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/transcription/transcription_agent.py

@@ -8,7 +8,7 @@ from spade.agent import Agent
 from spade.behaviour import CyclicBehaviour
 from spade.message import Message
 
-from control_backend.agents.transcription.speech_recognizer import SpeechRecognizer
+from .speech_recognizer import SpeechRecognizer
 from control_backend.core.config import settings
 from control_backend.core.zmq_context import context as zmq_context