Just a LaTeX issue and solution, in case anyone else ever spends half an afternoon banging their heads against this particular brick wall.
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LaTeX, apacite and bibliographies
LaTeX Includes
Latex offers a very nice way to divide large documents into manageable files – the include command. Combined with the includeonly command you have a very powerful method of compiling your document.
Typically, each included file is a chapter – this is apparently how it was designed, and is certainly how I – and every other LaTeX user I know – use it. Today I decided that one chapter was far too big, and split it up into a few smaller files for easy management. Took seconds, no problem.
Only later, when I was annotating a hard copy for my supervisor did I realise that every include finished with an implicit clearpage. Just what you want when you’re starting a chapter, and so I’d never noticed it. When you’re starting a new section though, that’s not what you want.
In this case, use the input command – same format, same effect, but no implicit clearpage. You lose the includeonly functionality, but it fixes your section breaks.
tldr/
Problem: Unwanted page breaks around include statements.
Solution: Use the near-identical input command instead.