fix(tools): decouple runtime from agent runner

tests/unit_tests/box/test_workspace.py

@@ -54,7 +54,9 @@ def test_classify_python_workspace_detects_package_and_requirements():
 def test_wrap_python_command_with_env_contains_bootstrap_and_command():
     command = wrap_python_command_with_env('python script.py')
 
-    assert 'python -m venv "$_LB_VENV_DIR"' in command
+    assert '_LB_SYSTEM_PYTHON="$(command -v python3 || command -v python || true)"' in command
+    assert '"$_LB_SYSTEM_PYTHON" -m venv "$_LB_VENV_DIR"' in command
+    assert 'kill -0 "$_LB_LOCK_OWNER"' in command
     assert 'export VIRTUAL_ENV="$_LB_VENV_DIR"' in command
     assert command.rstrip().endswith('python script.py')
 

tests/unit_tests/provider/test_mcp_box_integration.py

@@ -519,6 +519,7 @@ class TestPythonWorkspacePreparation:
         source.mkdir()
         (source / 'server.py').write_text('print("new")\n', encoding='utf-8')
         (source / 'requirements.txt').write_text('mcp==1.26.0\n', encoding='utf-8')
+        (source / '.env').write_text('TOKEN=new\n', encoding='utf-8')
 
         process_root = tmp_path / 'shared' / '.mcp' / 'u1'
         workspace = process_root / 'workspace'
@@ -526,6 +527,7 @@ class TestPythonWorkspacePreparation:
         (workspace / '.venv' / 'bin' / 'python').write_text('', encoding='utf-8')
         (workspace / '.langbot').mkdir()
         (workspace / '.langbot' / 'python-env.lock').mkdir()
+        (workspace / '.env').write_text('TOKEN=old\n', encoding='utf-8')
         (workspace / 'server.py').write_text('print("old")\n', encoding='utf-8')
         (workspace / 'removed.py').write_text('stale\n', encoding='utf-8')
         (workspace / 'removed_dir').mkdir()
@@ -535,6 +537,7 @@ class TestPythonWorkspacePreparation:
 
         assert (workspace / 'server.py').read_text(encoding='utf-8') == 'print("new")\n'
         assert (workspace / 'requirements.txt').read_text(encoding='utf-8') == 'mcp==1.26.0\n'
+        assert (workspace / '.env').read_text(encoding='utf-8') == 'TOKEN=new\n'
         assert not (workspace / 'removed.py').exists()
         assert not (workspace / 'removed_dir').exists()
         assert (workspace / '.venv' / 'bin' / 'python').exists()

tests/unit_tests/provider/test_skill_tools.py

@@ -193,6 +193,29 @@ class TestSkillPathHelpers:
 
         assert list(result.keys()) == ['visible']
 
+    def test_restore_activated_skills_uses_caller_provided_names_and_visibility(self):
+        from langbot.pkg.provider.tools.loaders.skill import (
+            ACTIVATED_SKILLS_KEY,
+            PIPELINE_BOUND_SKILLS_KEY,
+            get_activated_skill_names,
+            restore_activated_skills,
+        )
+
+        ap = _make_ap()
+        ap.skill_mgr = SimpleNamespace(
+            skills={
+                'visible': _make_skill_data(name='visible'),
+                'hidden': _make_skill_data(name='hidden'),
+            }
+        )
+        query = SimpleNamespace(variables={PIPELINE_BOUND_SKILLS_KEY: ['visible']})
+
+        restored = restore_activated_skills(ap, query, ['visible', 'hidden', 'visible', ''])
+
+        assert restored == ['visible']
+        assert list(query.variables[ACTIVATED_SKILLS_KEY].keys()) == ['visible']
+        assert get_activated_skill_names(query) == ['visible']
+
     def test_resolve_virtual_skill_path_allows_visible_skill_reads(self):
         from langbot.pkg.provider.tools.loaders.skill import (
             PIPELINE_BOUND_SKILLS_KEY,
@@ -282,6 +305,7 @@ class TestSkillToolLoader:
         assert result['activated'] is True
         assert result['skill_name'] == 'demo'
         assert result['mount_path'] == '/workspace/.skills/demo'
+        assert result['activated_skill_names'] == ['demo']
         assert 'Step 1' in result['content']
         assert set(query.variables[ACTIVATED_SKILLS_KEY].keys()) == {'demo'}