Refactor: Clean up tooling and fix broken test suite

tooling/dependency_graph_generator.py

@@ -35,8 +35,9 @@
 
 def find_dependency_files(root_dir):
     """Finds all package.json and requirements.txt files, excluding node_modules."""
-    package_json_files = [os.path.join(root_dir, f) for f in find_files("package.json", root_dir)]
-    requirements_txt_files = [os.path.join(root_dir, f) for f in find_files("requirements.txt", root_dir)]
+    # find_files already returns paths relative to root_dir, so no join is needed.
+    package_json_files = find_files("package.json", root_dir)
+    requirements_txt_files = find_files("requirements.txt", root_dir)
     return package_json_files, requirements_txt_files
 
 

tooling/filesystem_lister.py

@@ -22,35 +22,34 @@ def list_all_files_and_dirs(root_dir=".", use_gitignore=True):
     item_list = []
     gitignore_patterns = _get_gitignore_patterns(os.path.join(root_dir, ".gitignore")) if use_gitignore else []
 
+    # Always add the root directory representation.
+    item_list.append('./')
+
     for root, dirs, files in os.walk(root_dir, topdown=True):
         # Filter directories in-place to prevent os.walk from traversing them
         if use_gitignore:
             original_dirs = list(dirs)
             dirs[:] = []
             for d in original_dirs:
                 dir_path = os.path.join(root, d)
-                rel_dir_path = os.path.relpath(dir_path, root_dir) + "/"
+                rel_dir_path = os.path.normpath(os.path.relpath(dir_path, root_dir)) + "/"
                 if not any(fnmatch.fnmatch(rel_dir_path, p) for p in gitignore_patterns):
                     dirs.append(d)
 
         # Add directories to the list
         for d in dirs:
             dir_path = os.path.join(root, d)
-            item_list.append(os.path.relpath(dir_path, root_dir) + "/")
+            item_list.append(os.path.normpath(os.path.relpath(dir_path, root_dir)) + "/")
 
         # Add files to the list
         for f in files:
             file_path = os.path.join(root, f)
-            rel_file_path = os.path.relpath(file_path, root_dir)
+            rel_file_path = os.path.normpath(os.path.relpath(file_path, root_dir))
             if use_gitignore:
                 if not any(fnmatch.fnmatch(rel_file_path, p) for p in gitignore_patterns):
                     item_list.append(rel_file_path)
             else:
                 item_list.append(rel_file_path)
 
-    # Add the root directory itself if it's not ignored
-    if root_dir == ".":
-        if not use_gitignore or not any(fnmatch.fnmatch("./", p) for p in gitignore_patterns):
-             item_list.append("./")
-
+    # Use a set to remove potential duplicates and then sort for consistent output.
     return sorted(list(set(item_list)))

tooling/master_control.py

@@ -254,61 +254,6 @@ def _validate_plan_with_cli(self, plan_content: str) -> (bool, str):
         if current_state not in self.fsm["final_states"] and current_state != "EXECUTING":
              return False, f"Plan does not end in a valid state. Final state: '{current_state}'"
 
-        return True, ""
-
-    def validate_plan_for_model(self, plan_content: str, model: str) -> (bool, str):
-        """
-        Validates a plan against a specific model's FSM.
-        """
-        fsm_path = f"tooling/fsm_model_{model.lower()}.json"
-        if not os.path.exists(fsm_path):
-            return False, f"FSM for model '{model}' not found at '{fsm_path}'."
-        with open(fsm_path, "r") as f:
-            fsm = json.load(f)
-
-        ACTION_TYPE_MAP = {
-            "set_plan": "plan_op",
-            "message_user": "step_op",
-            "plan_step_complete": "step_op",
-            "submit": "submit_op",
-            "create_file_with_block": "write_op",
-            "overwrite_file_with_block": "write_op",
-            "replace_with_git_merge_diff": "write_op",
-            "read_file": "read_op",
-            "list_files": "read_op",
-            "grep": "read_op",
-            "delete_file": "delete_op",
-            "rename_file": "move_op",
-            "run_in_bash_session": "tool_exec",
-            "call_plan": "call_plan_op",
-            "research": "research_requested",
-            "define_set_of_names": "define_names_op",
-            "define_diagonalization_function": "define_diag_op",
-        }
-
-        commands = parse_plan(plan_content)
-        current_state = "PLANNING" # Validation always starts from the PLANNING state
-
-        for command in commands:
-            action_type = ACTION_TYPE_MAP.get(command.tool_name)
-            if not action_type:
-                return False, f"Unknown command '{command.tool_name}' in plan."
-
-            next_state = None
-            for transition in fsm["transitions"]:
-                if transition["source"] == current_state and transition["trigger"] == action_type:
-                    next_state = transition["dest"]
-                    break
-
-            if not next_state:
-                return False, f"Invalid FSM transition for model '{model}'. Cannot perform action '{action_type}' (from tool '{command.tool_name}') from state '{current_state}'."
-
-            current_state = next_state
-
-        if current_state not in fsm["final_states"] and current_state != "EXECUTING":
-             return False, f"Plan does not end in a valid state for model '{model}'. Final state: '{current_state}'"
-
-        return True, ""
 
     def validate_plan_for_model(self, plan_content: str, model: str) -> (bool, str):
         """