chore(agent-runner): align split runtime files with base

src/langbot/pkg/box/workspace.py

@@ -204,14 +204,14 @@ def wrap_python_command_with_env(command: str, *, mount_path: str = '/workspace'
         fi
 
         if [ "$_LB_NEEDS_BOOTSTRAP" -eq 1 ]; then
-          if [ -d "$_LB_LOCK_DIR" ] && [ ! -f "$_LB_LOCK_DIR/pid" ]; then
-            echo "Clearing stale Python environment lock without owner: $_LB_LOCK_DIR" >&2
-            rm -rf "$_LB_LOCK_DIR" 2>/dev/null || true
-          fi
-
           _LB_LOCK_WAIT=0
           while ! mkdir "$_LB_LOCK_DIR" 2>/dev/null; do
             if [ "$_LB_LOCK_WAIT" -ge 120 ]; then
+              _LB_LOCK_OWNER="$(cat "$_LB_LOCK_DIR/pid" 2>/dev/null || true)"
+              if [ -n "$_LB_LOCK_OWNER" ] && kill -0 "$_LB_LOCK_OWNER" 2>/dev/null; then
+                echo "Timed out waiting for active Python environment lock: $_LB_LOCK_DIR" >&2
+                exit 1
+              fi
               echo "Timed out waiting for Python environment lock, clearing stale lock: $_LB_LOCK_DIR" >&2
               rm -rf "$_LB_LOCK_DIR" 2>/dev/null || true
               if mkdir "$_LB_LOCK_DIR" 2>/dev/null; then

src/langbot/pkg/provider/tools/loaders/mcp_stdio.py

@@ -276,7 +276,7 @@ class BoxStdioSessionRuntime:
         # to delete them, so refresh source files in place and preserve runtime
         # directories instead of rmtree'ing the whole staging root.
         with _workspace_copy_lock(process_host_root):
-            preserved_names = {'.venv', 'venv', 'env', '.env', '.cache', '.tmp', '.langbot'}
+            preserved_names = {'.venv', 'venv', 'env', '.cache', '.tmp', '.langbot'}
             os.makedirs(process_host_workspace, exist_ok=True)
             for name in os.listdir(process_host_workspace):
                 if name in preserved_names:
@@ -288,6 +288,7 @@ class BoxStdioSessionRuntime:
                     try:
                         os.unlink(path)
                     except FileNotFoundError:
+                        # The entry may disappear between listdir and unlink if cleanup races us.
                         pass
             shutil.copytree(
                 source_path,
@@ -303,7 +304,6 @@ class BoxStdioSessionRuntime:
                     '.venv',
                     'venv',
                     'env',
-                    '.env',
                     '.cache',
                     '.tmp',
                     '.langbot',
@@ -401,18 +401,12 @@ class BoxStdioSessionRuntime:
         workspace_root = workspace_path.rstrip('/') or '/workspace'
         venv_dir = f'{workspace_root}/.venv'
         venv_bin = f'{venv_dir}/bin'
-        command = ' '.join(
-            [shlex.quote(payload['command']), *[shlex.quote(arg) for arg in payload.get('args', [])]]
-        )
+        command = ' '.join([shlex.quote(payload['command']), *[shlex.quote(arg) for arg in payload.get('args', [])]])
         wrapped = dict(payload)
         wrapped['command'] = 'sh'
         wrapped['args'] = [
             '-lc',
-            (
-                f'export VIRTUAL_ENV={shlex.quote(venv_dir)}; '
-                f'export PATH={shlex.quote(venv_bin)}:$PATH; '
-                f'exec {command}'
-            ),
+            (f'export VIRTUAL_ENV={shlex.quote(venv_dir)}; export PATH={shlex.quote(venv_bin)}:$PATH; exec {command}'),
         ]
         return wrapped
 

tests/unit_tests/box/test_workspace.py

@@ -56,10 +56,7 @@ def test_wrap_python_command_with_env_contains_bootstrap_and_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 'Clearing stale Python environment lock without owner: $_LB_LOCK_DIR' in command
-    assert 'clearing stale lock: $_LB_LOCK_DIR' in command
-    assert 'printf \'%s\\n\' "$$" > "$_LB_LOCK_DIR/pid"' in command
-    assert 'rm -rf "$_LB_LOCK_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()