), so
+        # set the topology explicitly. Most cases exercise the shared-fs (local
+        # stdio) path where local package_root validation applies.
+        service._shares_filesystem_with_box_override = shares_filesystem
+        return service
 
     def test_skips_skill_with_missing_package_root(self):
         logger = Mock()
@@ -1373,6 +1438,30 @@ class TestBuildSkillExtraMounts:
                 for call in logger.warning.call_args_list
             )
 
+    def test_trusts_box_paths_when_filesystem_not_shared(self):
+        """In separated deployments (Docker Compose, k8s sidecar,
+        --standalone-box, remote endpoint) the Box runtime owns its own
+        filesystem. package_root values it reports are NOT resolvable on the
+        LangBot side, so LangBot must trust them rather than dropping every
+        skill via a local isdir() check."""
+        logger = Mock()
+        skills = {
+            'a': {'name': 'a', 'package_root': '/box/skills/a'},
+            'b': {'name': 'b', 'package_root': '/box/skills/b'},
+        }
+        service = self._make_service(logger, skills, shares_filesystem=False)
+
+        mounts = service.build_skill_extra_mounts(make_query())
+
+        assert mounts == [
+            {'host_path': '/box/skills/a', 'mount_path': '/workspace/.skills/a', 'mode': 'rw'},
+            {'host_path': '/box/skills/b', 'mount_path': '/workspace/.skills/b', 'mode': 'rw'},
+        ]
+        # No skill is dropped, so no "missing" warning should be logged.
+        assert not any(
+            'package_root missing' in str(call.args[0]) for call in logger.warning.call_args_list
+        )
+
     def test_skips_skill_with_empty_package_root(self):
         logger = Mock()
         skills = {
@@ -1383,6 +1472,14 @@ class TestBuildSkillExtraMounts:
 
         assert service.build_skill_extra_mounts(make_query()) == []
 
+    def test_empty_package_root_skipped_even_when_not_shared(self):
+        """An empty package_root is always invalid regardless of topology."""
+        logger = Mock()
+        skills = {'no_root': {'name': 'no_root', 'package_root': ''}}
+        service = self._make_service(logger, skills, shares_filesystem=False)
+
+        assert service.build_skill_extra_mounts(make_query()) == []
+
     def test_returns_empty_when_no_skill_manager(self):
         logger = Mock()
         app = make_app(logger)
diff --git a/tests/unit_tests/provider/test_skill_tools.py b/tests/unit_tests/provider/test_skill_tools.py
index 00e04bfa..847480c1 100644
--- a/tests/unit_tests/provider/test_skill_tools.py
+++ b/tests/unit_tests/provider/test_skill_tools.py
@@ -62,15 +62,17 @@ class TestSkillManagerCache:
 
     @pytest.mark.asyncio
     async def test_reload_skills_drops_box_skills_with_missing_package_root(self):
-        """When Box reports a skill whose package_root is gone from the
-        LangBot-visible filesystem, the cache must drop it instead of
-        keeping a stale entry that would later produce a bad mount."""
+        """When LangBot shares a filesystem with Box (local stdio mode) and Box
+        reports a skill whose package_root is gone from that shared filesystem,
+        the cache must drop it instead of keeping a stale entry that would later
+        produce a bad mount."""
         from langbot.pkg.skill.manager import SkillManager
 
         with tempfile.TemporaryDirectory() as live_dir:
             ghost_dir = os.path.join(live_dir, '_does_not_exist')
             box_service = SimpleNamespace(
                 available=True,
+                shares_filesystem_with_box=True,
                 list_skills=AsyncMock(
                     return_value=[
                         _make_skill_data(name='alive', package_root=live_dir),
@@ -90,6 +92,37 @@ class TestSkillManagerCache:
         warning_messages = [str(call.args[0]) for call in ap.logger.warning.call_args_list]
         assert any('ghost' in msg and 'package_root missing' in msg for msg in warning_messages)
 
+    @pytest.mark.asyncio
+    async def test_reload_skills_trusts_box_paths_when_filesystem_not_shared(self):
+        """In separated deployments (Docker Compose, k8s sidecar,
+        --standalone-box, remote endpoint) the package_root reported by Box
+        lives on the Box runtime's filesystem and is not resolvable on the
+        LangBot side. The cache must keep every Box-reported skill rather than
+        dropping them all via a local isdir() check."""
+        from langbot.pkg.skill.manager import SkillManager
+
+        box_service = SimpleNamespace(
+            available=True,
+            shares_filesystem_with_box=False,
+            list_skills=AsyncMock(
+                return_value=[
+                    _make_skill_data(name='alpha', package_root='/box/skills/alpha'),
+                    _make_skill_data(name='beta', package_root='/box/skills/beta'),
+                ]
+            ),
+        )
+
+        ap = _make_ap()
+        ap.box_service = box_service
+        mgr = SkillManager(ap)
+
+        await mgr.reload_skills()
+
+        assert sorted(mgr.skills) == ['alpha', 'beta']
+        # No skill dropped → no "package_root missing" warning.
+        warning_messages = [str(call.args[0]) for call in ap.logger.warning.call_args_list]
+        assert not any('package_root missing' in msg for msg in warning_messages)
+
 
 class TestSkillActivationHelper:
     """Skill activation is now Tool-Call based.