Revert "refactor: clean up legacy code, rename hopper to entity_extractor, and add third-party notices"

This reverts commit 54fcef9887.

Please do not submit unrelated docs and codes in the same commit. I am reverting this commit so that the related files can be submitted in better-organized future commits.

artemis/graph/graph.py

@@ -511,6 +511,24 @@ def _get_active_subgoal_hashes(ctx: ArtemisContext) -> tuple[str, str | None]:
     return "default", None
 
 
+class _CyFunctionDetectorMeta(type):
+    def __instancecheck__(self, instance):
+        name = type(instance).__name__
+        return (
+            name
+            in (
+                "cyfunction",
+                "cython_function_or_method",
+                "builtin_function_or_method",
+            )
+            or "cyfunction" in name.lower()
+        )
+
+
+class CyFunctionDetector(metaclass=_CyFunctionDetectorMeta):
+    pass
+
+
 def check_plan_mutation_rejections(
     content_before: str, content_after: str, state: State | None = None
 ) -> str | None:
@@ -596,6 +614,7 @@ def _reject_checker_note_write(key: str, tool_call_id: str | None) -> ToolMessag
 
 
 class NoteArgs(BaseModel):
+    model_config = {"ignored_types": (CyFunctionDetector,)}
     key: str = Field(..., description=SAVE_NOTE_ARG_KEY_DESC)
     content: str = Field(..., description=SAVE_NOTE_ARG_CONTENT_DESC)
 
@@ -833,6 +852,7 @@ def wrap_note_tool(ctx: ArtemisContext, original_tool):
 
 
 class UpdateNoteArgs(BaseModel):
+    model_config = {"ignored_types": (CyFunctionDetector,)}
     key: str = Field(..., description=UPDATE_NOTE_ARG_KEY_DESC)
     target: str = Field(..., description=UPDATE_NOTE_ARG_TARGET_DESC)
     replacement: str = Field(..., description=UPDATE_NOTE_ARG_REPLACEMENT_DESC)