fix: Deprecate in memory function stores in agent.py

[mattzh72]

Description

Before, we were holding self.functions and self.functions_python in memory via link_tools. Here we get rid of link tools, and retrieve the tools when we need them from agent_state.

Small change - we directly pass in the actor object into calls, to reduce repeatedly retrieving the user based on the user_id.

Testing

Because this is a refactor, we rely on existing tests.