I use this really great tool for annotating engineering textbooks and university scripts.
However, particularly in science and engineering, sub and superscripts are part of everyday life. I think, for the purpose I use xournal, that limitation is actually the weakest point. The top wish would be a TeX functionality. On the other hand, I'd like to see the result (e.g. formula) rather than the TeX commands. Perhaps, it might be easier to implement, if one writes a TeX formula or text into a separate window (or frame) and cut+paste the result to the pdf.
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