I usually decouple the code that joins
lines from the actual program which parses the lines. Hence, the program makes the assumption that lines are not broken, and thus, is able to concentrate on its sole purpose.
This works out cleaner for me because I find that many programs require that lines be joined in the same way. Rather than duplicating code in many programs, I place the join-lines filter up front. It's also easier if the programs read from STDIN, so filters could be piped along in the *NIX environment.
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