fix: isolate Flow subprocesses from MCP stdin

src/openadapt_agent/runner.py

@@ -501,6 +501,7 @@ def run(
             try:
                 proc = subprocess.run(
                     cmd,
+                    stdin=subprocess.DEVNULL,
                     capture_output=True,
                     text=True,
                     timeout=self.config.timeout_s,
@@ -591,7 +592,11 @@ def certify(self, bundle_dir: Path) -> dict:
             cmd += ["--config", self.config.deployment_config]
         try:
             proc = subprocess.run(
-                cmd, capture_output=True, text=True, timeout=self.config.timeout_s
+                cmd,
+                stdin=subprocess.DEVNULL,
+                capture_output=True,
+                text=True,
+                timeout=self.config.timeout_s,
             )
         except subprocess.TimeoutExpired:
             return {"certified": None, "detail": "certify timed out"}

tests/conftest.py

@@ -67,13 +67,15 @@ def __init__(self, exit_code: int = 0, report: dict | None = None):
         self.exit_code = exit_code
         self.report = report
         self.calls: list[list[str]] = []
+        self.stdins: list[object] = []
         self.stdout = "stub stdout"
         self.stderr = ""
 
-    def __call__(self, cmd, capture_output=True, text=True, timeout=None):
+    def __call__(self, cmd, stdin=None, capture_output=True, text=True, timeout=None):
         import subprocess
 
         self.calls.append(list(cmd))
+        self.stdins.append(stdin)
         if "--run-dir" in cmd:
             run_dir = Path(cmd[cmd.index("--run-dir") + 1])
             run_dir.mkdir(parents=True, exist_ok=True)

tests/test_bridge.py

@@ -438,6 +438,7 @@ def test_certify_result_is_fixed_copy_unless_protected_export_enabled(
     cmd = stub.calls[0]
     assert cmd[1] == "certify"
     assert cmd[cmd.index("--policy") + 1] == "clinical-write"
+    assert stub.stdins == [runner_mod.subprocess.DEVNULL]
 
 
 def test_workflow_names_intents_recorded_values_and_paths_never_default_export(

tests/test_runner.py

@@ -48,6 +48,7 @@ def test_success_mapping(monkeypatch, runner_config, bundle_dir, success_report)
     assert cmd[0] == "openadapt-flow-stub" and cmd[1] == "run"
     assert "--params-file" in cmd and "--run-dir" in cmd
     assert "hello" not in " ".join(cmd)
+    assert stub.stdins == [subprocess.DEVNULL]
 
 
 def test_halt_maps_to_structured_halt_not_success(
@@ -259,7 +260,7 @@ def test_exit_two_is_governed_refusal(monkeypatch, runner_config, bundle_dir):
 
 
 def test_timeout_maps_to_timeout(monkeypatch, runner_config, bundle_dir):
-    def raise_timeout(cmd, capture_output=True, text=True, timeout=None):
+    def raise_timeout(cmd, stdin=None, capture_output=True, text=True, timeout=None):
         raise subprocess.TimeoutExpired(cmd, timeout, output=b"partial", stderr=b"")
 
     outcome = _run(monkeypatch, runner_config, raise_timeout, bundle_dir=bundle_dir)
@@ -269,7 +270,7 @@ def raise_timeout(cmd, capture_output=True, text=True, timeout=None):
 
 
 def test_missing_cli_maps_to_error(monkeypatch, runner_config, bundle_dir):
-    def raise_missing(cmd, capture_output=True, text=True, timeout=None):
+    def raise_missing(cmd, stdin=None, capture_output=True, text=True, timeout=None):
         raise FileNotFoundError(cmd[0])
 
     outcome = _run(monkeypatch, runner_config, raise_missing, bundle_dir=bundle_dir)