Speed up reply<->state check

[nritsche]

Speeds up the kotekan config check by minimizing the number of DeepDiff calls.

There's a bit of refactoring and test additions to facilitate the change, but the commit messages hopefully make the review easy.

The two fix commits fix an issue discovered when adding the test.

Closes #161

[anjakefala]

I did not notice anything outside of the things Tristan has already commented on. =)

[nritsche]

Thanks for reviewing!