Update Agent Docs

[jessegrabowski]

Agent docs in docs/agents/ptgp-vfe/ are out of date in light of recent changes. They need to be updated. Here is a partial list of things I found, but an exhaustive check needs to be conducted:

• reference/api.md:58 : training.py:728 → :898
• reference/workflow.md:120 : training.py:728 → :898
• pitfalls/sigma_collapse.md:66 : training.py:728 → :898
• reference/api.md:87 : Points(Z) missing Z_init arg
• reference/api.md:32 : sig missing compile_kwargs
• reference/discrete_inputs.md:93 : kmeans_init is :377 not :101