Improve error handling story

[begleynk]

So far Dossier has taken a "panic when you see something weird" attitude. This has been great getting the project off the ground quickly, but it won't work going forward.

I think the philosophy should instead be "we'll do our best to parse your input, even if it is malformed, and try to return something". We can output warnings into STDERR if there is a weird output, but generally we shouldn't panic like we do currently if we see something unexpected.

We could also have an option to make turn warnings into errors and return a non-zero status if the user so chooses.