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My (BiBTeX) references need to appear before my appendix, but my appendix contains new references. These references are flagged as undefined unless my bibliography appears AFTER the appendix. Is there a way to fix this?

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Please proivde a minimal example which shows such a behavior. Normally the output is independent from the order. –  Marco Daniel Oct 30 '11 at 7:40
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1 Answer

This kind of behaviour is usually fixed by compiling your document more than once.

Every time you compile your document latex reads and writes information to a few different files: \jobname.aux, \jobname.toc, etc. When you use biblatex you run bibtex, or biber, etc to update the bibliography auxiliary files. Once these files are updated, you re-compile the original document which will be able to read the updated reference & citation information.

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