Replace several internal protobufs with Go structs

[dmjb]

A number of internal-only types are defined as protobufs. These are used solely inside the engine code. Remove them and replace them with plain Go structs.

Summary

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Fixes #(related issue)

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Review Checklist:

• Reviewed my own code for quality and clarity.
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• Updated any affected documentation.
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[coveralls]

coverage: 53.026% (-0.02%) from 53.048%
when pulling f293fcb on decrease-internal-pbs
into 41e4833 on main.