fix(scripts): feed config-upgrade inline python on stdin, not argv (#6845)

* fix(scripts): feed config-upgrade inline python on stdin, not argv

On Windows setups where python/uv resolve through shim layers that
reparse arguments with cmd.exe (e.g. pyenv-win), the multi-line
`python -c "..."` payloads in config-upgrade.sh get mangled mid-flight
(observed as `IndentationError: unexpected indent` on a stray
`|| goto :error` line) and `make dev` fails before the Gateway starts.

Feed both inline scripts on stdin instead, which is safe across every
spawn chain, and load the checkout .env explicitly inside the resolver
probe: the default load_dotenv() discovery walks up from cwd/__file__,
which a stdin-fed script (`python -`) cannot satisfy. Pin both with a
static regression test.

* test(config): isolate upgrade fixtures from inherited dotenv selectors

---------

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>

backend/tests/AGENTS.md

@@ -10,6 +10,11 @@ ownership and capture cleanup. Retain the real XLSX conversion coverage.
 
 Backend tests must preserve the runtime invariants they exercise without changing production execution topology.
 
+Config-upgrade checkout fixtures clear inherited `DEER_FLOW_CONFIG_PATH`,
+`DEER_FLOW_PROJECT_ROOT` and `DEER_FLOW_ENV_FILE` before applying explicit test
+overrides. Exercise selector leaks through the real script with temporary
+configs; assert that the simulated developer config and its backup stay untouched.
+
 Image-context budget regressions use real PNG files through `view_image`, the
 state reducer, and both model-call wrappers. Check decoded payloads, cumulative
 base64 size and skipped file reads; keep count and byte limits independent.

backend/tests/test_config_version.py

@@ -653,7 +653,7 @@ def _run_config_upgrade_in_checkout(checkout: Path, **env_overrides: str):
     shutil.copy2(repo_root / "scripts" / "config-upgrade.sh", checkout / "scripts" / "config-upgrade.sh")
     shutil.copy2(repo_root / "config.example.yaml", checkout / "config.example.yaml")
 
-    env = {key: value for key, value in os.environ.items() if key not in {"DEER_FLOW_CONFIG_PATH", "DEER_FLOW_PROJECT_ROOT"}}
+    env = {key: value for key, value in os.environ.items() if key not in {"DEER_FLOW_CONFIG_PATH", "DEER_FLOW_PROJECT_ROOT", "DEER_FLOW_ENV_FILE"}}
     env["UV_PROJECT"] = str(repo_root / "backend")
     env.update(env_overrides)
     return subprocess.run(
@@ -776,3 +776,63 @@ def test_config_upgrade_creates_checkout_config_when_none_exists(tmp_path):
 
     assert "creating from example" in result.stdout
     assert (checkout / "config.yaml").read_bytes() == (checkout / "config.example.yaml").read_bytes()
+
+
+def test_config_upgrade_feeds_inline_python_on_stdin():
+    """The upgrade script must not pass its inline Python via a `python -c` argv payload.
+
+    On Windows setups where python/uv resolve through shim layers that reparse
+    arguments with cmd.exe (e.g. pyenv-win), multi-line argv payloads get
+    mangled mid-flight (observed as `IndentationError: unexpected indent` on
+    `|| goto :error`) and `make dev` fails before the Gateway starts. Feeding
+    the payload on stdin is safe across every spawn chain.
+    """
+    repo_root = Path(__file__).resolve().parents[2]
+    script = (repo_root / "scripts" / "config-upgrade.sh").read_text(encoding="utf-8")
+    assert 'python -c "' not in script
+    assert script.count("<<'DEERFLOW_UPGRADE_PY'") == 2
+
+
+@pytest.mark.skipif(SCRIPT_BASH is None, reason="repo shell-script tests need Git Bash on Windows")
+def test_config_upgrade_honors_deer_flow_env_file_over_checkout_dotenv(tmp_path):
+    """An explicit DEER_FLOW_ENV_FILE selection must win over the checkout .env.
+
+    The Gateway loads the selected env file and upgrades the config it points
+    at; this script must not pre-load the checkout .env first, or its values
+    would shadow the selected file's (load_dotenv uses override=False).
+    """
+    checkout = tmp_path / "checkout"
+    live = tmp_path / "live" / "config.yaml"
+    other = tmp_path / "other" / "config.yaml"
+    _write_outdated_config(checkout / "config.yaml")
+    _write_outdated_config(live)
+    _write_outdated_config(other)
+    (checkout / ".env").write_text(f"DEER_FLOW_CONFIG_PATH={other}\n", encoding="utf-8")
+    stage = checkout / "stage.env"
+    stage.write_text(f"DEER_FLOW_CONFIG_PATH={live}\n", encoding="utf-8")
+
+    result = _run_config_upgrade_in_checkout(checkout, DEER_FLOW_ENV_FILE=str(stage))
+    assert result.returncode == 0, result.stdout + result.stderr
+
+    assert yaml.safe_load(live.read_text(encoding="utf-8"))["config_version"] > 1
+    assert yaml.safe_load(other.read_text(encoding="utf-8"))["config_version"] == 1
+
+
+@pytest.mark.skipif(SCRIPT_BASH is None, reason="repo shell-script tests need Git Bash on Windows")
+def test_config_upgrade_checkout_helper_ignores_inherited_env_file(tmp_path, monkeypatch):
+    """A developer's exported selector must not redirect a fixture's upgrade."""
+    checkout = tmp_path / "checkout"
+    _write_outdated_config(checkout / "config.yaml")
+    developer_config = tmp_path / "developer" / "config.yaml"
+    developer_text = _write_outdated_config(developer_config)
+    developer_env = tmp_path / "developer.env"
+    developer_env.write_text(f"DEER_FLOW_CONFIG_PATH={developer_config}\n", encoding="utf-8")
+    monkeypatch.setenv("DEER_FLOW_ENV_FILE", str(developer_env))
+
+    result = _run_config_upgrade_in_checkout(checkout)
+    assert result.returncode == 0, result.stdout + result.stderr
+
+    assert developer_config.read_text(encoding="utf-8") == developer_text
+    assert not developer_config.with_suffix(".yaml.bak").exists()
+    expected_version = yaml.safe_load((checkout / "config.example.yaml").read_text(encoding="utf-8"))["config_version"]
+    assert yaml.safe_load((checkout / "config.yaml").read_text(encoding="utf-8"))["config_version"] == expected_version

scripts/config-upgrade.sh

@@ -22,10 +22,28 @@ fi
 # backend/config.yaml present, `make dev` reads the checkout copy. The import
 # loads .env as the Gateway does; DEER_FLOW_PROJECT_ROOT then defaults to the
 # checkout, as in serve.sh. Prints nothing when no config exists yet.
-CONFIG="$(cd "$REPO_ROOT/backend" && REPO_ROOT_WIN_PATH="$REPO_ROOT_WIN" uv run python -c "
+# Pass the payload on stdin instead of `python -c`: on Windows setups where
+# python/uv resolve through pyenv-win shim layers, arguments cross a cmd.exe
+# reparse boundary that mangles multi-line argv (observed as a bogus
+# "IndentationError: unexpected indent" on '|| goto :error'). stdin is safe.
+CONFIG="$(cd "$REPO_ROOT/backend" && REPO_ROOT_WIN_PATH="$REPO_ROOT_WIN" uv run python - <<'DEERFLOW_UPGRADE_PY'
 import os
 import sys
 
+from deerflow.env import load_selected_env_file
+
+# Honor an explicit DEER_FLOW_ENV_FILE selection first: values loaded here
+# keep precedence over anything app_config's import-time load discovers,
+# matching the Gateway. Only with no selector do we load the checkout .env
+# explicitly, so the probe does not depend on dotenv's frame-based discovery
+# anchoring inside the harness package. Bonus: loading before the import
+# below lets DEER_FLOW_PROJECT_ROOT in the checkout .env win over the
+# setdefault, as it does for the Gateway.
+if not load_selected_env_file():
+    from dotenv import load_dotenv
+
+    load_dotenv(os.path.join(os.environ['REPO_ROOT_WIN_PATH'], '.env'))
+
 from deerflow.config.app_config import AppConfig
 
 os.environ.setdefault('DEER_FLOW_PROJECT_ROOT', os.environ['REPO_ROOT_WIN_PATH'])
@@ -38,7 +56,8 @@ except FileNotFoundError as exc:
         sys.exit(f'ERROR {exc}')
 except ValueError as exc:
     sys.exit(f'ERROR {exc}')
-")"
+DEERFLOW_UPGRADE_PY
+)"
 
 if [ ! -f "$EXAMPLE" ]; then
     echo "✗ config.example.yaml not found at $EXAMPLE"
@@ -61,7 +80,7 @@ else
     EXAMPLE_WIN="$EXAMPLE"
 fi
 
-cd "$REPO_ROOT/backend" && CONFIG_WIN_PATH="$CONFIG_WIN" EXAMPLE_WIN_PATH="$EXAMPLE_WIN" uv run python -c "
+cd "$REPO_ROOT/backend" && CONFIG_WIN_PATH="$CONFIG_WIN" EXAMPLE_WIN_PATH="$EXAMPLE_WIN" uv run python - <<'DEERFLOW_UPGRADE_PY'
 import os
 import sys, shutil, copy, re, secrets
 from pathlib import Path
@@ -231,7 +250,7 @@ if migrated:
 added = []
 
 def merge(target, source, path=''):
-    \"\"\"Recursively merge source into target, adding missing keys only.\"\"\"
+    """Recursively merge source into target, adding missing keys only."""
     for key, value in source.items():
         key_path = f'{path}.{key}' if path else key
         if key not in target:
@@ -265,4 +284,4 @@ if not migrated and not added:
 print()
 print(f'OK config.yaml upgraded to version {example_version}.')
 print('  Please review the changes and set any new required values.')
-"
+DEERFLOW_UPGRADE_PY