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I write it as a note for me and if it can helps some other people,
it's fine.
To change the program used by **xdg-open** for opening some kind of
file, it's not that hard.
First, check the type of the file:
$ xdg-mime query filetype file.pdf
application/pdf
Then, choose the right tool for handling this type:
$ xdg-mime default mupdf.desktop application/pdf
Honestly, having firefox opening PDF files with GIMP **IS NOT FUN**.