fix: Claude reviewer empty output, worktree isolation false positives, and input file access

- Add -p flag to _CLAUDE_REVIEW_ARGS so reviewer uses print mode (stdin→stdout)
  instead of interactive mode which conflicts with plan permission mode
- Copy input files (plan, checklist) into worktree .cross-eval-inputs/ so
  agents in plan mode can access them without escaping the sandbox
- Simplify _snapshot_repo_state to use only git diff HEAD + untracked hashes,
  eliminating false positives from staging state changes (git diff --cached)
  and git status index drift during long-running pipelines

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

tests/test_config.py

@@ -1030,6 +1030,60 @@ class FixPresetBehaviorTest(unittest.TestCase):
         self.assertTrue(captured["agentic"])
         self.assertEqual(captured["phase_max"], 3)
 
+    def test_run_senior_model_override_applies_only_to_seniors(self) -> None:
+        captured: dict[str, list[str]] = {}
+
+        def _fake_run_pipeline(config, **kwargs):
+            captured["coder_args"] = list(config.agents[config.coders[0]].args)
+            captured["reviewer_args"] = list(config.agents[config.reviewers[0]].args)
+            captured["senior_args"] = list(config.agents[config.seniors[0]].args)
+            return PipelineResult(
+                iterations=[],
+                final_verdict="PASS",
+                run_dir=Path(".cross-eval/output"),
+            )
+
+        with patch("cross_eval.pipeline.run_pipeline", side_effect=_fake_run_pipeline):
+            exit_code = main([
+                "run",
+                "--preset", "review-fix",
+                "--coder", "claude",
+                "--reviewer", "claude",
+                "--senior", "claude",
+                "--senior-model", "sonnet",
+                "--dry-run",
+            ])
+
+        self.assertEqual(exit_code, 0)
+        self.assertIn("opus", captured["coder_args"])
+        self.assertIn("opus", captured["reviewer_args"])
+        self.assertIn("sonnet", captured["senior_args"])
+
+
+class OutputDirectoryResolutionTest(unittest.TestCase):
+    def test_load_config_resolves_output_dir_from_project_root(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            root = Path(tmpdir)
+            ce_dir = root / ".cross-eval"
+            ce_dir.mkdir()
+            (ce_dir / "plan.md").write_text("# plan\n", encoding="utf-8")
+            config_path = ce_dir / "config.yaml"
+            config_path.write_text(
+                (
+                    "inputs:\n"
+                    "  plan: plan.md\n"
+                    "coders: [claude-coder]\n"
+                    "reviewers: [claude-reviewer]\n"
+                    "pipeline: preset:simple\n"
+                    "output_dir: .cross-eval/output\n"
+                ),
+                encoding="utf-8",
+            )
+
+            config = load_config(config_path)
+
+        self.assertEqual(config.output_dir.resolve(), (root / ".cross-eval" / "output").resolve())
+
 
 if __name__ == "__main__":
     unittest.main()