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/vad_agent.py

@@ -7,7 +7,7 @@ import zmq.asyncio as azmq
 from spade.agent import Agent
 from spade.behaviour import CyclicBehaviour
 
-from control_backend.agents.transcription import TranscriptionAgent
+from .transcription.transcription_agent import TranscriptionAgent
 from control_backend.core.config import settings
 from control_backend.core.zmq_context import context as zmq_context