[paper] Fix formatting of citations

[giordano]

Note: I haven't tried to build the paper myself, but according to JOSS formatting instructions and Pandoc documentation, for citations where the paper is referred to in the text (rather than being mentioned in a parenthetical list) you should remove the square brackets. Also, according again to Pandon documentation for multiple citations together one should use the style [@ref1; @ref2] instead of [@ref1], [@ref2].

[LasNikas]

Thanks a lot! I tried to build the paper and it works.
The only thing was to update the upload-artifact action (see https://github.blog/changelog/2024-02-13-deprecation-notice-v1-and-v2-of-the-artifact-actions/)