test: reconcile master's unit tests with feat/sandbox refactors

The merge from master brought in new unit tests that target pre-refactor
APIs on feat/sandbox. Reconcile each:

- factories/app.py: FakeApp now exposes a Mock skill_mgr (with empty .skills
  dict + inert prompt-addition builder) and a Mock pipeline_service so the
  PreProcessor skill-index injection branch can run end-to-end in tests.

- pipeline/conftest.py: eagerly import langbot.pkg.pipeline.pipelinemgr so
  pipeline.stage is fully initialised before any individual stage test
  (preproc, longtext, ...) tries to lazy-load it. Without this preload,
  running test_preproc.py in isolation hit a circular-import error via the
  stage -> app -> pipelinemgr -> stage chain.

- provider/test_tool_manager.py: ToolManager now probes four loaders
  (native -> plugin -> mcp -> skill). Inject inert native + skill mocks in
  the execute_func_call fixture and assert all four shutdowns fire.

- utils/test_paths.py: drop the three cwd-dependent _check_if_source_install
  cases. The refactor walks Path(__file__).resolve().parents looking for
  pyproject.toml + main.py, so cwd no longer factors in and there's no
  file read to mock-fail. The positive case and caching test still apply.

- utils/test_version.py: delete entirely. is_newer and compare_version_str
  were removed when VersionManager was refactored to use the Space API for
  release checks (1b4107a9); the tests targeted a surface that no longer
  exists.

tests/factories/app.py

@@ -15,7 +15,7 @@ class FakeApp:
     def __init__(
         self,
         *,
-        command_prefix: list[str] = ["/", "!"],
+        command_prefix: list[str] = ['/', '!'],
         command_enable: bool = True,
         pipeline_concurrency: int = 10,
         admins: list[str] | None = None,
@@ -40,6 +40,8 @@ class FakeApp:
         self.telemetry = self._create_mock_telemetry()
         self.survey = None
         self.cmd_mgr = self._create_mock_cmd_mgr()
+        self.skill_mgr = self._create_mock_skill_mgr()
+        self.pipeline_service = self._create_mock_pipeline_service()
 
         # Apply any extra attributes for specific test scenarios
         for name, value in extra_attrs.items():
@@ -98,9 +100,9 @@ class FakeApp:
     ):
         instance_config = Mock()
         instance_config.data = {
-            "command": {"prefix": command_prefix, "enable": command_enable},
-            "concurrency": {"pipeline": pipeline_concurrency},
-            "admins": admins,
+            'command': {'prefix': command_prefix, 'enable': command_enable},
+            'concurrency': {'pipeline': pipeline_concurrency},
+            'admins': admins,
         }
         return instance_config
 
@@ -119,6 +121,20 @@ class FakeApp:
         cmd_mgr.execute = AsyncMock()
         return cmd_mgr
 
+    def _create_mock_skill_mgr(self):
+        """Mock SkillManager that returns no skill index addition by default."""
+        skill_mgr = Mock()
+        skill_mgr.skills = {}
+        skill_mgr.build_skill_aware_prompt_addition = Mock(return_value='')
+        skill_mgr.get_skill_index = Mock(return_value=[])
+        return skill_mgr
+
+    def _create_mock_pipeline_service(self):
+        """Mock PipelineService.get_pipeline returning empty extensions prefs."""
+        pipeline_service = AsyncMock()
+        pipeline_service.get_pipeline = AsyncMock(return_value={'extensions_preferences': {}})
+        return pipeline_service
+
     def capture_message(self, message):
         """Capture an outbound message for test assertions."""
         self._outbound_messages.append(message)
@@ -134,4 +150,4 @@ class FakeApp:
 
 def fake_app(**kwargs) -> FakeApp:
     """Create a FakeApp instance with optional overrides."""
-    return FakeApp(**kwargs)
+    return FakeApp(**kwargs)