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>

cross_eval/config.py

@@ -62,12 +62,7 @@ _CLAUDE_CODER_ARGS = list(_CLAUDE_BASE_ARGS) + [
     "bypassPermissions",
 ]
 
-_CLAUDE_REVIEW_ARGS = [
-    "--setting-sources",
-    "user",
-    "--disable-slash-commands",
-    "--model",
-    "opus",
+_CLAUDE_REVIEW_ARGS = list(_CLAUDE_BASE_ARGS) + [
     "--permission-mode",
     "plan",
 ]
@@ -425,6 +420,8 @@ def load_config(path: Path) -> PipelineConfig:
 
 def _parse_raw(raw: dict[str, Any], config_path: Path) -> PipelineConfig:
     """Parse raw YAML dict into PipelineConfig."""
+    project_root = config_path.parent.parent if config_path.parent.name == ".cross-eval" else config_path.parent
+
     # --- agents ---
     agents: dict[str, AgentConfig] = {}
     for name, agent_data in raw.get("agents", {}).items():
@@ -494,8 +491,12 @@ def _parse_raw(raw: dict[str, Any], config_path: Path) -> PipelineConfig:
     if isinstance(pipeline_raw, str) and pipeline_raw.startswith("preset:"):
         preset_name = pipeline_raw.split(":", 1)[1]
 
+    output_dir = Path(raw.get("output_dir", ".cross-eval/output"))
+    if not output_dir.is_absolute():
+        output_dir = project_root / output_dir
+
     config = PipelineConfig(
-        output_dir=Path(raw.get("output_dir", ".cross-eval/output")),
+        output_dir=output_dir,
         max_iterations=int(raw.get("max_iterations", 3)),
         min_iterations=int(raw.get("min_iterations", 1)),
         verbose=bool(raw.get("verbose", False)),