conductor(checkpoint): Checkpoint end of Phase 2

src/app_controller.py

@@ -2489,6 +2489,7 @@ class AppController:
    "active_preset": self.ui_global_preset_name,
   }
   self.config["ai"]["system_prompt"] = self.ui_global_system_prompt
+  self.config["ai"]["tool_instructions"] = self.ui_global_tool_instructions
   self.config["projects"] = {"paths": self.project_paths, "active": self.active_project_path}
   from src import bg_shader
   # Update gui section while preserving other keys like bg_shader_enabled