fix CI: lazy import refresh_decision in CLI, update MCP tools test

- Make refresh_decision import lazy inside _cmd_increment to avoid
  ModuleNotFoundError when running as installed entrypoint
- Update test_registered_tool_surface_is_v2_navigation_only to include
  refresh_code_index in expected tool set
- Fix CLI test mock paths to patch refresh_decision.choose_refresh_mode
  instead of java_codebase_rag.cli.choose_refresh_mode

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

Author: HumanBean17

java_codebase_rag/cli.py

@@ -22,7 +22,6 @@
     resolve_operator_config,
 )
 from java_codebase_rag.pipeline import clip, run_build_ast_graph, run_build_ast_graph_incremental, run_cocoindex_drop, run_cocoindex_update
-from refresh_decision import choose_refresh_mode
 from java_ontology import VALID_UNRESOLVED_CALL_REASONS
 
 _REFRESH_DEPRECATION = (
@@ -279,6 +278,8 @@ def _cmd_increment(args: argparse.Namespace) -> int:
     cfg.apply_to_os_environ()
 
     def work() -> int:
+        from refresh_decision import choose_refresh_mode
+
         env = cfg.subprocess_env()
         verbose = bool(args.verbose)
 

tests/test_cli_increment.py

@@ -65,7 +65,7 @@ def test_increment_dispatches_kuzu_incremental(tmp_path: Path) -> None:
         patch("java_codebase_rag.cli._resolved_from_ns", return_value=cfg),
         patch("java_codebase_rag.cli._startup_hints"),
         patch("java_codebase_rag.cli.run_cocoindex_update", return_value=_mock_completed_process()),
-        patch("java_codebase_rag.cli.choose_refresh_mode", return_value=decision),
+        patch("refresh_decision.choose_refresh_mode", return_value=decision),
         patch("java_codebase_rag.cli.run_build_ast_graph_incremental", return_value=_mock_completed_process()) as mock_incr,
         patch("java_codebase_rag.cli.run_build_ast_graph", return_value=_mock_completed_process()) as mock_full,
         patch("sys.stdout", new_callable=io.StringIO),
@@ -94,7 +94,7 @@ def test_increment_dispatches_kuzu_full_fallback(tmp_path: Path) -> None:
         patch("java_codebase_rag.cli._resolved_from_ns", return_value=cfg),
         patch("java_codebase_rag.cli._startup_hints"),
         patch("java_codebase_rag.cli.run_cocoindex_update", return_value=_mock_completed_process()),
-        patch("java_codebase_rag.cli.choose_refresh_mode", return_value=decision),
+        patch("refresh_decision.choose_refresh_mode", return_value=decision),
         patch("java_codebase_rag.cli.run_build_ast_graph_incremental", return_value=_mock_completed_process()) as mock_incr,
         patch("java_codebase_rag.cli.run_build_ast_graph", return_value=_mock_completed_process()) as mock_full,
         patch("sys.stdout", new_callable=io.StringIO),
@@ -123,7 +123,7 @@ def test_increment_removes_kuzu_warning(tmp_path: Path) -> None:
         patch("java_codebase_rag.cli._resolved_from_ns", return_value=cfg),
         patch("java_codebase_rag.cli._startup_hints"),
         patch("java_codebase_rag.cli.run_cocoindex_update", return_value=_mock_completed_process()),
-        patch("java_codebase_rag.cli.choose_refresh_mode", return_value=decision),
+        patch("refresh_decision.choose_refresh_mode", return_value=decision),
         patch("java_codebase_rag.cli.run_build_ast_graph_incremental", return_value=_mock_completed_process()),
         patch("sys.stdout", new_callable=io.StringIO),
         patch("sys.stderr", new_callable=io.StringIO) as mock_stderr,

tests/test_mcp_tools.py

@@ -25,9 +25,10 @@ async def test_registered_tool_surface_is_v2_navigation_only(mcp_server) -> None
         "describe",
         "neighbors",
         "resolve",
+        "refresh_code_index",
     }
     assert names == expected
-    assert len(names) == 5
+    assert len(names) == 6
 
 
 async def test_all_tools_have_non_empty_description(mcp_server) -> None: