bibtex never run

[l0drex]

I have trouble getting my references into the pdf. It seems to me that bibtex is never run, because I do get my references when I do this:

1. Compile in Setzer, with "remove temporary files" disabled
2. Run bibtex main.tex manually from command line
3. Compile again

I have Setzer installed from flathub.

[esijg]

Do the inline citation appear as [?] or something similar. I am running into that problem and I realized it seems to happen if the path gets too long.

As an example. If the bib and tex file are stored in /var/home/esi/Folder1/Folder2/Folder3/Folder4/Folder4/Folder5/Folder6 everything works fine but if they are stored in /var/home/esi/Folder1/Folder2/Folder3/Folder4/Folder4/Folder5/Folder61 references stop working.

My files

article.tex

\documentclass{article}
\begin{document}

This is a test if references work \cite{test}

\bibliography{references} 
\bibliographystyle{apalike}

\end{document}

references.bib

@article{test,
    title = {Does this work?},
    author = {Tester Testson},
}