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/__init__.py

@@ -0,0 +1,4 @@
+from .belief_collector.belief_collector import BeliefCollectorAgent
+from .llm.llm import LLMAgent
+from .ri_communication_agent import RICommunicationAgent
+from .vad_agent import VADAgent