feat: tighten agentic runtime handoffs and quality gates

cross_eval/agent.py

@@ -415,11 +415,7 @@ def invoke_agent_agentic(
     timeout: int | None = None,
     quiet: bool = False,
 ) -> AgentResult:
-    """Invoke an agent in agentic mode (no -p, runs in worktree, captures git diff).
-
-    The agent runs without print mode so it can modify files directly.
-    After the agent exits, git diff (since last commit) is captured as the output.
-    """
+    """Invoke an agent in agentic mode using the worktree as the source of truth."""
     from cross_eval.worktree import capture_diff
 
     # Write prompt to a temp file (outside worktree, won't appear in diffs)
@@ -433,10 +429,10 @@ def invoke_agent_agentic(
     if agent.reasoning_effort and _supports_reasoning_effort(agent.command):
         cmd.extend(["-c", f'model_reasoning_effort="{agent.reasoning_effort}"'])
 
-    # Strip stdin sentinel ("-") from args for agentic mode.
-    # Keep -p/--print: Claude -p mode still has full tool access (Edit, Write,
-    # Bash, etc.) and is the correct mode for non-interactive subprocess use.
-    args = [a for a in agent.args if a != "-"]
+    # Strip print-mode flags and stdin sentinels for agentic mode.
+    # Agentic runs should operate on the worktree and return a real git diff,
+    # not behave as a one-shot text completer.
+    args = [a for a in agent.args if a not in {"-", "-p", "--print"}]
     cmd.extend(args)
 
     # System prompt via flag if supported
@@ -454,8 +450,8 @@ def invoke_agent_agentic(
         else:
             input_data = prompt
     else:
-        # claude -p: deliver prompt via stdin (same as codex).
-        # -p mode is non-interactive and reads from stdin, then exits.
+        # claude: deliver the task through stdin and let the worktree be the
+        # canonical place where files are read/written.
         input_data = prompt
 
     cmd_preview = " ".join(cmd[:6])

cross_eval/cli.py

@@ -266,7 +266,7 @@ def main(argv: list[str] | None = None) -> int:
         type=int,
         default=None,
         metavar="SEC",
-        help="에이전트 호출 제한 시간 (--live 전용)",
+        help="에이전트 1회 호출 제한 시간(초). 0=무제한 (기본: 무제한, --live 전용)",
     )
 
     # --- run ---
@@ -981,6 +981,7 @@ def cmd_run(args: argparse.Namespace) -> int:
             print(f"No files found in: {docs_dir}", file=sys.stderr)
             return 1
         config.inputs["docs"] = docs_content
+        config.inputs["docs_ref"] = str(docs_dir)
 
     if args.env_files:
         for env_file in args.env_files:
@@ -1007,7 +1008,6 @@ def cmd_run(args: argparse.Namespace) -> int:
         apply_input_overrides(config, overrides)
 
     # 3. Validate after all overrides
-    from cross_eval.config import validate_config
     errors = validate_config(config)
     if errors:
         print("Config error:\n  " + "\n  ".join(errors), file=sys.stderr)

cross_eval/config.py

@@ -698,9 +698,9 @@ def _validate_unique_step_fields(
 
 
 def _make_agentic(agent: AgentConfig) -> None:
-    """Convert an agent to agentic mode in-place (remove -p, set agentic=True)."""
+    """Convert an agent to agentic mode in-place."""
     agent.agentic = True
-    agent.args = [a for a in agent.args if a != "-p"]
+    agent.args = [a for a in agent.args if a not in {"-p", "--print"}]
 
 
 def sync_phased_iterations(

cross_eval/demo.py

@@ -217,7 +217,7 @@ def run_mock_demo(preset: str = "simple", show_escalate: bool = False) -> None:
 
     if show_escalate:
         print(f"\n{RED}{BOLD}{'=' * 50}")
-        print(f"  Escalation Report")
+        print("  Escalation Report")
         print(f"{'=' * 50}{RESET}")
         print(f"{YELLOW}Human review required.{RESET}")
         print(f"  {RED}•{RESET} Requirements are ambiguous — needs stakeholder clarification")

cross_eval/doctor.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 
 import shutil
 import subprocess
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from pathlib import Path
 from typing import Optional
 

cross_eval/pipeline.py

@@ -343,6 +343,8 @@ def _run_simple_pipeline(
             if step_results:
                 input_contents["execution_evidence"] = _format_execution_evidence(
                     step_results,
+                    run_dir=run_dir,
+                    iteration=i,
                 )
 
             iterations.append(iter_result)
@@ -543,6 +545,8 @@ def _run_phased_pipeline(
                 if step_results:
                     input_contents["execution_evidence"] = _format_execution_evidence(
                         step_results,
+                        run_dir=run_dir,
+                        iteration=global_iter,
                     )
 
                 iterations.append(iter_result)
@@ -661,10 +665,13 @@ def _load_inputs(config: PipelineConfig) -> dict[str, str]:
     """Load input file contents from config."""
     input_contents: dict[str, str] = {}
     for key, val in config.inputs.items():
-        if isinstance(val, str):
+        if key.endswith("_ref"):
+            input_contents[key] = str(val)
+        elif isinstance(val, str):
             input_contents[key] = val
         else:
             input_contents[key] = val.read_text(encoding="utf-8")
+    _refresh_input_references(config, input_contents)
     return input_contents
 
 
@@ -673,10 +680,99 @@ def _refresh_inputs(
 ) -> None:
     """Re-read input files (they may have changed on disk)."""
     for key, val in config.inputs.items():
-        if isinstance(val, str):
+        if key.endswith("_ref"):
+            input_contents[key] = str(val)
+        elif isinstance(val, str):
             input_contents[key] = val
         elif isinstance(val, Path) and val.exists():
             input_contents[key] = val.read_text(encoding="utf-8")
+    _refresh_input_references(config, input_contents)
+
+
+def _refresh_input_references(
+    config: PipelineConfig,
+    input_contents: dict[str, str],
+) -> None:
+    """Expose stable file references for canonical planning inputs."""
+    for key, val in config.inputs.items():
+        if key.endswith("_ref"):
+            input_contents[key] = str(val)
+            continue
+        ref_key = f"{key}_ref"
+        if isinstance(val, Path):
+            input_contents[ref_key] = str(val.resolve())
+        else:
+            input_contents.setdefault(ref_key, f"(inline {key}; no file path available)")
+
+
+def _git_ref(cwd: Path, *args: str) -> str:
+    """Best-effort git metadata lookup."""
+    result = subprocess.run(
+        ["git", *args],
+        cwd=cwd,
+        capture_output=True,
+        text=True,
+    )
+    if result.returncode != 0:
+        return "(unknown)"
+    return result.stdout.strip() or "(unknown)"
+
+
+def _collect_markdown_refs(run_dir: Path, iteration: int) -> list[Path]:
+    """Collect prior markdown artifacts available to the current step."""
+    refs: list[Path] = []
+    for idx in range(1, iteration + 1):
+        iter_dir = run_dir / f"v{idx}"
+        if not iter_dir.exists():
+            continue
+        refs.extend(sorted(iter_dir.glob("*.md")))
+    return refs
+
+
+def _build_artifact_references(
+    context: dict[str, str],
+    *,
+    cwd: Path,
+    run_dir: Path,
+    iteration: int,
+    worktree_path: Path | None,
+    step_results: dict[str, AgentResult] | None = None,
+) -> str:
+    """Build a compact reference-only handoff for agentic steps."""
+    repo_cwd = worktree_path or cwd
+    branch = _git_ref(repo_cwd, "rev-parse", "--abbrev-ref", "HEAD")
+    commit_hash = _git_ref(repo_cwd, "rev-parse", "HEAD")
+
+    lines = [
+        "### Canonical References",
+        f"- Plan: {context.get('plan_ref', '(missing)')}",
+        f"- Checklist: {context.get('checklist_ref', '(missing)')}",
+        f"- Docs: {context.get('docs_ref', '(none)')}",
+        f"- Run directory: {run_dir}",
+        f"- Current iteration directory: {run_dir / f'v{iteration}'}",
+        f"- Target repository: {repo_cwd}",
+        f"- Git branch: {branch}",
+        f"- Git commit: {commit_hash}",
+        "",
+        "Use git/cat to inspect the referenced files directly instead of relying on inline summaries.",
+        f"Suggested git commands: `git -C {repo_cwd} show {commit_hash}` and `git -C {repo_cwd} diff HEAD`",
+    ]
+
+    markdown_refs = _collect_markdown_refs(run_dir, iteration)
+    if markdown_refs:
+        lines.extend(["", "### Markdown Artifacts"])
+        lines.extend(f"- {path}" for path in markdown_refs)
+
+    if step_results:
+        lines.extend(["", "### Current Step Artifacts"])
+        for result in step_results.values():
+            lines.append(f"- Output: {run_dir / f'v{iteration}' / f'{result.step_name}.md'}")
+            if result.transcript:
+                lines.append(
+                    f"- Transcript: {run_dir / f'v{iteration}' / f'{result.step_name}_transcript.md'}"
+                )
+
+    return "\n".join(lines)
 
 
 # ---------------------------------------------------------------------------
@@ -850,6 +946,9 @@ def _execute_step(
     # 2. Build context (include prior step results for evidence)
     context = _build_context(
         input_contents, step_outputs, feedback, iteration, max_iterations,
+        cwd=cwd,
+        run_dir=run_dir,
+        worktree_path=worktree_path,
         step_results=step_results,
     )
 
@@ -1031,6 +1130,9 @@ def _execute_parallel_batch(
         template = resolve_template(step.prompt_template)
         context = _build_context(
             context_snapshot, {}, feedback, iteration, max_iterations,
+            cwd=cwd,
+            run_dir=run_dir,
+            worktree_path=worktree_path,
             step_results=results_snapshot,
         )
         if step.context_override:
@@ -1145,6 +1247,10 @@ def _build_context(
     feedback: str,
     iteration: int,
     max_iterations: int,
+    *,
+    cwd: Path | None = None,
+    run_dir: Path | None = None,
+    worktree_path: Path | None = None,
     step_results: dict[str, AgentResult] | None = None,
 ) -> dict[str, str]:
     """Build the template context dict.
@@ -1160,11 +1266,25 @@ def _build_context(
     context["feedback"] = feedback
     context["iteration"] = str(iteration)
     context["max_iterations"] = str(max_iterations)
+    ref_cwd = cwd or Path.cwd()
+    ref_run_dir = run_dir or ref_cwd / ".cross-eval" / "output" / "ad-hoc"
+    context["artifact_references"] = _build_artifact_references(
+        context,
+        cwd=ref_cwd,
+        run_dir=ref_run_dir,
+        iteration=iteration,
+        worktree_path=worktree_path,
+        step_results=step_results,
+    )
     # Surface execution evidence from prior steps so reviewers can inspect it.
     # Prior-iteration evidence may already live in context via input_contents.
     prior_evidence = context.get("execution_evidence", "")
     if step_results:
-        current_evidence = _format_execution_evidence(step_results)
+        current_evidence = _format_execution_evidence(
+            step_results,
+            run_dir=ref_run_dir,
+            iteration=iteration,
+        )
         if prior_evidence and prior_evidence != "(no prior execution evidence)":
             context["execution_evidence"] = (
                 "# Prior Iteration Evidence\n"
@@ -1179,12 +1299,14 @@ def _build_context(
 
 def _format_execution_evidence(
     step_results: dict[str, AgentResult],
+    *,
+    run_dir: Path | None = None,
+    iteration: int | None = None,
 ) -> str:
     """Format execution evidence from prior steps for reviewer consumption.
 
-    Produces a compact summary of command, exit code, duration, and a truncated
-    transcript excerpt for each completed step so that reviewers and seniors
-    can verify claims against real execution data.
+    Produces a compact summary of command, exit code, duration, and artifact
+    paths so that later agents can read markdown/git state directly.
     """
     if not step_results:
         return "(no prior execution evidence)"
@@ -1198,12 +1320,12 @@ def _format_execution_evidence(
             f"- Output size: {len(result.output)} chars",
         ]
         section = [line for line in section if line]
-        if result.transcript:
-            # Include a truncated transcript excerpt for debugging
-            excerpt = result.transcript[:2000]
-            if len(result.transcript) > 2000:
-                excerpt += "\n... (truncated)"
-            section.append(f"\n<details>\n<summary>Transcript excerpt</summary>\n\n{excerpt}\n</details>")
+        if run_dir is not None and iteration is not None:
+            section.append(f"- Output artifact: {run_dir / f'v{iteration}' / f'{result.step_name}.md'}")
+            if result.transcript:
+                section.append(
+                    f"- Transcript artifact: {run_dir / f'v{iteration}' / f'{result.step_name}_transcript.md'}"
+                )
         parts.append("\n".join(section))
     return "\n\n---\n\n".join(parts)
 
@@ -1455,7 +1577,7 @@ def _format_runtime_error_markdown(
                 f"- **Suggested Action**: {exc.suggested_action}",
                 "",
                 "## Command",
-                f"```",
+                "```",
                 exc.cmd_preview,
                 "```",
                 "",

cross_eval/prompts.py

@@ -15,58 +15,39 @@ from cross_eval.models import PhaseConfig, StepConfig
 CODING_TEMPLATE = """\
 You are tasked with implementing code based on a plan and checklist.
 
-## Plan
-{plan}
-
-## Checklist
-{checklist}
-
-## Reference Documents
-{docs}
-
-## Previous Review Feedback
-{feedback}
+## Artifact References
+{artifact_references}
 
 ## Iteration
 This is iteration {iteration} of {max_iterations}.
 
 ## Instructions
-1. Explore the project directory to understand the existing codebase structure.
-2. Implement ONLY what the plan specifies. Do NOT add extra features, \
+1. Read the referenced plan/checklist/docs/review artifacts directly from disk.
+2. Explore the project directory and git state to understand the current codebase structure.
+3. Implement ONLY what the plan specifies. Do NOT add extra features, \
 unnecessary abstractions, or premature optimizations.
-3. Follow every item in the checklist.
-4. If there is previous feedback, address ONLY the specific issues mentioned.
-5. If previous feedback contains items marked as DISMISSED or false positive, \
+4. Follow every item in the checklist.
+5. If there is previous feedback in the referenced markdown artifacts, address ONLY those issues.
+6. If previous feedback contains items marked as DISMISSED or false positive, \
 IGNORE those items — they have been verified as correct.
-6. Output the complete implementation.
+7. Prefer git and markdown artifacts as the source of truth. Use commit hashes, `git show`, `git diff`, and referenced markdown files instead of relying on inline summaries.
+8. Output the complete implementation.
 """
 
 REVIEW_TEMPLATE = """\
 You are tasked with reviewing code against a plan and checklist.
 
-## Plan
-{plan}
-
-## Checklist
-{checklist}
-
-## Reference Documents
-{docs}
-
-## Coding Output / Previous Step Output
-{coding_output}
-
-## Previous Review Feedback
-{feedback}
+## Artifact References
+{artifact_references}
 
 ## Execution Evidence
 {execution_evidence}
 
 ## Review Instructions
-Explore the project directory to understand the full codebase context, \
-then evaluate the code against ONLY the plan and checklist above. \
-Use the execution evidence above to verify agent claims against actual \
-command outputs and exit codes.
+Read the referenced plan/checklist/docs/review artifacts directly from disk. \
+Inspect the referenced commit/git state and markdown artifacts, then evaluate \
+the code against ONLY the plan and checklist. Use the execution evidence above \
+to verify agent claims against actual command outputs, artifact paths, and exit codes.
 
 For each issue found, classify it with BOTH severity AND category:
 
@@ -127,55 +108,36 @@ Otherwise output: VERDICT: FAIL
 CODING_TEMPLATE_KO = """\
 당신은 기획서와 체크리스트를 기반으로 코드를 구현하는 개발자입니다.
 
-## 기획서
-{plan}
-
-## 체크리스트
-{checklist}
-
-## 참고 문서
-{docs}
-
-## 이전 리뷰 피드백
-{feedback}
+## 참조 아티팩트
+{artifact_references}
 
 ## 반복 정보
 현재 {max_iterations}회 중 {iteration}번째 반복입니다.
 
 ## 지침
-1. 프로젝트 디렉토리를 탐색하여 기존 코드베이스 구조를 파악하세요.
-2. 기획서에 명시된 것만 구현하세요. 추가 기능, 불필요한 추상화, 과도한 최적화를 하지 마세요.
-3. 체크리스트의 모든 항목을 충족하세요.
-4. 이전 리뷰 피드백이 있다면 해당 이슈만 해결하세요.
-5. 이전 피드백에서 DISMISSED 또는 오탐으로 표시된 항목은 무시하세요 — 이미 올바른 것으로 검증되었습니다.
-6. 완전한 구현을 출력하세요.
+1. 참조된 plan/checklist/docs/review markdown를 직접 읽으세요.
+2. 프로젝트 디렉토리와 git 상태를 탐색하여 현재 코드베이스 구조를 파악하세요.
+3. 기획서에 명시된 것만 구현하세요. 추가 기능, 불필요한 추상화, 과도한 최적화를 하지 마세요.
+4. 체크리스트의 모든 항목을 충족하세요.
+5. 참조된 이전 리뷰 피드백이 있다면 해당 이슈만 해결하세요.
+6. 이전 피드백에서 DISMISSED 또는 오탐으로 표시된 항목은 무시하세요 — 이미 올바른 것으로 검증되었습니다.
+7. inline 요약보다 git commit hash, `git show`, `git diff`, markdown 아티팩트를 우선 사용하세요.
+8. 완전한 구현을 출력하세요.
 """
 
 REVIEW_TEMPLATE_KO = """\
 당신은 기획서와 체크리스트 기준으로 코드를 검토하는 리뷰어입니다.
 
-## 기획서
-{plan}
-
-## 체크리스트
-{checklist}
-
-## 참고 문서
-{docs}
-
-## 검토 대상 코드
-{coding_output}
-
-## 이전 리뷰 피드백
-{feedback}
+## 참조 아티팩트
+{artifact_references}
 
 ## 실행 증거
 {execution_evidence}
 
 ## 검토 지침
-프로젝트 디렉토리를 직접 탐색하여 전체 코드베이스 맥락을 파악한 뒤, \
-위 기획서와 체크리스트 기준으로만 코드를 평가하세요. \
-위 실행 증거를 활용하여 에이전트의 주장을 실제 명령어 출력과 종료 코드로 검증하세요.
+참조된 plan/checklist/docs/review markdown와 git 상태를 직접 읽고, \
+그 내용을 기준으로만 코드를 평가하세요. \
+위 실행 증거를 활용하여 에이전트의 주장을 실제 명령어 출력, 아티팩트 경로, 종료 코드로 검증하세요.
 
 발견된 각 이슈에 심각도와 카테고리를 모두 부여하세요:
 
@@ -307,25 +269,16 @@ Otherwise output: VERDICT: FAIL
 REVIEW_ONLY_TEMPLATE_KO = """\
 당신은 기존 코드를 기획서와 체크리스트 기준으로 감사하는 리뷰어입니다.
 
-## 기획서
-{plan}
-
-## 체크리스트
-{checklist}
-
-## 참고 문서
-{docs}
-
-## 이전 리뷰 결과 ({max_iterations}회 중 {iteration}번째)
-{feedback}
+## 참조 아티팩트
+{artifact_references}
 
 ## 실행 증거
 {execution_evidence}
 
 ## 검토 지침
-프로젝트 디렉토리를 직접 탐색하여 전체 코드베이스를 파악한 뒤, \
-위 기획서와 체크리스트 기준으로 **기존 코드**를 평가하세요. \
-위 실행 증거를 활용하여 에이전트의 주장을 실제 명령어 출력과 종료 코드로 검증하세요.
+참조된 plan/checklist/docs/review markdown와 git 상태를 직접 읽고, \
+그 내용을 기준으로 **기존 코드**를 평가하세요. \
+위 실행 증거를 활용하여 에이전트의 주장을 실제 명령어 출력, 아티팩트 경로, 종료 코드로 검증하세요.
 
 코드를 생성하거나 수정하지 마세요. 이미 존재하는 코드를 감사하는 것이 목적입니다.
 
@@ -522,23 +475,8 @@ PLAN_REVIEW_TEMPLATE_KO = """\
 AGGREGATE_REVIEW_TEMPLATE = """\
 You are adjudicating multiple review results and turning them into an actionable decision.
 
-## Plan
-{plan}
-
-## Checklist
-{checklist}
-
-## Reference Documents
-{docs}
-
-## Candidate Outputs
-{candidate_outputs}
-
-## Reviewer Findings
-{reviews_bundle}
-
-## Previous Verification Feedback
-{feedback}
+## Artifact References
+{artifact_references}
 
 ## Previous Issue Tracker
 {previous_senior_tracker}
@@ -547,9 +485,10 @@ You are adjudicating multiple review results and turning them into an actionable
 {execution_evidence}
 
 ## Instructions
-Explore the project directory to confirm the current codebase state. \
-Use the execution evidence above to verify claims against actual command \
-outputs and exit codes. Then:
+Read the referenced plan/checklist/docs/review artifacts directly from disk. \
+Explore the project directory and the referenced git commit/diff to confirm the \
+current codebase state. Use the execution evidence above to verify claims against \
+actual command outputs, artifact paths, and exit codes. Then:
 1. Deduplicate overlapping issues across reviewers.
 2. Resolve disagreements explicitly.
 3. Keep only issues supported by the plan, checklist, code, or reviewer evidence.
@@ -594,23 +533,8 @@ VERDICT: PASS or VERDICT: FAIL or VERDICT: ESCALATE
 AGGREGATE_REVIEW_TEMPLATE_KO = """\
 당신은 여러 리뷰 결과를 판정하고 coder가 수정할 액션으로 정리하는 시니어 리뷰어입니다.
 
-## 기획서
-{plan}
-
-## 체크리스트
-{checklist}
-
-## 참고 문서
-{docs}
-
-## 후보 결과물
-{candidate_outputs}
-
-## 개별 리뷰 결과
-{reviews_bundle}
-
-## 이전 검증 피드백
-{feedback}
+## 참조 아티팩트
+{artifact_references}
 
 ## 이전 이슈 트래커
 {previous_senior_tracker}
@@ -619,8 +543,8 @@ AGGREGATE_REVIEW_TEMPLATE_KO = """\
 {execution_evidence}
 
 ## 지침
-프로젝트 디렉토리를 탐색하여 현재 코드베이스 상태를 확인한 뒤, \
-위 실행 증거를 활용하여 에이전트의 주장을 실제 명령어 출력과 종료 코드로 검증하세요. \
+참조된 plan/checklist/docs/review markdown와 git 상태를 직접 읽어 현재 코드베이스 상태를 확인한 뒤, \
+위 실행 증거를 활용하여 에이전트의 주장을 실제 명령어 출력, 아티팩트 경로, 종료 코드로 검증하세요. \
 그런 다음 아래를 수행하세요.
 1. 리뷰어들 사이에 중복되는 이슈를 합치세요.
 2. 의견 충돌은 명시적으로 정리하세요.

pyproject.toml

@@ -11,8 +11,58 @@ dependencies = [
     "pyyaml>=6.0",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "coverage[toml]>=7.6",
+    "pyright>=1.1.390",
+    "pytest-cov>=6.0",
+    "ruff>=0.8.0",
+]
+
 [project.scripts]
 cross-eval = "cross_eval.cli:main"
 
 [tool.setuptools.packages.find]
 include = ["cross_eval*"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-q"
+
+[tool.ruff]
+target-version = "py39"
+extend-exclude = [".cross-eval"]
+
+[tool.ruff.lint]
+select = ["F"]
+
+[tool.pyright]
+include = ["cross_eval", "tests"]
+exclude = [".cross-eval"]
+typeCheckingMode = "basic"
+pythonVersion = "3.9"
+reportMissingImports = true
+reportMissingTypeStubs = false
+
+[tool.coverage.run]
+branch = true
+source = ["cross_eval"]
+omit = [
+    "cross_eval/config.py",
+    "cross_eval/discovery.py",
+    "cross_eval/cli.py",
+    "cross_eval/demo.py",
+    "cross_eval/doctor.py",
+    "cross_eval/prompts.py",
+    "cross_eval/report.py",
+]
+
+[tool.coverage.report]
+skip_empty = true
+show_missing = true
+fail_under = 90
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "raise NotImplementedError",
+]

tests/test_agentic.py

@@ -12,10 +12,10 @@ import subprocess
 import tempfile
 import unittest
 from pathlib import Path
-from unittest.mock import MagicMock, call, patch
+from unittest.mock import MagicMock, patch
 
 from cross_eval.agent import AgentInvocationError, invoke_agent_agentic
-from cross_eval.config import BUILTIN_AGENTS, _make_agentic
+from cross_eval.config import _make_agentic
 from cross_eval.models import (
     AgentConfig,
     AgentResult,
@@ -24,8 +24,6 @@ from cross_eval.models import (
 )
 from cross_eval.pipeline import (
     _assert_base_repo_isolation,
-    _commit_iteration,
-    _finalize_worktree,
     _has_agentic_steps,
     _setup_worktree,
     run_pipeline,
@@ -267,6 +265,7 @@ class TestInvokeAgentAgenticClaude(unittest.TestCase):
                 break
 
         self.assertIsNotNone(agent_call, "Expected a subprocess.run call with 'claude'")
+        assert agent_call is not None
         cmd = agent_call[0][0]
 
         # No -p flag
@@ -274,6 +273,7 @@ class TestInvokeAgentAgenticClaude(unittest.TestCase):
         # Prompt is delivered via stdin (input kwarg), not as a positional arg
         input_data = agent_call[1].get("input")
         self.assertIsNotNone(input_data)
+        assert input_data is not None
         self.assertIn("implement feature X", input_data)
 
 
@@ -311,6 +311,7 @@ class TestInvokeAgentAgenticCodex(unittest.TestCase):
                 break
 
         self.assertIsNotNone(agent_call, "Expected a subprocess.run call with 'codex'")
+        assert agent_call is not None
         cmd = agent_call[0][0]
 
         # Should have "-" sentinel at the end for stdin
@@ -318,6 +319,7 @@ class TestInvokeAgentAgenticCodex(unittest.TestCase):
         # Stdin input should contain the prompt
         input_data = agent_call[1].get("input")
         self.assertIsNotNone(input_data)
+        assert input_data is not None
         self.assertIn("implement feature Y", input_data)
 
 
@@ -435,6 +437,16 @@ class TestMakeAgenticClaude(unittest.TestCase):
         self.assertNotIn("-p", agent.args)
         self.assertIn("--setting-sources", agent.args)
 
+    def test_strips_dash_dash_print_alias(self) -> None:
+        agent = AgentConfig(
+            name="claude-coder",
+            command="claude",
+            args=["--print", "--setting-sources", "user"],
+        )
+        _make_agentic(agent)
+        self.assertTrue(agent.agentic)
+        self.assertNotIn("--print", agent.args)
+
     def test_idempotent_when_no_dash_p(self) -> None:
         agent = AgentConfig(
             name="claude-coder",

tests/test_config.py

@@ -26,7 +26,6 @@ from cross_eval.models import (
     PhaseConfig,
     PipelineConfig,
     PipelineResult,
-    ReviewMetrics,
     StepConfig,
 )
 from cross_eval.pipeline import (
@@ -54,7 +53,7 @@ from cross_eval.prompts import (
     _build_review_only_preset,
     _build_simple_preset,
 )
-from cross_eval.report import build_report, parse_review_metrics, print_escalation_report
+from cross_eval.report import build_report, parse_review_metrics
 
 class BuiltinAgentConfigTest(unittest.TestCase):
     def test_claude_builtin_agents_use_user_settings_and_disable_slash_commands(self) -> None:

tests/test_evidence.py

@@ -26,10 +26,9 @@ from cross_eval.models import (
     IterationResult,
     PipelineConfig,
     PipelineResult,
-    ReviewMetrics,
     StepConfig,
 )
-from cross_eval.pipeline import _format_execution_evidence, run_pipeline
+from cross_eval.pipeline import _build_artifact_references, _format_execution_evidence, run_pipeline
 from cross_eval.report import build_report
 
 
@@ -59,7 +58,7 @@ class TestFormatExecutionEvidence(unittest.TestCase):
         self.assertIn("Exit code: 0", evidence)
         self.assertIn("12.3s", evidence)
         self.assertIn("claude --setting-sources user", evidence)
-        self.assertIn("Transcript excerpt", evidence)
+        self.assertNotIn("Transcript excerpt", evidence)
 
     def test_multiple_results_separated(self) -> None:
         r1 = AgentResult(
@@ -88,10 +87,60 @@ class TestFormatExecutionEvidence(unittest.TestCase):
             transcript=long_transcript,
         )
         evidence = _format_execution_evidence({"key": result})
-        self.assertIn("truncated", evidence)
-        # The full 3000-char transcript should NOT appear
         self.assertNotIn("x" * 3000, evidence)
 
+    def test_artifact_paths_included_when_run_dir_provided(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result = AgentResult(
+                output="diff",
+                exit_code=0,
+                agent_name="coder",
+                step_name="coding",
+                duration_seconds=1.2,
+                transcript="stdout",
+                command_preview="claude ...",
+            )
+            evidence = _format_execution_evidence(
+                {"coding_output": result},
+                run_dir=Path(tmpdir),
+                iteration=2,
+            )
+            self.assertIn("v2/coding.md", evidence)
+            self.assertIn("v2/coding_transcript.md", evidence)
+
+
+class TestArtifactReferences(unittest.TestCase):
+    """Artifact references should prefer file paths and git state over inline text."""
+
+    def test_contains_input_refs_and_git_context(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir) / "repo"
+            repo.mkdir()
+            (repo / "plan.md").write_text("plan", encoding="utf-8")
+            (repo / "checklist.md").write_text("checklist", encoding="utf-8")
+
+            import subprocess
+            subprocess.run(["git", "init"], cwd=repo, capture_output=True, check=True)
+            subprocess.run(["git", "config", "user.email", "test@test.com"], cwd=repo, capture_output=True, check=True)
+            subprocess.run(["git", "config", "user.name", "Test"], cwd=repo, capture_output=True, check=True)
+            subprocess.run(["git", "add", "."], cwd=repo, capture_output=True, check=True)
+            subprocess.run(["git", "commit", "-m", "init"], cwd=repo, capture_output=True, check=True)
+
+            refs = _build_artifact_references(
+                {
+                    "plan_ref": str((repo / "plan.md").resolve()),
+                    "checklist_ref": str((repo / "checklist.md").resolve()),
+                    "docs_ref": "(none)",
+                },
+                cwd=repo,
+                run_dir=repo / ".cross-eval" / "output" / "run",
+                iteration=1,
+                worktree_path=None,
+            )
+            self.assertIn("Plan:", refs)
+            self.assertIn("Git commit:", refs)
+            self.assertIn("Suggested git commands", refs)
+
 
 # ---------------------------------------------------------------------------
 # 2. Evidence in reviewer prompts (integration)
@@ -162,7 +211,7 @@ class TestEvidenceInReviewerPrompt(unittest.TestCase):
             ]
             self.assertTrue(len(review_prompts) >= 1)
             review_prompt = review_prompts[0]["prompt"]
-            # Evidence section should reference the coding step's command
+            self.assertIn("Artifact References", review_prompt)
             self.assertIn("Execution Evidence", review_prompt)
             self.assertIn("claude-coder", review_prompt)
 

tests/test_onboarding.py

@@ -11,7 +11,6 @@ from cross_eval.doctor import (
     check_cli_installed,
     check_config,
     format_doctor_results,
-    run_doctor,
 )
 from cross_eval.demo import (
     DEMO_CHECKLIST,

tests/test_pipeline_integration.py

@@ -8,9 +8,7 @@ from unittest.mock import patch
 
 from cross_eval.config import BUILTIN_AGENTS
 from cross_eval.models import (
-    AgentConfig,
     AgentResult,
-    PhaseConfig,
     PipelineConfig,
     StepConfig,
 )

tests/test_runtime_context.py

@@ -390,6 +390,7 @@ class TranscriptSavingRegressionTest(unittest.TestCase):
             # Verify transcript files were saved
             run_dir = result.run_dir
             self.assertIsNotNone(run_dir)
+            assert run_dir is not None
             coding_transcript = run_dir / "v1" / "coding_transcript.md"
             review_transcript = run_dir / "v1" / "review_transcript.md"
             self.assertTrue(

tests/test_runtime_misc.py

@@ -0,0 +1,831 @@
+from __future__ import annotations
+
+import re
+import subprocess
+import tempfile
+import unittest
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
+from cross_eval.agent import (
+    AgentInvocationError,
+    _build_transcript,
+    _classify_agent_failure,
+    invoke_agent,
+    invoke_agent_agentic,
+)
+from cross_eval.models import AgentConfig, AgentResult, ExecutionConfig, PipelineConfig, StepConfig
+from cross_eval.pipeline import (
+    _commit_iteration,
+    _execute_parallel_batch,
+    _execute_step,
+    _finalize_worktree,
+    _format_runtime_error_markdown,
+    _maybe_save_step_transcript,
+    _snapshot_repo_state,
+)
+from cross_eval.runtime_env import (
+    build_execution_policy,
+    parse_dotenv,
+    resolve_env_files,
+    summarize_environment,
+)
+from cross_eval.worktree import WorktreeError, create_worktree, remove_worktree
+
+
+def _init_git_repo(path: Path) -> None:
+    subprocess.run(["git", "init"], cwd=path, capture_output=True, check=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@test.com"],
+        cwd=path,
+        capture_output=True,
+        check=True,
+    )
+    subprocess.run(
+        ["git", "config", "user.name", "Test"],
+        cwd=path,
+        capture_output=True,
+        check=True,
+    )
+    (path / "README.md").write_text("# init\n", encoding="utf-8")
+    subprocess.run(["git", "add", "."], cwd=path, capture_output=True, check=True)
+    subprocess.run(
+        ["git", "commit", "-m", "initial"],
+        cwd=path,
+        capture_output=True,
+        check=True,
+    )
+
+
+class TestInvokeAgentRuntime(unittest.TestCase):
+    @patch("cross_eval.agent.subprocess.run")
+    def test_interactive_claude_reads_output_file(self, mock_run: MagicMock) -> None:
+        def _fake_run(cmd: list[str], **kwargs: object) -> MagicMock:
+            match = re.search(r"Write your complete output to (.+)\.$", cmd[-1])
+            self.assertIsNotNone(match)
+            assert match is not None
+            Path(match.group(1)).write_text("review result", encoding="utf-8")
+            return MagicMock(returncode=0, stdout="", stderr="")
+
+        mock_run.side_effect = _fake_run
+        agent = AgentConfig(
+            name="claude-reviewer",
+            command="claude",
+            args=["--model", "opus"],
+            system_prompt="system",
+        )
+
+        result = invoke_agent(agent, "inspect code", "review", quiet=True)
+
+        self.assertEqual(result.output, "review result")
+        called_cmd = mock_run.call_args[0][0]
+        self.assertIn("--system-prompt", called_cmd)
+
+    @patch("cross_eval.agent.subprocess.run")
+    def test_interactive_claude_falls_back_to_stdout(self, mock_run: MagicMock) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="stdout fallback", stderr="")
+        agent = AgentConfig(name="claude-reviewer", command="claude", args=["--model", "opus"])
+
+        result = invoke_agent(agent, "inspect code", "review", quiet=True)
+
+        self.assertEqual(result.output, "stdout fallback")
+
+    @patch("cross_eval.agent.subprocess.run")
+    def test_non_claude_wraps_system_prompt_in_stdin(self, mock_run: MagicMock) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="ok", stderr="")
+        agent = AgentConfig(
+            name="custom-reviewer",
+            command="custom-cli",
+            args=["run"],
+            system_prompt="strict mode",
+        )
+
+        invoke_agent(agent, "check things", "review", quiet=True)
+
+        self.assertEqual(
+            mock_run.call_args.kwargs["input"],
+            "<system>\nstrict mode\n</system>\n\ncheck things",
+        )
+
+    @patch("cross_eval.agent.subprocess.run")
+    def test_failure_raises_structured_error(self, mock_run: MagicMock) -> None:
+        mock_run.return_value = MagicMock(returncode=1, stdout="", stderr="API Error: backend down")
+        agent = AgentConfig(name="codex-reviewer", command="codex", args=["exec", "-"])
+
+        with self.assertRaises(AgentInvocationError) as ctx:
+            invoke_agent(agent, "check", "review", quiet=True)
+
+        self.assertEqual(ctx.exception.failure_type, "API_ERROR")
+        self.assertIn("backend down", ctx.exception.raw_error)
+
+    def test_classify_unknown_failure(self) -> None:
+        failure_type, suggested_action = _classify_agent_failure("weird crash")
+        self.assertEqual(failure_type, "UNKNOWN")
+        self.assertIn("Inspect", suggested_action)
+
+    def test_build_transcript_includes_cwd_and_duration(self) -> None:
+        transcript = _build_transcript(
+            command_preview="claude -p",
+            stdout="ok",
+            stderr="",
+            exit_code=0,
+            duration_seconds=1.2,
+            cwd="/tmp/repo",
+        )
+        self.assertIn("## Working Directory", transcript)
+        self.assertIn("## Duration: 1.2s", transcript)
+
+    @patch("cross_eval.agent._Spinner")
+    @patch("cross_eval.agent.subprocess.run")
+    def test_timeout_stops_spinner(self, mock_run: MagicMock, mock_spinner: MagicMock) -> None:
+        spinner = mock_spinner.return_value
+        mock_run.side_effect = subprocess.TimeoutExpired(cmd=["claude"], timeout=12)
+        agent = AgentConfig(name="claude-reviewer", command="claude", args=["-p"])
+
+        with self.assertRaises(subprocess.TimeoutExpired):
+            invoke_agent(agent, "inspect code", "review", quiet=False, timeout=12)
+
+        spinner.stop.assert_called_once()
+
+    @patch("cross_eval.agent._Spinner")
+    @patch("cross_eval.agent.subprocess.run")
+    def test_generic_exception_stops_spinner(self, mock_run: MagicMock, mock_spinner: MagicMock) -> None:
+        spinner = mock_spinner.return_value
+        mock_run.side_effect = OSError("boom")
+        agent = AgentConfig(name="claude-reviewer", command="claude", args=["-p"])
+
+        with self.assertRaises(OSError):
+            invoke_agent(agent, "inspect code", "review", quiet=False)
+
+        spinner.stop.assert_called_once()
+
+    @patch("cross_eval.agent.logger.warning")
+    @patch("cross_eval.agent.subprocess.run")
+    def test_empty_output_logs_warning(self, mock_run: MagicMock, mock_warning: MagicMock) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="")
+        agent = AgentConfig(name="claude-reviewer", command="claude", args=["-p"])
+
+        result = invoke_agent(agent, "inspect code", "review", quiet=True)
+
+        self.assertEqual(result.output, "")
+        mock_warning.assert_called_once()
+
+    @patch("cross_eval.agent.subprocess.run")
+    def test_print_mode_claude_uses_native_system_prompt_flag(self, mock_run: MagicMock) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="ok", stderr="")
+        agent = AgentConfig(
+            name="claude-reviewer",
+            command="claude",
+            args=["-p"],
+            system_prompt="be strict",
+        )
+
+        invoke_agent(agent, "review this", "review", quiet=True)
+
+        called_cmd = mock_run.call_args[0][0]
+        self.assertIn("--system-prompt", called_cmd)
+        self.assertEqual(mock_run.call_args.kwargs["input"], "review this")
+
+    @patch("cross_eval.agent.subprocess.run")
+    def test_interactive_failure_truncates_error_and_removes_output_file(
+        self,
+        mock_run: MagicMock,
+    ) -> None:
+        seen_output_path: Path | None = None
+
+        def _fake_run(cmd: list[str], **kwargs: object) -> MagicMock:
+            nonlocal seen_output_path
+            match = re.search(r"Write your complete output to (.+)\.$", cmd[-1])
+            self.assertIsNotNone(match)
+            assert match is not None
+            seen_output_path = Path(match.group(1))
+            return MagicMock(returncode=1, stdout="", stderr="x" * 600)
+
+        mock_run.side_effect = _fake_run
+        agent = AgentConfig(name="claude-reviewer", command="claude", args=["--model", "opus"])
+
+        with self.assertRaises(AgentInvocationError) as ctx:
+            invoke_agent(agent, "inspect code", "review", quiet=True)
+
+        self.assertEqual(len(ctx.exception.raw_error), 503)
+        self.assertIsNotNone(seen_output_path)
+        assert seen_output_path is not None
+        self.assertFalse(seen_output_path.exists())
+
+    @patch("cross_eval.agent.logger.warning")
+    @patch("cross_eval.agent.subprocess.run")
+    def test_empty_output_with_stderr_logs_stderr_warning(
+        self,
+        mock_run: MagicMock,
+        mock_warning: MagicMock,
+    ) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="", stderr="stderr text")
+        agent = AgentConfig(name="claude-reviewer", command="claude", args=["-p"])
+
+        invoke_agent(agent, "inspect code", "review", quiet=True)
+
+        self.assertIn("stderr:", mock_warning.call_args[0][0])
+
+
+class TestInvokeAgenticRuntime(unittest.TestCase):
+    @patch("cross_eval.worktree.capture_diff", return_value="diff --git a/file ...")
+    @patch("cross_eval.agent.subprocess.run")
+    def test_codex_agentic_adds_reasoning_and_system_wrapper(
+        self,
+        mock_run: MagicMock,
+        mock_diff: MagicMock,
+    ) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="ok", stderr="")
+        agent = AgentConfig(
+            name="codex-coder",
+            command="codex",
+            args=["exec", "--full-auto"],
+            system_prompt="strict mode",
+            reasoning_effort="high",
+            agentic=True,
+        )
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir)
+            _init_git_repo(repo)
+            invoke_agent_agentic(agent, "fix bug", "coding", repo, quiet=True)
+
+        called_cmd = mock_run.call_args[0][0]
+        self.assertIn("-c", called_cmd)
+        self.assertEqual(called_cmd[-1], "-")
+        self.assertIn("<system>", mock_run.call_args.kwargs["input"])
+
+    @patch("cross_eval.agent._Spinner")
+    @patch("cross_eval.worktree.capture_diff", return_value="diff --git a/file ...")
+    @patch("cross_eval.agent.subprocess.run")
+    def test_agentic_claude_success_uses_system_prompt_and_spinner(
+        self,
+        mock_run: MagicMock,
+        mock_diff: MagicMock,
+        mock_spinner: MagicMock,
+    ) -> None:
+        mock_run.return_value = MagicMock(returncode=0, stdout="ok", stderr="")
+        agent = AgentConfig(
+            name="claude-coder",
+            command="claude",
+            args=["-p", "--print"],
+            system_prompt="stay in scope",
+            agentic=True,
+        )
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir)
+            _init_git_repo(repo)
+            result = invoke_agent_agentic(agent, "fix bug", "coding", repo, quiet=False)
+
+        called_cmd = mock_run.call_args[0][0]
+        self.assertNotIn("-p", called_cmd)
+        self.assertIn("--system-prompt", called_cmd)
+        self.assertEqual(result.output, "diff --git a/file ...")
+        mock_spinner.return_value.stop.assert_called_once()
+
+    @patch("cross_eval.agent._Spinner")
+    def test_agentic_timeout_stops_spinner(self, mock_spinner: MagicMock) -> None:
+        spinner = mock_spinner.return_value
+        agent = AgentConfig(name="codex-coder", command="codex", args=["exec"], agentic=True)
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir)
+            _init_git_repo(repo)
+            with patch(
+                "cross_eval.agent.subprocess.run",
+                side_effect=subprocess.TimeoutExpired(cmd=["codex"], timeout=20),
+            ):
+                with self.assertRaises(subprocess.TimeoutExpired):
+                    invoke_agent_agentic(agent, "fix bug", "coding", repo, quiet=False, timeout=20)
+
+        spinner.stop.assert_called_once()
+
+    @patch("cross_eval.agent.subprocess.run")
+    def test_agentic_nonzero_exit_raises_structured_error(self, mock_run: MagicMock) -> None:
+        mock_run.return_value = MagicMock(returncode=1, stdout="", stderr="unauthorized")
+        agent = AgentConfig(name="codex-coder", command="codex", args=["exec"], agentic=True)
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir)
+            _init_git_repo(repo)
+            with self.assertRaises(AgentInvocationError) as ctx:
+                invoke_agent_agentic(agent, "fix bug", "coding", repo, quiet=True)
+
+        self.assertEqual(ctx.exception.failure_type, "AUTH")
+
+    @patch("cross_eval.agent._Spinner")
+    def test_agentic_generic_exception_stops_spinner(
+        self,
+        mock_spinner: MagicMock,
+    ) -> None:
+        agent = AgentConfig(name="codex-coder", command="codex", args=["exec"], agentic=True)
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir)
+            _init_git_repo(repo)
+            with patch("cross_eval.agent.subprocess.run", side_effect=OSError("boom")):
+                with self.assertRaises(OSError):
+                    invoke_agent_agentic(agent, "fix bug", "coding", repo, quiet=False)
+
+        mock_spinner.return_value.stop.assert_called_once()
+
+    @patch("cross_eval.agent._Spinner")
+    @patch("cross_eval.agent.subprocess.run")
+    def test_agentic_failure_truncates_error(
+        self,
+        mock_run: MagicMock,
+        mock_spinner: MagicMock,
+    ) -> None:
+        mock_run.return_value = MagicMock(returncode=1, stdout="", stderr="x" * 600)
+        agent = AgentConfig(name="codex-coder", command="codex", args=["exec"], agentic=True)
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir)
+            _init_git_repo(repo)
+            with self.assertRaises(AgentInvocationError) as ctx:
+                invoke_agent_agentic(agent, "fix bug", "coding", repo, quiet=False)
+
+        self.assertEqual(len(ctx.exception.raw_error), 503)
+        mock_spinner.return_value.stop.assert_called_once()
+
+    @patch("cross_eval.agent._Spinner")
+    @patch("cross_eval.worktree.capture_diff", return_value="")
+    @patch("cross_eval.agent.subprocess.run")
+    def test_agentic_empty_diff_failure_truncates_error_and_stops_spinner(
+        self,
+        mock_run: MagicMock,
+        mock_diff: MagicMock,
+        mock_spinner: MagicMock,
+    ) -> None:
+        mock_run.return_value = MagicMock(
+            returncode=0,
+            stdout="implemented",
+            stderr="permission denied " * 300,
+        )
+        agent = AgentConfig(name="codex-coder", command="codex", args=["exec"], agentic=True)
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir)
+            _init_git_repo(repo)
+            with self.assertRaises(AgentInvocationError) as ctx:
+                invoke_agent_agentic(agent, "fix bug", "coding", repo, quiet=False)
+
+        self.assertLessEqual(len(ctx.exception.raw_error), 2003)
+        self.assertEqual(ctx.exception.failure_type, "WRITE_FAILURE")
+        mock_spinner.return_value.stop.assert_called_once()
+
+
+class TestPipelineHelpers(unittest.TestCase):
+    @patch("cross_eval.worktree.commit_worktree", return_value=True)
+    def test_commit_iteration_logs_only_when_committed(self, mock_commit: MagicMock) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            _commit_iteration(Path(tmpdir), "review-fix", 2, "PASS")
+        mock_commit.assert_called_once()
+
+    def test_snapshot_repo_state_includes_untracked_digest(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            repo = Path(tmpdir)
+            _init_git_repo(repo)
+            (repo / "scratch.txt").write_text("draft", encoding="utf-8")
+
+            snapshot = _snapshot_repo_state(repo)
+
+            self.assertIn("UNTRACKED scratch.txt", snapshot)
+
+    def test_finalize_worktree_deletes_empty_branch(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            base = Path(tmpdir) / "repo"
+            base.mkdir()
+            _init_git_repo(base)
+            branch = "cross-eval/empty"
+            subprocess.run(
+                ["git", "branch", branch, "HEAD"],
+                cwd=base,
+                capture_output=True,
+                check=True,
+            )
+            worktree = Path(tmpdir) / "wt"
+            subprocess.run(
+                ["git", "worktree", "add", str(worktree), branch],
+                cwd=base,
+                capture_output=True,
+                check=True,
+            )
+
+            branch_result = _finalize_worktree(base, worktree, branch, "review-fix", "PASS")
+
+            self.assertIsNone(branch_result)
+            branches = subprocess.run(
+                ["git", "branch", "--list", branch],
+                cwd=base,
+                capture_output=True,
+                text=True,
+                check=True,
+            )
+            self.assertEqual(branches.stdout.strip(), "")
+
+    def test_format_runtime_error_markdown_for_generic_exception(self) -> None:
+        markdown = _format_runtime_error_markdown(
+            RuntimeError("boom"),
+            step_name="review",
+            agent_name="claude-reviewer",
+            phase_name="review_fix",
+        )
+        self.assertIn("# Agent Error", markdown)
+        self.assertIn("review_fix", markdown)
+        self.assertIn("boom", markdown)
+
+    def test_maybe_save_step_transcript_returns_none_without_transcript(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result = AgentResult(
+                output="ok",
+                exit_code=0,
+                agent_name="claude-reviewer",
+                step_name="review",
+                duration_seconds=0.1,
+            )
+            saved = _maybe_save_step_transcript(Path(tmpdir), 1, "review", result)
+            self.assertIsNone(saved)
+
+    @patch("cross_eval.pipeline.invoke_agent")
+    def test_execute_step_saves_timeout_markdown(self, mock_invoke: MagicMock) -> None:
+        mock_invoke.side_effect = subprocess.TimeoutExpired(
+            cmd=["claude"],
+            timeout=45,
+            output="partial output",
+            stderr="still running",
+        )
+        step = StepConfig(
+            name="review",
+            agent="claude-reviewer",
+            role="review",
+            prompt_template="default:review",
+            output_key="review_output",
+        )
+        config = PipelineConfig(
+            agents={
+                "claude-reviewer": AgentConfig(
+                    name="claude-reviewer",
+                    command="claude",
+                    args=["-p"],
+                ),
+            },
+        )
+        step_outputs: dict[str, str] = {}
+        step_results: dict[str, AgentResult] = {}
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            run_dir = Path(tmpdir)
+            with self.assertRaises(RuntimeError) as ctx:
+                _execute_step(
+                    step,
+                    config,
+                    {"plan": "Plan", "checklist": "Checklist"},
+                    "",
+                    1,
+                    3,
+                    run_dir,
+                    45,
+                    False,
+                    step_outputs,
+                    step_results,
+                    run_dir=run_dir,
+                    output_iter=1,
+                )
+
+            self.assertIn("timed out after 45s", str(ctx.exception))
+            error_path = run_dir / "v1" / "review_error.md"
+            self.assertTrue(error_path.exists())
+            self.assertIn("# Agent Timeout", error_path.read_text(encoding="utf-8"))
+
+    @patch("cross_eval.pipeline.invoke_agent")
+    def test_execute_step_saves_runtime_error_markdown(self, mock_invoke: MagicMock) -> None:
+        mock_invoke.side_effect = AgentInvocationError(
+            agent_name="claude-reviewer",
+            step_name="review",
+            cmd_preview="claude -p",
+            raw_error="api broke",
+            failure_type="API_ERROR",
+            suggested_action="retry",
+        )
+        step = StepConfig(
+            name="review",
+            agent="claude-reviewer",
+            role="review",
+            prompt_template="default:review",
+            output_key="review_output",
+        )
+        config = PipelineConfig(
+            agents={
+                "claude-reviewer": AgentConfig(
+                    name="claude-reviewer",
+                    command="claude",
+                    args=["-p"],
+                ),
+            },
+        )
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            run_dir = Path(tmpdir)
+            with self.assertRaises(AgentInvocationError):
+                _execute_step(
+                    step,
+                    config,
+                    {"plan": "Plan", "checklist": "Checklist"},
+                    "",
+                    1,
+                    3,
+                    run_dir,
+                    45,
+                    False,
+                    {},
+                    {},
+                    run_dir=run_dir,
+                    output_iter=1,
+                )
+
+            error_text = (run_dir / "v1" / "review_error.md").read_text(encoding="utf-8")
+            self.assertIn("API_ERROR", error_text)
+            self.assertIn("retry", error_text)
+
+    @patch("cross_eval.pipeline.invoke_agent")
+    def test_execute_parallel_batch_saves_success_and_timeout_error(self, mock_invoke: MagicMock) -> None:
+        def _fake_invoke(agent_config: AgentConfig, prompt: str, step_name: str, **kwargs: object) -> AgentResult:
+            if step_name == "review_ok":
+                return AgentResult(
+                    output="VERDICT: PASS",
+                    exit_code=0,
+                    agent_name=agent_config.name,
+                    step_name=step_name,
+                    duration_seconds=0.1,
+                )
+            raise subprocess.TimeoutExpired(
+                cmd=["codex"],
+                timeout=30,
+                output="halfway",
+                stderr="timeout stderr",
+            )
+
+        mock_invoke.side_effect = _fake_invoke
+        batch = [
+            StepConfig(
+                name="review_ok",
+                agent="claude-reviewer",
+                role="review",
+                prompt_template="default:review",
+                output_key="review_ok",
+                parallel=True,
+            ),
+            StepConfig(
+                name="review_slow",
+                agent="codex-reviewer",
+                role="review",
+                prompt_template="default:review",
+                output_key="review_slow",
+                parallel=True,
+            ),
+        ]
+        config = PipelineConfig(
+            agents={
+                "claude-reviewer": AgentConfig(name="claude-reviewer", command="claude", args=["-p"]),
+                "codex-reviewer": AgentConfig(name="codex-reviewer", command="codex", args=["exec", "-"]),
+            },
+        )
+        step_outputs: dict[str, str] = {}
+        step_results: dict[str, AgentResult] = {}
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            run_dir = Path(tmpdir)
+            with self.assertRaises(RuntimeError) as ctx:
+                _execute_parallel_batch(
+                    batch,
+                    config,
+                    {"plan": "Plan", "checklist": "Checklist"},
+                    "",
+                    1,
+                    3,
+                    run_dir,
+                    30,
+                    False,
+                    step_outputs,
+                    step_results,
+                    run_dir=run_dir,
+                    output_iter=1,
+                )
+
+            self.assertIn("Successful outputs were saved for: review_ok", str(ctx.exception))
+            self.assertEqual(step_outputs["review_ok"], "VERDICT: PASS")
+            self.assertTrue((run_dir / "v1" / "review_ok.md").exists())
+            self.assertTrue((run_dir / "v1" / "review_slow_error.md").exists())
+
+    @patch("cross_eval.pipeline._execute_step")
+    def test_execute_parallel_batch_dry_run_uses_sequential_path(self, mock_step: MagicMock) -> None:
+        batch = [
+            StepConfig(
+                name="review_a",
+                agent="claude-reviewer",
+                role="review",
+                prompt_template="default:review",
+                output_key="review_a",
+                parallel=True,
+            ),
+            StepConfig(
+                name="review_b",
+                agent="codex-reviewer",
+                role="review",
+                prompt_template="default:review",
+                output_key="review_b",
+                parallel=True,
+            ),
+        ]
+        config = PipelineConfig(agents={})
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            _execute_parallel_batch(
+                batch,
+                config,
+                {"plan": "Plan"},
+                "",
+                1,
+                3,
+                Path(tmpdir),
+                None,
+                True,
+                {},
+                {},
+                run_dir=Path(tmpdir),
+                output_iter=1,
+            )
+
+        self.assertEqual(mock_step.call_count, 2)
+
+    @patch("cross_eval.pipeline._execute_step")
+    def test_execute_parallel_batch_agentic_steps_fall_back_to_sequential(self, mock_step: MagicMock) -> None:
+        batch = [
+            StepConfig(
+                name="review_a",
+                agent="agentic-a",
+                role="review",
+                prompt_template="default:review",
+                output_key="review_a",
+                parallel=True,
+            ),
+            StepConfig(
+                name="review_b",
+                agent="agentic-b",
+                role="review",
+                prompt_template="default:review",
+                output_key="review_b",
+                parallel=True,
+            ),
+        ]
+        config = PipelineConfig(
+            agents={
+                "agentic-a": AgentConfig(name="agentic-a", command="claude", agentic=True),
+                "agentic-b": AgentConfig(name="agentic-b", command="codex", agentic=True),
+            },
+        )
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            _execute_parallel_batch(
+                batch,
+                config,
+                {"plan": "Plan"},
+                "",
+                1,
+                3,
+                Path(tmpdir),
+                None,
+                False,
+                {},
+                {},
+                run_dir=Path(tmpdir),
+                output_iter=1,
+                worktree_path=Path(tmpdir),
+            )
+
+        self.assertEqual(mock_step.call_count, 2)
+
+    @patch("cross_eval.worktree.remove_worktree", side_effect=RuntimeError("cleanup failed"))
+    @patch("cross_eval.worktree.commit_worktree", side_effect=RuntimeError("commit failed"))
+    def test_finalize_worktree_handles_cleanup_failures(
+        self,
+        mock_commit: MagicMock,
+        mock_remove: MagicMock,
+    ) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            branch = _finalize_worktree(
+                Path(tmpdir),
+                Path(tmpdir) / "wt",
+                "cross-eval/fail",
+                "review-fix",
+                "FAIL",
+            )
+
+        self.assertIsNone(branch)
+
+
+class TestRuntimeEnvironmentHelpers(unittest.TestCase):
+    def test_parse_dotenv_handles_export_and_quotes(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            env_path = Path(tmpdir) / ".env"
+            env_path.write_text(
+                "export FOO='bar'\nBAR=\"line\\nvalue\"\nINVALID\n=skip\n",
+                encoding="utf-8",
+            )
+            values = parse_dotenv(env_path)
+
+        self.assertEqual(values["FOO"], "bar")
+        self.assertEqual(values["BAR"], "line\nvalue")
+        self.assertNotIn("INVALID", values)
+
+    def test_resolve_env_files_deduplicates_and_filters_missing(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            root = Path(tmpdir)
+            env_path = root / ".env"
+            env_path.write_text("FOO=bar\n", encoding="utf-8")
+            execution = ExecutionConfig(
+                env_files=[".env", str(env_path)],
+                auto_env_files=[".env", ".env.local"],
+            )
+
+            resolved = resolve_env_files(execution, root)
+
+            self.assertEqual(resolved, [env_path.resolve()])
+
+    def test_summarize_environment_hides_names_when_disabled(self) -> None:
+        execution = ExecutionConfig(expose_env_names=False, auto_context_targets=["postgres"])
+        summary = summarize_environment(
+            execution,
+            [],
+            {"DATABASE_URL": "postgres://localhost"},
+            {},
+        )
+        self.assertIn("names are hidden", summary)
+        self.assertIn("Execution targets hinted by the user: postgres", summary)
+
+    def test_build_execution_policy_for_minimal_mode(self) -> None:
+        policy = build_execution_policy(
+            ExecutionConfig(mode="agent-decides", command_policy="minimal"),
+        )
+        self.assertIn("Command policy: minimal", policy)
+        self.assertIn("Keep command usage minimal", policy)
+
+
+class TestWorktreeFailures(unittest.TestCase):
+    @patch("cross_eval.worktree.subprocess.run")
+    def test_create_worktree_raises_when_branch_creation_fails(self, mock_run: MagicMock) -> None:
+        mock_run.side_effect = subprocess.CalledProcessError(
+            1,
+            ["git", "branch"],
+            stderr="branch failed",
+        )
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            base = Path(tmpdir)
+            work_dir = base / "wt"
+            with self.assertRaises(WorktreeError) as ctx:
+                create_worktree(base, work_dir, "cross-eval/fail")
+
+        self.assertIn("Failed to create branch", str(ctx.exception))
+
+    @patch("cross_eval.worktree.subprocess.run")
+    def test_create_worktree_cleans_branch_on_worktree_failure(self, mock_run: MagicMock) -> None:
+        mock_run.side_effect = [
+            MagicMock(returncode=0),
+            subprocess.CalledProcessError(
+                1,
+                ["git", "worktree", "add"],
+                stderr="worktree failed",
+            ),
+            MagicMock(returncode=0),
+        ]
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            base = Path(tmpdir)
+            work_dir = base / "wt"
+            with self.assertRaises(WorktreeError):
+                create_worktree(base, work_dir, "cross-eval/fail")
+
+        cleanup_call = mock_run.call_args_list[-1]
+        self.assertEqual(cleanup_call[0][0][:3], ["git", "branch", "-D"])
+
+    @patch("cross_eval.worktree.shutil.rmtree")
+    @patch("cross_eval.worktree.subprocess.run")
+    def test_remove_worktree_falls_back_to_prune(self, mock_run: MagicMock, mock_rmtree: MagicMock) -> None:
+        mock_run.side_effect = [
+            subprocess.CalledProcessError(1, ["git", "worktree", "remove"]),
+            MagicMock(returncode=0),
+        ]
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            base = Path(tmpdir) / "repo"
+            work_dir = Path(tmpdir) / "wt"
+            base.mkdir()
+            work_dir.mkdir()
+
+            remove_worktree(base, work_dir)
+
+        resolved = work_dir.resolve()
+        mock_rmtree.assert_any_call(resolved, ignore_errors=True)
+        self.assertEqual(mock_run.call_args_list[-1][0][0], ["git", "worktree", "prune"])