I do not have any general answer, but I do have an example of a proof checker that is small enough. The accompanying paper should make it easier to understand and it should give some idea of how the proof system was designed. I should mention that it does not handle HO proofs. One interesting feature is that it dumps HO proof obligations that essentially say "the calculus rules I use are sound." (And most of those proof obligations are handled by some tactics in Coq automatically.)
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