fix(tools): harden agent runner tool runtimes

tests/unit_tests/provider/test_mcp_box_integration.py

@@ -180,7 +180,7 @@ class TestMCPServerBoxConfig:
         assert cfg.host_path is None
         assert cfg.host_path_mode == 'ro'
         assert cfg.env == {}
-        assert cfg.startup_timeout_sec == 120
+        assert cfg.startup_timeout_sec == 300
         assert cfg.cpus is None
         assert cfg.memory_mb is None
         assert cfg.pids_limit is None
@@ -494,6 +494,52 @@ class TestBuildBoxProcessPayload:
         assert payload['args'] == ['/opt/other/server.py', '--flag']
 
 
+# ── Python Workspace Preparation ────────────────────────────────────
+
+
+class TestPythonWorkspacePreparation:
+    def test_requirements_workspace_uses_venv_bootstrap(self, mcp_module, tmp_path):
+        host_path = tmp_path / 'mcp-source'
+        host_path.mkdir()
+        (host_path / 'requirements.txt').write_text('mcp==1.26.0\n', encoding='utf-8')
+
+        command = mcp_module.BoxStdioSessionRuntime.detect_install_command(
+            str(host_path),
+            '/workspace/.mcp/u1/workspace',
+        )
+
+        assert command is not None
+        assert 'python -m venv "$_LB_VENV_DIR"' in command
+        assert 'python -m pip install -r "/workspace/.mcp/u1/workspace/requirements.txt"' in command
+        assert 'pip install --no-cache-dir -r' not in command
+
+    def test_staging_refresh_removes_stale_source_files_but_preserves_runtime_dirs(self, mcp_module, tmp_path):
+        source = tmp_path / 'source'
+        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')
+
+        process_root = tmp_path / 'shared' / '.mcp' / 'u1'
+        workspace = process_root / 'workspace'
+        (workspace / '.venv' / 'bin').mkdir(parents=True)
+        (workspace / '.venv' / 'bin' / 'python').write_text('', encoding='utf-8')
+        (workspace / '.langbot').mkdir()
+        (workspace / '.langbot' / 'python-env.lock').mkdir()
+        (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()
+        (workspace / 'removed_dir' / 'old.txt').write_text('stale\n', encoding='utf-8')
+
+        mcp_module.BoxStdioSessionRuntime._copy_workspace_tree(str(source), str(process_root), str(workspace))
+
+        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 not (workspace / 'removed.py').exists()
+        assert not (workspace / 'removed_dir').exists()
+        assert (workspace / '.venv' / 'bin' / 'python').exists()
+        assert (workspace / '.langbot' / 'python-env.lock').is_dir()
+
+
 # ── get_runtime_info_dict ───────────────────────────────────────────
 
 

tests/unit_tests/provider/test_skill_tools.py

@@ -456,7 +456,9 @@ class TestNativeToolLoaderSkillPaths:
                 SimpleNamespace(query_id='q1', variables={PIPELINE_BOUND_SKILLS_KEY: ['demo']}),
             )
 
-            assert result == {'ok': True, 'content': 'demo instructions'}
+            assert result['ok'] is True
+            assert result['content'] == 'demo instructions'
+            assert result['truncated'] is False
 
     @pytest.mark.asyncio
     async def test_exec_in_activated_skill_mount_rewrites_command_and_refreshes(self):
@@ -485,7 +487,7 @@ class TestNativeToolLoaderSkillPaths:
                 query,
             )
 
-            assert result == {'ok': True}
+            assert result['ok'] is True
             tool_parameters = ap.box_service.execute_tool.await_args.args[0]
             assert tool_parameters['command'] == 'python /workspace/.skills/demo/scripts/run.py'
             assert tool_parameters['workdir'] == '/workspace/.skills/demo'