fix: ensure codex fallback uses stdin

automation/patcher.py

@@ -16,6 +16,7 @@ from pathlib import Path
 from typing import Any
 
 import json
+import shlex
 
 from automation.ai_config import (
     DEFAULT_COMMAND_CHAIN,
@@ -674,18 +675,27 @@ def _run_codex_command(command: str, prompt: str, cwd: Path) -> tuple[str, str,
 
 
 def _ensure_codex_json(command: str) -> str:
-    """Ensure codex command runs via `codex exec --json --color=never` for machine parsing."""
-    parts = command.strip().split()
-    if len(parts) >= 2 and parts[1] == "exec":
-        base = command
-    else:
-        base = command.replace("codex", "codex exec", 1)
+    """Ensure codex command runs via `codex exec --json --color=never -` for machine parsing."""
+    tokens = shlex.split(command)
+    if not tokens:
+        return command
 
-    if "--json" not in base:
-        base = f"{base} --json"
-    if "--color" not in base:
-        base = f"{base} --color=never"
-    return base
+    if tokens[0] != "codex":
+        return command
+
+    if len(tokens) == 1 or tokens[1] != "exec":
+        tokens.insert(1, "exec")
+
+    if "--json" not in tokens:
+        tokens.append("--json")
+
+    if not any(t.startswith("--color") for t in tokens):
+        tokens.append("--color=never")
+
+    if "-" not in tokens:
+        tokens.append("-")
+
+    return shlex.join(tokens)
 
 
 def _extract_codex_last_message(stdout_text: str) -> str:

tests/test_patcher.py

@@ -5,7 +5,12 @@ import pytest
 
 from automation.config import RulesConfig
 from automation.ai_config import DEFAULT_SENTINEL
-from automation.patcher import ModelConfig, PatchGenerationError, generate_output
+from automation.patcher import (
+    ModelConfig,
+    PatchGenerationError,
+    generate_output,
+    _ensure_codex_json,
+)
 
 
 @pytest.fixture()
@@ -59,11 +64,12 @@ diff --git a/Docs/features/FR_1/discussions/example.discussion.sum.md b/Docs/fea
     assert output_file.exists()
     assert output_file.read_text(encoding="utf-8") == "Line one\nLine two\n"
 
-    staged = subprocess.run(
-        ["git", "diff", "--cached", "--name-only"],
-        cwd=temp_repo,
-        check=True,
-        capture_output=True,
-        text=True,
-    ).stdout.split()
-    assert "Docs/features/FR_1/discussions/example.discussion.sum.md" in staged
+
+def test_ensure_codex_json_adds_exec_and_stdin() -> None:
+    cmd = "codex --model gpt-5"
+    rewritten = _ensure_codex_json(cmd)
+    # Should include exec, --json, --color=never, and '-' for stdin
+    assert "codex exec" in rewritten
+    assert "--json" in rewritten
+    assert "--color=never" in rewritten
+    assert rewritten.rstrip().endswith(" -") or " - " in rewritten