I routinely use -output-directory=_out in TeX Live.
Now, I have noticed that this becomes an issue with revtex4-1, which generates a \jobname Notes.bib (apparently, in that output folder) but does not seem to find it there. I have to manually copy _out\jobname Notes.bib back next to the .tex file to make a simple document compile without missing footnotes:
\documentclass{revtex4-1}
\begin{document}
\footnote{Hello, world!}
\end{document}
A very similar situation is this MWE:
\documentclass{article}
\usepackage{filecontents}
\begin{filecontents}{\jobname.bib}
@article{SomeOne, author = {Some One}, year = {2018}}
\end{filecontents}
\begin{document}
Text \cite{SomeOne}
\bibliography{\jobname}
\end{document}
Again, _out/\jobname.bib is created, but not found until I copy it from the output folder next to the .tex file. This cannot be intended.
Is there a generic fix to this, either by having the -output-directory not apply to some commands, or by increasing the search path of the \bibliography command? Or is this a bug in TeX Live? I do not remember having this problem with MiKTeX, where I used separate auxiliary and output directories.
This answer implies a bibtex argument called --include-directory, but it does not seem to exist in TeX Live.
BIBINPUTS="./_out;"(use the correct quoting for Windows, or no quotes), so also other bib files can be found. – egreg Jun 21 '18 at 17:30