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It seems as this is not possible. You could report this behaviour to the maintainer of the subfiles package. The problem is that subfiles misinterprets your paths. In my opinion, you are having three options here: 1. You may omit the mystyle.sty and copy your header in the thesis.tex. tesi/thesis.tex % arara: pdflatex ...

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Apparently I totally misunderstood the environment variable IPELATEXDIR. I always thought it had to be set to the location to which pdflatex points. But the environment variable indicates the location where temporary latex files are stored. By default it is. ~/.ipe/latexrun. After I changed it back I still got the same error. This was caused due to the fact ...

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