fix(config): improve configuration merges #1285
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The library we were using does not provide a good way to handle exceptions et al.
Even if it did, we probably need to handle this in a case-by-case basis, as the correct thing to do for each property is different.
This removes the library, introducing a manual merge process, and starts adding tests to verify it all.
Ideally, we should also document what happens for each option.
closes #932
closes #241