Refactor checkpoint verifcation

[j-atkins]

As per review in #269, verify in checkpoint.py can be refactored, see original comment:

I feel that a lot of the logic can be refactored out. Theres a lot of info needed about the structure of the problems file, and triggering the writing of said file. This can become very difficult if we start reading/writing this file in a different part of the code.

Originally posted by @VeckoTheGecko in #269 (comment)