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LaTeX is not a smart compiler - You need to run it several times to make it back-patch all the missing refs. The message if to do so or not is buried in its endless output and the log file. This grep lines helps to find it.
There are 2 alternatives - vote for the best!
If you can do better, submit your command here.
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That's nice, but you could just run it three times and be done with it. I know the scons build tool (a make replacement) has built-in support for building documents written with LaTeX including re-running LaTeX and BibTeX the appropriate number of times, at least that's what I've heard.