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Yes, it's something I've always wanted to look at. transient seems a much better fit because its use-case is exactly what pandoc-mode does: call a shell command with lots of different command line arguments.
The current hydra-based implementation has a big advantage (for me as the maintainer, I mean). If a new option or switch is added to pandoc, it usually takes only a single line of code to add support for it to pandoc-mode. It took a bit of work to set that up, but it works quite nicely, now. I will have to look at transient more closely to see if that can be made to work.
Thanks for this awesome package.
Instead of using hydra, maybe it is more elegant to implement the UI with transient.
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