Generalize warning/error logging for analysis modules
There should be some kind of "message logger" or other way to record and print/save warnings and errors generated by analysis modules and the main analyzer. At present, messages are printed as they occur during replay, and the only record of them is the terminal's scrollback buffer. Users can redirect/copy replay output manually to a file, but this is rarely done. Message logging should be automatic, and a summary should be printed at the end of analysis.
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