I am working with pdflatex on a nested tex file (eg: Main.tex+Chapter1.tex+...) and as my work folder is quite a mess already, I want to have the build files in a subdirectory. Checking the dedicated box in texmaker, hence using the -output-directory option, it works well except for bibtex. I have read the other topics, tried different solutions which weren't working because of the nested files, and finally settled to writing a small bash script that I can call within texmaker.
This works well, bibtex generates the bbl which looks fine, but when running pdflatex afterwards, it looks like there is no bbl at all. I tried placing the bbl in the build directory or in the parent one with the same disappointing results.
Can anyone tell me when and how pdflatex includes the contents of that bbl file, and where it might look for it?