fix: 统一输出文件目录结构 - Closes #3

- 新增 PROJECT_OUTPUT (项目根/output/)，统一所有输出文件
- IR 中间产物 → output/ir/，最终交付物 → output/final/
- agent_poller.py 新增 pr-status/merge-pr/close-issue/lifecycle 命令
- DEV_AGENT.md 同步更新完整闭环流程
- 更新 conftest/test_sample 中的默认路径

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

tests/test_config.py

@@ -1,5 +1,6 @@
 """Unit tests for config.py pure functions."""
 
+import os
 import sys
 from pathlib import Path
 
@@ -21,6 +22,10 @@ def test_set_input_file():
 def test_config_constants_exist():
     """Verify all expected path constants are defined."""
     assert config.BASE_DIR
+    assert config.PROJECT_ROOT
+    assert config.PROJECT_OUTPUT
+    assert config.IR_OUTPUT
+    assert config.FINAL_OUTPUT
     assert config.OUTPUT_DIR
     assert config.PROMPTS_DIR
     assert config.TESTS_DIR
@@ -33,6 +38,23 @@ def test_config_constants_exist():
     assert config.IR_AUDIT_REPORT_MD
 
 
+def test_output_dir_is_under_project_root():
+    """PROJECT_OUTPUT, IR_OUTPUT, FINAL_OUTPUT should all be under PROJECT_ROOT."""
+    assert config.PROJECT_OUTPUT.startswith(config.PROJECT_ROOT)
+    assert config.IR_OUTPUT.startswith(config.PROJECT_OUTPUT)
+    assert config.FINAL_OUTPUT.startswith(config.PROJECT_OUTPUT)
+
+
+def test_output_dir_structure():
+    """IR files should go to output/ir/, final deliverable to output/final/."""
+    assert config.IR_OUTPUT.endswith(os.path.join("output", "ir"))
+    assert config.FINAL_OUTPUT.endswith(os.path.join("output", "final"))
+    assert config.SEMANTIC_INDEX_JSON.startswith(config.IR_OUTPUT)
+    assert config.IR_FRAGMENTS_JSON.startswith(config.IR_OUTPUT)
+    assert config.IR_FINAL_JSON.startswith(config.FINAL_OUTPUT)
+    assert config.IR_AUDIT_REPORT_MD.startswith(config.FINAL_OUTPUT)
+
+
 def test_ensemble_temperatures_count():
     """Should have exactly 3 ensemble temperatures."""
     assert len(config.ENSEMBLE_TEMPERATURES) == 3