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To solve your first problem, I would define two commands - one for important terms, which should be used when you want the index entry even in the Epub file, the second for all instances you want in the PDF version. The second issue can be solved using multiple TeX files - separate file for the print on demand, another for other uses. Document text can be ...

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If you have an eps file called img.eps in a directory build, you can include it like this: \documentclass{article} \usepackage{graphicx} \graphicspath{ {build/} } \begin{document} Include graphics here: \includegraphics{img} \end{document} Compile with pdflatex and it automatically converts the file, leaving the pdf in the build directory, and compiles ...

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Biber's option --output-directory may help you here. From Biber's --help output --output-directory [directory] Output files (including log files) are output to directory instead of the current directory. Input files are also looked for in directory before current directory (but after "--input_directory" if that is specified). for ...

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