refactor: improve logging and module structure

Changed some folders to not be modules and organized some `__init__.py`
files.

ref: N25B-223

src/control_backend/agents/ri_communication_agent.py

@@ -1,5 +1,4 @@
 import asyncio
-import json
 import logging
 from spade.agent import Agent
 from spade.behaviour import CyclicBehaviour
@@ -7,8 +6,7 @@ import zmq
 
 from control_backend.core.config import settings
 from control_backend.core.zmq_context import context
-from control_backend.schemas.message import Message
-from control_backend.agents.ri_command_agent import RICommandAgent
+from .ri_command_agent import RICommandAgent
 
 logger = logging.getLogger(__name__)