Good points. Anyway I guess you can agree on the fact that when no conflicts are presents, there are no problems.
An algorithm that I really like is "do the sure things automatically and let the human solve the unsure things".
BTW, in Eclipse class name clash is not infrequent, so of course you point out important problems.
Nonetheless I think that often asking the user "do you mean A::Class or B::Class?" is a better option than leave the user to write all down. It's not only a matter of speed, but also of method: having an automatic tool that does automatically things that you're usually doing over and over, let you to forget about those things and rely on the automatic tool. In other words: I would always be sure to include the headers - or to be asked to.
Good software has to do things right. No matter how often (usually, rarely, always).
~Aki
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