Refine the implementation of __clean_messages().

[EdSchouten]

• Suppress 'There were undefined references' unconditionally. The check that was done for it is inaccurate, as this message may also be printed when other types of things (citations, hyper references) are undefined. Even if we were to print it in corner cases, there would be nothing actionable.

• Swallow warnings containing 'Rerun to get X right' and regarding undefined references when there are errors. We tend to generate a lot of them upon error, even though they are likely a result of LaTeX not completing in the first place.