fix: preserve agentic branch when intermediate commits exist

_finalize_worktree was returning None and deleting the branch when the
final commit was empty, even though _commit_iteration had already
committed changes during the pipeline. Now checks git log for any
commits on the branch before deciding to clean up.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

cross_eval/pipeline.py

@@ -263,8 +263,6 @@ def _finalize_worktree(
         )
         if committed:
             logger.info("  Agentic changes committed on branch: %s", branch_name)
-        else:
-            logger.warning("  No agentic changes to commit (empty diff)")
     except Exception:
         logger.warning("  Failed to commit agentic changes", exc_info=True)
 
@@ -273,16 +271,25 @@ def _finalize_worktree(
     except Exception:
         logger.warning("Failed to clean up worktree: %s", worktree_path)
 
-    # Check if branch has any commits beyond the base — if not, delete it
-    if not committed:
+    # Check if branch has any commits beyond the base (including intermediate
+    # commits from _commit_iteration, not just the final commit).
+    has_branch_commits = False
     try:
-            # Check if branch has diverged from its base
         result = subprocess.run(
             ["git", "log", "--oneline", f"HEAD..{branch_name}"],
             cwd=cwd, capture_output=True, text=True,
         )
-            if not result.stdout.strip():
-                # No commits on branch beyond base — clean up
+        has_branch_commits = bool(result.stdout.strip())
+    except Exception:
+        pass
+
+    if has_branch_commits:
+        if not committed:
+            logger.info("  Agentic changes on branch: %s (from intermediate commits)", branch_name)
+        return branch_name
+
+    # No commits on branch at all — clean up
+    try:
         subprocess.run(
             ["git", "branch", "-D", branch_name],
             cwd=cwd, capture_output=True,
@@ -291,7 +298,9 @@ def _finalize_worktree(
     except Exception:
         pass  # best-effort cleanup
 
-    return branch_name if committed else None
+    if not committed:
+        logger.warning("  No agentic changes to commit (empty diff)")
+    return None
 
 
 def _run_simple_pipeline(

tests/test_config.py

@@ -71,8 +71,11 @@ class BuiltinAgentConfigTest(unittest.TestCase):
 
         self.assertIn("--dangerously-skip-permissions", coder_args)
         self.assertIn("bypassPermissions", coder_args)
-        self.assertIn("plan", reviewer_args)
-        self.assertIn("plan", senior_args)
+        # Reviewers/seniors use -p without --permission-mode plan
+        self.assertIn("-p", reviewer_args)
+        self.assertIn("-p", senior_args)
+        self.assertNotIn("plan", reviewer_args)
+        self.assertNotIn("plan", senior_args)
 
     def test_codex_builtin_agents_skip_git_repo_check(self) -> None:
         for agent_name in ("codex-coder", "codex-reviewer", "codex-senior"):